Starting phenix.real_space_refine on Sun Sep 13 19:10:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zwo_11492/09_2026/6zwo_11492_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zwo_11492/09_2026/6zwo_11492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zwo_11492/09_2026/6zwo_11492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zwo_11492/09_2026/6zwo_11492.map" model { file = "/net/cci-nas-00/data/ceres_data/6zwo_11492/09_2026/6zwo_11492_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zwo_11492/09_2026/6zwo_11492_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.102 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 Zn 1 6.06 5 P 12 5.49 5 S 159 5.16 5 C 15858 2.51 5 N 4396 2.21 5 O 4568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24994 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 12841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1592, 12841 Classifications: {'peptide': 1592} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 64, 'TRANS': 1527} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 8931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8931 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1079} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 2, 'GLU:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'AGS': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23377 SG CYS F1520 123.208 91.400 26.960 1.00 61.03 S ATOM 23403 SG CYS F1523 123.708 91.698 23.353 1.00 65.32 S ATOM 23877 SG CYS F1651 123.596 88.159 24.988 1.00 48.61 S Time building chain proxies: 5.37, per 1000 atoms: 0.21 Number of scatterers: 24994 At special positions: 0 Unit cell: (165.312, 163.968, 149.184, 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) Zn 1 29.99 S 159 16.00 P 12 15.00 O 4568 8.00 N 4396 7.00 C 15858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F4801 " pdb="ZN ZN F4801 " - pdb=" NE2 HIS F1515 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1520 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1523 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1651 " Number of angles added : 3 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 11 sheets defined 65.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 792 through 809 Processing helix chain 'B' and resid 816 through 829 removed outlier: 3.605A pdb=" N ASP B 826 " --> pdb=" O ILE B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 847 removed outlier: 4.086A pdb=" N ALA B 840 " --> pdb=" O LYS B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 861 removed outlier: 3.990A pdb=" N ARG B 859 " --> pdb=" O VAL B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 871 removed outlier: 3.846A pdb=" N PHE B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 892 Processing helix chain 'B' and resid 895 through 902 Processing helix chain 'B' and resid 929 through 936 removed outlier: 3.541A pdb=" N VAL B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 960 removed outlier: 3.519A pdb=" N ILE B 958 " --> pdb=" O ALA B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 983 removed outlier: 3.781A pdb=" N GLY B 983 " --> pdb=" O PHE B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1004 Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1005 through 1007 No H-bonds generated for 'chain 'B' and resid 1005 through 1007' Processing helix chain 'B' and resid 1008 through 1023 removed outlier: 3.871A pdb=" N GLN B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1029 No H-bonds generated for 'chain 'B' and resid 1027 through 1029' Processing helix chain 'B' and resid 1030 through 1039 removed outlier: 3.698A pdb=" N ILE B1034 " --> pdb=" O TYR B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1064 removed outlier: 3.753A pdb=" N LEU B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1070 Processing helix chain 'B' and resid 1071 through 1073 No H-bonds generated for 'chain 'B' and resid 1071 through 1073' Processing helix chain 'B' and resid 1074 through 1084 removed outlier: 3.595A pdb=" N MET B1078 " --> pdb=" O LEU B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1101 Processing helix chain 'B' and resid 1115 through 1123 removed outlier: 3.557A pdb=" N LEU B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B1122 " --> pdb=" O ILE B1118 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B1123 " --> pdb=" O VAL B1119 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1142 Processing helix chain 'B' and resid 1149 through 1151 No H-bonds generated for 'chain 'B' and resid 1149 through 1151' Processing helix chain 'B' and resid 1152 through 1165 removed outlier: 4.080A pdb=" N HIS B1157 " --> pdb=" O SER B1153 " (cutoff:3.500A) Proline residue: B1158 - end of helix removed outlier: 3.861A pdb=" N ASP B1164 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B1165 " --> pdb=" O ARG B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1182 Processing helix chain 'B' and resid 1185 through 1189 removed outlier: 3.683A pdb=" N TYR B1188 " --> pdb=" O GLY B1185 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1202 removed outlier: 3.942A pdb=" N LYS B1197 " --> pdb=" O PRO B1193 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B1198 " --> pdb=" O MET B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1206 through 1218 Processing helix chain 'B' and resid 1228 through 1238 Processing helix chain 'B' and resid 1265 through 1270 Processing helix chain 'B' and resid 1276 through 1294 removed outlier: 3.802A pdb=" N ASP B1294 " --> pdb=" O GLU B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1308 removed outlier: 4.164A pdb=" N ALA B1305 " --> pdb=" O ARG B1301 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU B1306 " --> pdb=" O SER B1302 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1317 removed outlier: 3.698A pdb=" N ALA B1314 " --> pdb=" O TYR B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1327 Processing helix chain 'B' and resid 1330 through 1348 removed outlier: 4.051A pdb=" N GLN B1348 " --> pdb=" O ALA B1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1366 removed outlier: 3.915A pdb=" N THR B1354 " --> pdb=" O ILE B1350 " (cutoff:3.500A) Processing helix chain 'B' and resid 1376 through 1378 No H-bonds generated for 'chain 'B' and resid 1376 through 1378' Processing helix chain 'B' and resid 1379 through 1389 removed outlier: 3.708A pdb=" N LYS B1389 " --> pdb=" O GLU B1385 " (cutoff:3.500A) Processing helix chain 'B' and resid 1392 through 1407 removed outlier: 3.875A pdb=" N LYS B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B1407 " --> pdb=" O GLU B1403 " (cutoff:3.500A) Processing helix chain 'B' and resid 1409 through 1423 removed outlier: 3.567A pdb=" N LYS B1422 " --> pdb=" O SER B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1425 through 1440 removed outlier: 3.534A pdb=" N ALA B1429 " --> pdb=" O GLN B1425 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B1440 " --> pdb=" O ALA B1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 1446 through 1453 removed outlier: 3.785A pdb=" N TYR B1450 " --> pdb=" O GLN B1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1468 Processing helix chain 'B' and resid 1476 through 1488 removed outlier: 3.887A pdb=" N ARG B1480 " --> pdb=" O LEU B1476 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1499 removed outlier: 3.541A pdb=" N LEU B1493 " --> pdb=" O GLU B1489 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B1499 " --> pdb=" O GLN B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1505 through 1524 removed outlier: 4.006A pdb=" N GLN B1509 " --> pdb=" O ASN B1505 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1510 " --> pdb=" O ASP B1506 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS B1511 " --> pdb=" O GLU B1507 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1525 through 1534 removed outlier: 3.759A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B1534 " --> pdb=" O GLU B1530 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1554 removed outlier: 3.535A pdb=" N GLN B1554 " --> pdb=" O LEU B1550 " (cutoff:3.500A) Processing helix chain 'B' and resid 1558 through 1579 removed outlier: 3.685A pdb=" N ASP B1569 " --> pdb=" O ASP B1565 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) Processing helix chain 'B' and resid 1582 through 1598 removed outlier: 5.041A pdb=" N GLY B1588 " --> pdb=" O SER B1584 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA B1589 " --> pdb=" O ARG B1585 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B1592 " --> pdb=" O GLY B1588 " (cutoff:3.500A) Processing helix chain 'B' and resid 1598 through 1608 Processing helix chain 'B' and resid 1611 through 1624 removed outlier: 3.730A pdb=" N TRP B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B1624 " --> pdb=" O TRP B1620 " (cutoff:3.500A) Processing helix chain 'B' and resid 1629 through 1641 removed outlier: 3.871A pdb=" N LYS B1635 " --> pdb=" O GLU B1631 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1663 removed outlier: 4.008A pdb=" N LYS B1655 " --> pdb=" O ARG B1651 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B1656 " --> pdb=" O THR B1652 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1678 Processing helix chain 'B' and resid 1693 through 1708 removed outlier: 3.590A pdb=" N ALA B1708 " --> pdb=" O MET B1704 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1729 removed outlier: 3.508A pdb=" N GLN B1715 " --> pdb=" O ILE B1711 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN B1727 " --> pdb=" O THR B1723 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B1728 " --> pdb=" O MET B1724 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN B1729 " --> pdb=" O GLN B1725 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1763 Processing helix chain 'B' and resid 1768 through 1784 Processing helix chain 'B' and resid 1786 through 1809 removed outlier: 3.535A pdb=" N TRP B1790 " --> pdb=" O TRP B1786 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B1808 " --> pdb=" O TYR B1804 " (cutoff:3.500A) Processing helix chain 'B' and resid 1875 through 1896 Proline residue: B1883 - end of helix removed outlier: 3.856A pdb=" N SER B1893 " --> pdb=" O PHE B1889 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B1894 " --> pdb=" O ARG B1890 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B1895 " --> pdb=" O SER B1891 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B1896 " --> pdb=" O ILE B1892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1899 through 1914 Processing helix chain 'B' and resid 1916 through 1930 removed outlier: 3.955A pdb=" N GLU B1921 " --> pdb=" O PRO B1917 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B1922 " --> pdb=" O ASP B1918 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B1928 " --> pdb=" O VAL B1924 " (cutoff:3.500A) Processing helix chain 'B' and resid 1932 through 1937 removed outlier: 3.732A pdb=" N TRP B1935 " --> pdb=" O ILE B1932 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN B1937 " --> pdb=" O THR B1934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1944 Processing helix chain 'B' and resid 1950 through 1968 Processing helix chain 'B' and resid 1972 through 1981 removed outlier: 3.660A pdb=" N LYS B1981 " --> pdb=" O THR B1977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1984 through 1999 Processing helix chain 'B' and resid 2003 through 2021 removed outlier: 3.851A pdb=" N ARG B2018 " --> pdb=" O GLU B2014 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B2019 " --> pdb=" O GLU B2015 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B2020 " --> pdb=" O LEU B2016 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B2021 " --> pdb=" O ILE B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2042 removed outlier: 3.616A pdb=" N ARG B2036 " --> pdb=" O GLU B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2043 through 2059 removed outlier: 4.072A pdb=" N GLU B2049 " --> pdb=" O LYS B2045 " (cutoff:3.500A) Proline residue: B2053 - end of helix Processing helix chain 'B' and resid 2064 through 2075 Processing helix chain 'B' and resid 2076 through 2091 removed outlier: 3.589A pdb=" N GLN B2082 " --> pdb=" O LEU B2078 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2113 removed outlier: 3.710A pdb=" N LEU B2097 " --> pdb=" O ASN B2093 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN B2099 " --> pdb=" O LYS B2095 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B2113 " --> pdb=" O ARG B2109 " (cutoff:3.500A) Processing helix chain 'B' and resid 2123 through 2127 Processing helix chain 'B' and resid 2192 through 2211 removed outlier: 3.650A pdb=" N GLU B2196 " --> pdb=" O LEU B2192 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG B2197 " --> pdb=" O ARG B2193 " (cutoff:3.500A) Processing helix chain 'B' and resid 2212 through 2217 Processing helix chain 'B' and resid 2246 through 2257 removed outlier: 4.327A pdb=" N ASP B2252 " --> pdb=" O ALA B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2262 through 2272 Processing helix chain 'B' and resid 2274 through 2278 removed outlier: 3.535A pdb=" N HIS B2277 " --> pdb=" O ASP B2274 " (cutoff:3.500A) Processing helix chain 'B' and resid 2279 through 2293 Processing helix chain 'B' and resid 2297 through 2306 removed outlier: 3.520A pdb=" N LYS B2306 " --> pdb=" O LEU B2302 " (cutoff:3.500A) Processing helix chain 'B' and resid 2309 through 2335 removed outlier: 3.534A pdb=" N TRP B2313 " --> pdb=" O SER B2309 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B2326 " --> pdb=" O ARG B2322 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET B2327 " --> pdb=" O SER B2323 " (cutoff:3.500A) Processing helix chain 'B' and resid 2380 through 2385 Processing helix chain 'B' and resid 2394 through 2410 Processing helix chain 'B' and resid 2410 through 2423 removed outlier: 3.714A pdb=" N VAL B2414 " --> pdb=" O HIS B2410 " (cutoff:3.500A) Processing helix chain 'B' and resid 2429 through 2433 removed outlier: 3.686A pdb=" N MET B2432 " --> pdb=" O TRP B2429 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP B2433 " --> pdb=" O ARG B2430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2429 through 2433' Processing helix chain 'B' and resid 2493 through 2508 removed outlier: 4.515A pdb=" N ALA B2497 " --> pdb=" O LEU B2493 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B2498 " --> pdb=" O ASN B2494 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B2503 " --> pdb=" O GLN B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2533 Processing helix chain 'B' and resid 2534 through 2539 Processing helix chain 'B' and resid 2540 through 2541 No H-bonds generated for 'chain 'B' and resid 2540 through 2541' Processing helix chain 'B' and resid 2542 through 2546 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 52 through 70 Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.791A pdb=" N ILE F 84 " --> pdb=" O HIS F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.539A pdb=" N LEU F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 removed outlier: 4.349A pdb=" N LEU F 128 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 157 removed outlier: 3.663A pdb=" N GLN F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 147 " --> pdb=" O ARG F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.646A pdb=" N PHE F 161 " --> pdb=" O ALA F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 175 removed outlier: 3.568A pdb=" N THR F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.686A pdb=" N ILE F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.875A pdb=" N VAL F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 205 " --> pdb=" O VAL F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 removed outlier: 3.849A pdb=" N THR F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 235 removed outlier: 3.945A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.516A pdb=" N ILE F 253 " --> pdb=" O LEU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 273 through 292 removed outlier: 3.541A pdb=" N ARG F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 302 removed outlier: 3.553A pdb=" N ASN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 315 removed outlier: 3.509A pdb=" N VAL F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 323 through 335 removed outlier: 3.678A pdb=" N LEU F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 353 removed outlier: 3.625A pdb=" N ALA F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 362 Processing helix chain 'F' and resid 363 through 368 removed outlier: 4.071A pdb=" N PHE F 368 " --> pdb=" O LEU F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 377 removed outlier: 3.750A pdb=" N THR F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 402 removed outlier: 3.735A pdb=" N ASN F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 414 removed outlier: 3.709A pdb=" N GLY F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 438 removed outlier: 3.927A pdb=" N ARG F 422 " --> pdb=" O HIS F 418 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN F 435 " --> pdb=" O LEU F 431 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR F 436 " --> pdb=" O HIS F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.775A pdb=" N MET F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 486 removed outlier: 3.552A pdb=" N ARG F 466 " --> pdb=" O PRO F 462 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY F 486 " --> pdb=" O MET F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 509 removed outlier: 3.510A pdb=" N HIS F 496 " --> pdb=" O LEU F 492 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP F 509 " --> pdb=" O HIS F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 535 removed outlier: 3.676A pdb=" N LEU F 529 " --> pdb=" O GLU F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 557 Processing helix chain 'F' and resid 567 through 582 Processing helix chain 'F' and resid 598 through 615 removed outlier: 3.597A pdb=" N LEU F 613 " --> pdb=" O THR F 609 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER F 615 " --> pdb=" O PHE F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 639 removed outlier: 3.708A pdb=" N LEU F 623 " --> pdb=" O GLY F 619 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP F 625 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY F 639 " --> pdb=" O ASN F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 652 Processing helix chain 'F' and resid 654 through 657 removed outlier: 3.724A pdb=" N GLN F 657 " --> pdb=" O THR F 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 654 through 657' Processing helix chain 'F' and resid 658 through 668 removed outlier: 3.534A pdb=" N PHE F 662 " --> pdb=" O HIS F 658 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE F 663 " --> pdb=" O TYR F 659 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS F 668 " --> pdb=" O GLY F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 679 removed outlier: 3.770A pdb=" N LYS F 674 " --> pdb=" O PRO F 670 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET F 675 " --> pdb=" O HIS F 671 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS F 679 " --> pdb=" O MET F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 681 through 689 Processing helix chain 'F' and resid 695 through 703 Processing helix chain 'F' and resid 711 through 723 removed outlier: 3.821A pdb=" N VAL F 715 " --> pdb=" O GLY F 711 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 717 " --> pdb=" O ALA F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 735 Processing helix chain 'F' and resid 736 through 741 Processing helix chain 'F' and resid 746 through 759 removed outlier: 3.937A pdb=" N TRP F 750 " --> pdb=" O PHE F 746 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU F 753 " --> pdb=" O ASN F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 763 through 778 removed outlier: 3.540A pdb=" N SER F 767 " --> pdb=" O ASN F 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 780 through 789 removed outlier: 3.543A pdb=" N ALA F 786 " --> pdb=" O ALA F 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 806 removed outlier: 3.569A pdb=" N LEU F 802 " --> pdb=" O GLY F 798 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 810 Processing helix chain 'F' and resid 811 through 821 removed outlier: 6.366A pdb=" N TYR F 817 " --> pdb=" O LYS F 813 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU F 820 " --> pdb=" O SER F 816 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG F 821 " --> pdb=" O TYR F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 823 through 834 removed outlier: 3.790A pdb=" N GLU F 829 " --> pdb=" O ALA F 825 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS F 830 " --> pdb=" O LYS F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 852 removed outlier: 4.197A pdb=" N VAL F 840 " --> pdb=" O ASN F 836 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 881 through 887 removed outlier: 3.610A pdb=" N VAL F 887 " --> pdb=" O TYR F 883 " (cutoff:3.500A) Processing helix chain 'F' and resid 890 through 898 removed outlier: 3.865A pdb=" N HIS F 894 " --> pdb=" O LYS F 890 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 911 Processing helix chain 'F' and resid 917 through 934 Processing helix chain 'F' and resid 936 through 945 removed outlier: 3.626A pdb=" N ASN F 941 " --> pdb=" O ASN F 937 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU F 942 " --> pdb=" O TRP F 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 948 through 959 removed outlier: 3.818A pdb=" N LYS F 957 " --> pdb=" O LEU F 953 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS F 959 " --> pdb=" O LEU F 955 " (cutoff:3.500A) Processing helix chain 'F' and resid 961 through 976 removed outlier: 3.638A pdb=" N VAL F 969 " --> pdb=" O ARG F 965 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 976 " --> pdb=" O LEU F 972 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 988 removed outlier: 3.660A pdb=" N CYS F 987 " --> pdb=" O ASP F 983 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS F 988 " --> pdb=" O ILE F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 1432 through 1436 removed outlier: 3.751A pdb=" N ILE F1436 " --> pdb=" O ILE F1433 " (cutoff:3.500A) Processing helix chain 'F' and resid 1480 through 1487 removed outlier: 4.002A pdb=" N GLN F1485 " --> pdb=" O HIS F1481 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN F1486 " --> pdb=" O LEU F1482 " (cutoff:3.500A) Processing helix chain 'F' and resid 1488 through 1493 Processing helix chain 'F' and resid 1522 through 1529 removed outlier: 3.964A pdb=" N ILE F1526 " --> pdb=" O TYR F1522 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU F1527 " --> pdb=" O CYS F1523 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F1528 " --> pdb=" O VAL F1524 " (cutoff:3.500A) Processing helix chain 'F' and resid 1609 through 1623 removed outlier: 3.552A pdb=" N LYS F1614 " --> pdb=" O ILE F1610 " (cutoff:3.500A) Processing helix chain 'F' and resid 1628 through 1643 removed outlier: 4.018A pdb=" N HIS F1632 " --> pdb=" O SER F1628 " (cutoff:3.500A) Processing helix chain 'F' and resid 1649 through 1661 removed outlier: 3.861A pdb=" N GLU F1655 " --> pdb=" O CYS F1651 " (cutoff:3.500A) Processing helix chain 'F' and resid 1666 through 1677 removed outlier: 3.943A pdb=" N PHE F1677 " --> pdb=" O ILE F1673 " (cutoff:3.500A) Processing helix chain 'F' and resid 1682 through 1694 removed outlier: 3.550A pdb=" N HIS F1686 " --> pdb=" O PHE F1682 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 21 Processing helix chain 'H' and resid 25 through 31 removed outlier: 3.990A pdb=" N MET H 29 " --> pdb=" O GLY H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 101 removed outlier: 3.690A pdb=" N ASN H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 124 removed outlier: 4.040A pdb=" N SER H 122 " --> pdb=" O GLN H 118 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 146 Processing sheet with id=AA1, first strand: chain 'B' and resid 2120 through 2122 removed outlier: 4.234A pdb=" N GLN B2161 " --> pdb=" O LYS B2171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2153 through 2156 removed outlier: 6.443A pdb=" N SER B2234 " --> pdb=" O LEU B2230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2243 through 2245 Processing sheet with id=AA4, first strand: chain 'D' and resid 34 through 39 removed outlier: 3.888A pdb=" N ARG D 36 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 19 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 15 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS D 317 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.676A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER D 80 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 93 removed outlier: 3.769A pdb=" N SER D 90 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 136 removed outlier: 6.659A pdb=" N GLY D 146 " --> pdb=" O ASN D 132 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D 134 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE D 144 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU D 136 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU D 142 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 178 removed outlier: 6.983A pdb=" N VAL D 188 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA D 176 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA D 186 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS D 194 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS D 215 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 196 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 211 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 223 through 228 removed outlier: 3.597A pdb=" N GLN D 225 " --> pdb=" O CYS D 238 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.681A pdb=" N ALA D 294 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU D 307 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU D 296 " --> pdb=" O LYS D 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 990 through 992 1281 hydrogen bonds defined for protein. 3795 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: 5.77 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 8481 1.37 - 1.51: 6388 1.51 - 1.65: 10389 1.65 - 1.79: 22 1.79 - 1.93: 225 Bond restraints: 25505 Sorted by residual: bond pdb=" O24 IHP B2602 " pdb=" P4 IHP B2602 " ideal model delta sigma weight residual 1.532 1.619 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" O3G AGS B2601 " pdb=" PG AGS B2601 " ideal model delta sigma weight residual 1.570 1.484 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" O3G AGS F4802 " pdb=" PG AGS F4802 " ideal model delta sigma weight residual 1.570 1.484 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" O34 IHP B2602 " pdb=" P4 IHP B2602 " ideal model delta sigma weight residual 1.533 1.618 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C5 AGS B2601 " pdb=" C6 AGS B2601 " ideal model delta sigma weight residual 1.407 1.329 0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 25500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 34185 2.07 - 4.13: 303 4.13 - 6.20: 82 6.20 - 8.26: 15 8.26 - 10.33: 9 Bond angle restraints: 34594 Sorted by residual: angle pdb=" N1 AGS F4802 " pdb=" C2 AGS F4802 " pdb=" N3 AGS F4802 " ideal model delta sigma weight residual 128.45 118.12 10.33 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N1 AGS B2601 " pdb=" C2 AGS B2601 " pdb=" N3 AGS B2601 " ideal model delta sigma weight residual 128.45 118.21 10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N VAL B2389 " pdb=" CA VAL B2389 " pdb=" C VAL B2389 " ideal model delta sigma weight residual 113.42 109.69 3.73 1.17e+00 7.31e-01 1.02e+01 angle pdb=" PB AGS F4802 " pdb=" O3B AGS F4802 " pdb=" PG AGS F4802 " ideal model delta sigma weight residual 129.21 120.05 9.16 3.00e+00 1.11e-01 9.33e+00 angle pdb=" N MET H 26 " pdb=" CA MET H 26 " pdb=" C MET H 26 " ideal model delta sigma weight residual 111.37 116.41 -5.04 1.65e+00 3.67e-01 9.32e+00 ... (remaining 34589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.79: 15054 32.79 - 65.59: 390 65.59 - 98.38: 37 98.38 - 131.17: 1 131.17 - 163.97: 4 Dihedral angle restraints: 15486 sinusoidal: 6316 harmonic: 9170 Sorted by residual: dihedral pdb=" CA GLY F 367 " pdb=" C GLY F 367 " pdb=" N PHE F 368 " pdb=" CA PHE F 368 " ideal model delta harmonic sigma weight residual -180.00 -149.27 -30.73 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" O1B AGS F4802 " pdb=" O3B AGS F4802 " pdb=" PB AGS F4802 " pdb=" PG AGS F4802 " ideal model delta sinusoidal sigma weight residual 138.55 -57.48 -163.97 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O1A AGS B2601 " pdb=" O3A AGS B2601 " pdb=" PA AGS B2601 " pdb=" PB AGS B2601 " ideal model delta sinusoidal sigma weight residual 82.37 -70.69 153.06 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 15483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3608 0.068 - 0.135: 314 0.135 - 0.203: 7 0.203 - 0.271: 3 0.271 - 0.338: 3 Chirality restraints: 3935 Sorted by residual: chirality pdb=" C3' AGS F4802 " pdb=" C2' AGS F4802 " pdb=" C4' AGS F4802 " pdb=" O3' AGS F4802 " both_signs ideal model delta sigma weight residual False -2.37 -2.71 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C3' AGS B2601 " pdb=" C2' AGS B2601 " pdb=" C4' AGS B2601 " pdb=" O3' AGS B2601 " both_signs ideal model delta sigma weight residual False -2.37 -2.70 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C4' AGS B2601 " pdb=" C3' AGS B2601 " pdb=" C5' AGS B2601 " pdb=" O4' AGS B2601 " both_signs ideal model delta sigma weight residual False -2.41 -2.69 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3932 not shown) Planarity restraints: 4391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 76 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 77 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 77 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 77 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 384 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO F 385 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 385 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 385 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1473 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B1474 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B1474 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1474 " -0.023 5.00e-02 4.00e+02 ... (remaining 4388 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 669 2.71 - 3.26: 25105 3.26 - 3.81: 38637 3.81 - 4.35: 50548 4.35 - 4.90: 85416 Nonbonded interactions: 200375 Sorted by model distance: nonbonded pdb=" O LEU B 894 " pdb=" OH TYR B1583 " model vdw 2.167 3.040 nonbonded pdb=" OD1 ASP D 53 " pdb=" OG SER D 55 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B2332 " pdb=" OD2 ASP B2512 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU B2025 " pdb=" NH2 ARG B2170 " model vdw 2.270 3.120 nonbonded pdb=" NH2 ARG F 910 " pdb=" O GLU F 946 " model vdw 2.281 3.120 ... (remaining 200370 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.910 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 25510 Z= 0.197 Angle : 0.585 10.331 34597 Z= 0.303 Chirality : 0.040 0.338 3935 Planarity : 0.003 0.043 4391 Dihedral : 14.816 163.965 9518 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.26 % Allowed : 9.93 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.14), residues: 3096 helix: -1.26 (0.11), residues: 1869 sheet: -1.92 (0.34), residues: 184 loop : -2.51 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 533 TYR 0.021 0.001 TYR F1522 PHE 0.015 0.001 PHE F 573 TRP 0.018 0.001 TRP D 297 HIS 0.004 0.001 HIS B2340 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (25505) covalent geometry : angle 0.58391 / 0.30 (34594) hydrogen bonds : bond 0.14464 / 9.51 ( 1281) hydrogen bonds : angle 5.80883 / 4.14 ( 3795) metal coordination : bond 0.09222 / 4.81 ( 4) metal coordination : angle 3.63158 / 2.03 ( 3) Misc. bond : bond 0.10417 / 5.48 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 383 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 2045 LYS cc_start: 0.8641 (mptt) cc_final: 0.8289 (mptt) REVERT: B 2143 THR cc_start: 0.8098 (t) cc_final: 0.7782 (t) REVERT: D 155 TRP cc_start: 0.6719 (t60) cc_final: 0.6396 (t60) REVERT: D 185 MET cc_start: 0.8135 (tmm) cc_final: 0.7679 (tmt) REVERT: F 57 LEU cc_start: 0.7608 (pp) cc_final: 0.7312 (tp) REVERT: F 137 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7447 (tm-30) REVERT: F 247 ASP cc_start: 0.7287 (m-30) cc_final: 0.7058 (m-30) REVERT: F 453 MET cc_start: 0.8364 (mmm) cc_final: 0.8160 (mmm) REVERT: F 852 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7885 (m) REVERT: F 1617 LEU cc_start: 0.8492 (mt) cc_final: 0.8259 (mt) outliers start: 34 outliers final: 16 residues processed: 413 average time/residue: 0.7210 time to fit residues: 341.0003 Evaluate side-chains 260 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1768 THR Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 791 ASN B 797 ASN B 838 GLN B 967 HIS B1014 GLN B1045 ASN B1049 GLN B1202 HIS B1687 HIS B1715 GLN B1719 HIS B1722 GLN B1744 HIS B1809 GLN D 41 GLN D 44 GLN D 64 HIS D 71 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 94 ASN F 145 GLN F 359 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN F 418 HIS F 447 HIS F 496 HIS F 505 HIS F 539 GLN F 540 HIS F 549 ASN F 846 GLN F 848 ASN F 908 ASN F 958 GLN F1535 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099970 restraints weight = 35686.074| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.75 r_work: 0.3023 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25510 Z= 0.178 Angle : 0.586 9.925 34597 Z= 0.299 Chirality : 0.043 0.259 3935 Planarity : 0.004 0.049 4391 Dihedral : 8.197 149.934 3521 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.30 % Allowed : 16.34 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 3096 helix: -0.37 (0.12), residues: 1918 sheet: -1.48 (0.35), residues: 194 loop : -2.10 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1955 TYR 0.015 0.002 TYR B1700 PHE 0.017 0.001 PHE B1122 TRP 0.027 0.001 TRP D 99 HIS 0.007 0.001 HIS B1594 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (25505) covalent geometry : angle 0.58582 / 0.30 (34594) hydrogen bonds : bond 0.04582 / 3.05 ( 1281) hydrogen bonds : angle 4.48385 / 3.26 ( 3795) metal coordination : bond 0.01118 / 0.58 ( 4) metal coordination : angle 2.58467 / 1.39 ( 3) Misc. bond : bond 0.00166 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 264 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: B 791 ASN cc_start: 0.3740 (OUTLIER) cc_final: 0.3480 (t0) REVERT: B 823 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7520 (mp) REVERT: B 853 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 994 MET cc_start: 0.8693 (tpp) cc_final: 0.8389 (mmm) REVERT: B 1174 MET cc_start: 0.8814 (mmm) cc_final: 0.8542 (mmm) REVERT: B 1525 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6413 (mp10) REVERT: B 2045 LYS cc_start: 0.9011 (mptt) cc_final: 0.8653 (mptt) REVERT: B 2430 ARG cc_start: 0.7712 (ttp-170) cc_final: 0.7491 (ttp-170) REVERT: D 44 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: D 185 MET cc_start: 0.8348 (tmm) cc_final: 0.8083 (tmt) REVERT: D 255 MET cc_start: 0.8468 (tpp) cc_final: 0.8206 (tpt) REVERT: D 273 MET cc_start: 0.8737 (mmt) cc_final: 0.8381 (tpt) REVERT: F 55 ARG cc_start: 0.8048 (ptm160) cc_final: 0.7842 (ptp-110) REVERT: F 79 PHE cc_start: 0.7169 (m-80) cc_final: 0.6795 (m-80) REVERT: F 137 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7400 (tm-30) REVERT: F 254 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8346 (pp) REVERT: F 922 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8145 (mmmt) REVERT: F 946 GLU cc_start: 0.7547 (mp0) cc_final: 0.7320 (mp0) REVERT: F 964 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7914 (pp) REVERT: F 1679 ASP cc_start: 0.8103 (t0) cc_final: 0.7369 (m-30) REVERT: H 104 LYS cc_start: 0.7950 (ptpp) cc_final: 0.7692 (ptmm) outliers start: 89 outliers final: 39 residues processed: 323 average time/residue: 0.6224 time to fit residues: 234.0618 Evaluate side-chains 277 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1236 MET Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1525 GLN Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 535 SER Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 9 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 225 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 216 optimal weight: 0.6980 chunk 271 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1106 ASN D 44 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 94 ASN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 758 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102142 restraints weight = 35711.064| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.83 r_work: 0.3053 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25510 Z= 0.115 Angle : 0.528 9.490 34597 Z= 0.269 Chirality : 0.040 0.186 3935 Planarity : 0.004 0.050 4391 Dihedral : 7.963 145.248 3516 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.22 % Allowed : 17.27 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3096 helix: 0.17 (0.12), residues: 1914 sheet: -1.27 (0.35), residues: 194 loop : -1.89 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1955 TYR 0.012 0.001 TYR F 565 PHE 0.014 0.001 PHE F 573 TRP 0.012 0.001 TRP D 99 HIS 0.005 0.001 HIS B2410 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (25505) covalent geometry : angle 0.52808 / 0.27 (34594) hydrogen bonds : bond 0.03684 / 2.44 ( 1281) hydrogen bonds : angle 4.18826 / 3.05 ( 3795) metal coordination : bond 0.00782 / 0.41 ( 4) metal coordination : angle 1.58620 / 0.95 ( 3) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 253 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7409 (t80) REVERT: B 994 MET cc_start: 0.8649 (tpp) cc_final: 0.8361 (mmm) REVERT: B 1174 MET cc_start: 0.8815 (mmm) cc_final: 0.8576 (mmm) REVERT: B 1235 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8489 (mtm110) REVERT: B 1467 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6862 (mtt) REVERT: B 1529 MET cc_start: 0.8629 (ttt) cc_final: 0.8363 (ttt) REVERT: B 2045 LYS cc_start: 0.8973 (mptt) cc_final: 0.8633 (mptt) REVERT: B 2429 TRP cc_start: 0.7652 (OUTLIER) cc_final: 0.7287 (p90) REVERT: B 2515 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6785 (t70) REVERT: D 44 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: D 135 CYS cc_start: 0.7937 (t) cc_final: 0.7112 (p) REVERT: D 155 TRP cc_start: 0.6700 (t60) cc_final: 0.6359 (t60) REVERT: D 185 MET cc_start: 0.8386 (tmm) cc_final: 0.8137 (tmt) REVERT: D 255 MET cc_start: 0.8490 (tpp) cc_final: 0.8253 (tpt) REVERT: D 273 MET cc_start: 0.8738 (mmt) cc_final: 0.8499 (tpt) REVERT: F 55 ARG cc_start: 0.8016 (ptm160) cc_final: 0.7814 (ptp-110) REVERT: F 57 LEU cc_start: 0.7723 (pp) cc_final: 0.7422 (tp) REVERT: F 79 PHE cc_start: 0.7234 (m-80) cc_final: 0.6835 (m-80) REVERT: F 137 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7391 (tm-30) REVERT: F 254 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8185 (pp) REVERT: F 852 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8364 (m) REVERT: F 960 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: F 964 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7873 (pp) REVERT: F 1679 ASP cc_start: 0.8154 (t0) cc_final: 0.7387 (m-30) REVERT: F 1683 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7568 (tm) outliers start: 87 outliers final: 41 residues processed: 308 average time/residue: 0.6213 time to fit residues: 223.8817 Evaluate side-chains 289 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1236 MET Chi-restraints excluded: chain B residue 1467 MET Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 1998 MET Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2089 MET Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2515 HIS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 960 GLU Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1521 LEU Chi-restraints excluded: chain F residue 1683 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 203 optimal weight: 1.9990 chunk 308 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 293 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 286 optimal weight: 0.1980 chunk 296 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1719 HIS B2340 HIS B2385 ASN B2401 HIS D 44 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102746 restraints weight = 35463.582| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.83 r_work: 0.3031 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25510 Z= 0.113 Angle : 0.523 9.152 34597 Z= 0.265 Chirality : 0.040 0.179 3935 Planarity : 0.004 0.057 4391 Dihedral : 7.841 147.418 3512 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.71 % Allowed : 17.38 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 3096 helix: 0.41 (0.12), residues: 1930 sheet: -1.09 (0.35), residues: 192 loop : -1.84 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1955 TYR 0.012 0.001 TYR B2275 PHE 0.014 0.001 PHE B1122 TRP 0.012 0.001 TRP B1916 HIS 0.005 0.001 HIS B1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (25505) covalent geometry : angle 0.52282 / 0.27 (34594) hydrogen bonds : bond 0.03499 / 2.33 ( 1281) hydrogen bonds : angle 4.05095 / 2.96 ( 3795) metal coordination : bond 0.00442 / 0.23 ( 4) metal coordination : angle 1.33551 / 0.89 ( 3) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 258 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7420 (t80) REVERT: B 994 MET cc_start: 0.8666 (tpp) cc_final: 0.8383 (mmm) REVERT: B 1141 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7623 (ttp-110) REVERT: B 1174 MET cc_start: 0.8895 (mmm) cc_final: 0.8599 (mmm) REVERT: B 1235 ARG cc_start: 0.8741 (mtm110) cc_final: 0.8396 (mtm110) REVERT: B 1529 MET cc_start: 0.8669 (ttt) cc_final: 0.8239 (ttt) REVERT: B 1595 MET cc_start: 0.8728 (ttm) cc_final: 0.8461 (ttm) REVERT: B 2045 LYS cc_start: 0.8982 (mptt) cc_final: 0.8700 (mmtt) REVERT: B 2143 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8319 (t) REVERT: B 2429 TRP cc_start: 0.7716 (OUTLIER) cc_final: 0.7337 (p90) REVERT: B 2432 MET cc_start: 0.6543 (mtp) cc_final: 0.6136 (mpt) REVERT: B 2515 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.6742 (t70) REVERT: D 44 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: D 135 CYS cc_start: 0.7986 (t) cc_final: 0.7236 (p) REVERT: D 155 TRP cc_start: 0.6640 (t60) cc_final: 0.6283 (t60) REVERT: D 185 MET cc_start: 0.8439 (tmm) cc_final: 0.8219 (tmt) REVERT: D 255 MET cc_start: 0.8514 (tpp) cc_final: 0.8288 (tpt) REVERT: D 273 MET cc_start: 0.8774 (mmt) cc_final: 0.8500 (tpt) REVERT: F 57 LEU cc_start: 0.7730 (pp) cc_final: 0.7440 (tp) REVERT: F 76 LYS cc_start: 0.8788 (tttt) cc_final: 0.8578 (tttt) REVERT: F 79 PHE cc_start: 0.7320 (m-80) cc_final: 0.6956 (m-80) REVERT: F 137 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7359 (tm-30) REVERT: F 254 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8176 (pp) REVERT: F 531 ASN cc_start: 0.8609 (t0) cc_final: 0.8385 (t0) REVERT: F 629 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7420 (t0) REVERT: F 852 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8393 (m) REVERT: F 954 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8359 (ptmm) REVERT: F 960 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: F 964 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7784 (pp) REVERT: F 1679 ASP cc_start: 0.8220 (t0) cc_final: 0.7440 (m-30) outliers start: 100 outliers final: 54 residues processed: 327 average time/residue: 0.6284 time to fit residues: 241.5531 Evaluate side-chains 305 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1141 ARG Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 1998 MET Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2079 MET Chi-restraints excluded: chain B residue 2089 MET Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2413 SER Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain B residue 2515 HIS Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 960 GLU Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 71 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 284 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B2499 GLN D 44 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 696 HIS F 995 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100382 restraints weight = 35595.611| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.80 r_work: 0.3020 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25510 Z= 0.174 Angle : 0.574 9.342 34597 Z= 0.289 Chirality : 0.042 0.183 3935 Planarity : 0.004 0.057 4391 Dihedral : 7.916 147.607 3512 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.96 % Allowed : 18.12 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3096 helix: 0.42 (0.12), residues: 1926 sheet: -0.94 (0.35), residues: 191 loop : -1.78 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1955 TYR 0.012 0.001 TYR F 839 PHE 0.019 0.001 PHE B1122 TRP 0.026 0.001 TRP D 297 HIS 0.006 0.001 HIS B1594 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (25505) covalent geometry : angle 0.57349 / 0.29 (34594) hydrogen bonds : bond 0.04132 / 2.75 ( 1281) hydrogen bonds : angle 4.14015 / 3.02 ( 3795) metal coordination : bond 0.00595 / 0.31 ( 4) metal coordination : angle 1.69881 / 0.97 ( 3) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 253 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7443 (t80) REVERT: B 1141 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7603 (ttp-110) REVERT: B 1174 MET cc_start: 0.8883 (mmm) cc_final: 0.8583 (mmm) REVERT: B 1235 ARG cc_start: 0.8721 (mtm110) cc_final: 0.8391 (mtm110) REVERT: B 1368 ASP cc_start: 0.7626 (p0) cc_final: 0.7418 (p0) REVERT: B 1501 TRP cc_start: 0.7792 (t-100) cc_final: 0.7572 (t-100) REVERT: B 1529 MET cc_start: 0.8672 (ttt) cc_final: 0.8253 (ttt) REVERT: B 1578 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7552 (ttm) REVERT: B 1996 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8419 (tmtm) REVERT: B 2045 LYS cc_start: 0.8959 (mptt) cc_final: 0.8674 (mmtt) REVERT: B 2143 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8584 (p) REVERT: B 2322 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8552 (mtm-85) REVERT: B 2429 TRP cc_start: 0.7629 (OUTLIER) cc_final: 0.7246 (p90) REVERT: D 44 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: D 135 CYS cc_start: 0.8109 (t) cc_final: 0.7438 (p) REVERT: D 185 MET cc_start: 0.8429 (tmm) cc_final: 0.8151 (tmt) REVERT: D 255 MET cc_start: 0.8576 (tpp) cc_final: 0.8322 (tpt) REVERT: D 273 MET cc_start: 0.8748 (mmt) cc_final: 0.8467 (tpt) REVERT: F 57 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7451 (tp) REVERT: F 79 PHE cc_start: 0.7569 (m-80) cc_final: 0.7224 (m-80) REVERT: F 137 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7214 (tm-30) REVERT: F 254 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8320 (pp) REVERT: F 272 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: F 531 ASN cc_start: 0.8613 (t0) cc_final: 0.8406 (t0) REVERT: F 629 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7414 (t0) REVERT: F 922 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8120 (mmmt) REVERT: F 954 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8381 (ptmm) REVERT: F 960 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: F 964 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7901 (pp) REVERT: F 998 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7493 (ttmt) REVERT: F 1516 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7866 (p) REVERT: F 1679 ASP cc_start: 0.8196 (t0) cc_final: 0.7440 (m-30) REVERT: F 1683 LEU cc_start: 0.7902 (tp) cc_final: 0.7638 (tm) outliers start: 107 outliers final: 64 residues processed: 332 average time/residue: 0.6135 time to fit residues: 239.6423 Evaluate side-chains 325 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 245 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1038 MET Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1141 ARG Chi-restraints excluded: chain B residue 1236 MET Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1571 LEU Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1578 MET Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 1998 MET Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2079 MET Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2281 MET Chi-restraints excluded: chain B residue 2322 ARG Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2413 SER Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 535 SER Chi-restraints excluded: chain F residue 550 LEU Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 960 GLU Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 998 LYS Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1516 THR Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1620 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 201 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 171 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 209 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1719 HIS D 44 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101052 restraints weight = 35594.795| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.70 r_work: 0.3064 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25510 Z= 0.117 Angle : 0.538 9.772 34597 Z= 0.270 Chirality : 0.040 0.179 3935 Planarity : 0.004 0.066 4391 Dihedral : 7.830 148.149 3510 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.78 % Allowed : 19.01 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3096 helix: 0.63 (0.12), residues: 1927 sheet: -0.99 (0.37), residues: 180 loop : -1.68 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B1955 TYR 0.020 0.001 TYR F1643 PHE 0.014 0.001 PHE B1122 TRP 0.018 0.001 TRP D 297 HIS 0.006 0.001 HIS B1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (25505) covalent geometry : angle 0.53746 / 0.27 (34594) hydrogen bonds : bond 0.03528 / 2.34 ( 1281) hydrogen bonds : angle 4.00864 / 2.93 ( 3795) metal coordination : bond 0.00461 / 0.24 ( 4) metal coordination : angle 1.29517 / 0.87 ( 3) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 259 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7269 (t80) REVERT: B 886 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7536 (ttm170) REVERT: B 994 MET cc_start: 0.8611 (tpp) cc_final: 0.8328 (mmm) REVERT: B 1141 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7558 (ttp-110) REVERT: B 1174 MET cc_start: 0.8869 (mmm) cc_final: 0.8589 (mmm) REVERT: B 1529 MET cc_start: 0.8659 (ttt) cc_final: 0.8229 (ttt) REVERT: B 1996 LYS cc_start: 0.8661 (tmmt) cc_final: 0.8413 (tmtm) REVERT: B 2045 LYS cc_start: 0.8940 (mptt) cc_final: 0.8541 (mptt) REVERT: B 2143 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8352 (t) REVERT: B 2322 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8568 (mtm-85) REVERT: B 2429 TRP cc_start: 0.7630 (OUTLIER) cc_final: 0.7246 (p90) REVERT: B 2432 MET cc_start: 0.6320 (mtp) cc_final: 0.6024 (mpt) REVERT: D 44 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: D 135 CYS cc_start: 0.8063 (t) cc_final: 0.7385 (p) REVERT: D 155 TRP cc_start: 0.6539 (t60) cc_final: 0.6176 (t60) REVERT: D 255 MET cc_start: 0.8517 (tpp) cc_final: 0.8271 (tpt) REVERT: D 273 MET cc_start: 0.8717 (mmt) cc_final: 0.8431 (tpt) REVERT: F 57 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7416 (tp) REVERT: F 79 PHE cc_start: 0.7706 (m-80) cc_final: 0.7399 (m-80) REVERT: F 137 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7177 (tm-30) REVERT: F 254 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8175 (pp) REVERT: F 272 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: F 629 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7379 (t0) REVERT: F 790 MET cc_start: 0.8704 (ptp) cc_final: 0.8355 (pmm) REVERT: F 852 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8380 (m) REVERT: F 922 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8071 (mmmt) REVERT: F 954 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8363 (ptmm) REVERT: F 960 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: F 964 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7783 (pp) REVERT: F 998 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7476 (ttmt) REVERT: F 1516 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7850 (p) REVERT: F 1679 ASP cc_start: 0.8165 (t0) cc_final: 0.7457 (m-30) REVERT: H 29 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8203 (mpp) REVERT: H 107 GLN cc_start: 0.7343 (mp10) cc_final: 0.7131 (mp-120) outliers start: 102 outliers final: 60 residues processed: 337 average time/residue: 0.6135 time to fit residues: 243.4268 Evaluate side-chains 326 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 249 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1141 ARG Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1571 LEU Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 1998 MET Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2079 MET Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2322 ARG Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2413 SER Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 535 SER Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 802 LEU Chi-restraints excluded: chain F residue 811 ILE Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 960 GLU Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 998 LYS Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1516 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 5 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 308 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 878 GLN B1719 HIS D 44 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.133028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102145 restraints weight = 35394.149| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.81 r_work: 0.3028 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25510 Z= 0.117 Angle : 0.542 10.432 34597 Z= 0.270 Chirality : 0.040 0.177 3935 Planarity : 0.004 0.072 4391 Dihedral : 7.801 148.165 3510 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.89 % Allowed : 19.38 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 3096 helix: 0.72 (0.12), residues: 1930 sheet: -0.92 (0.37), residues: 179 loop : -1.60 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B1955 TYR 0.016 0.001 TYR F 565 PHE 0.015 0.001 PHE B1122 TRP 0.018 0.001 TRP D 297 HIS 0.008 0.001 HIS B1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (25505) covalent geometry : angle 0.54167 / 0.27 (34594) hydrogen bonds : bond 0.03468 / 2.30 ( 1281) hydrogen bonds : angle 3.96295 / 2.90 ( 3795) metal coordination : bond 0.00406 / 0.21 ( 4) metal coordination : angle 1.18020 / 0.78 ( 3) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 250 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7297 (t80) REVERT: B 994 MET cc_start: 0.8667 (tpp) cc_final: 0.8376 (mmm) REVERT: B 1141 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7622 (ttp-110) REVERT: B 1174 MET cc_start: 0.8917 (mmm) cc_final: 0.8625 (mmm) REVERT: B 1495 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7820 (tp-100) REVERT: B 1529 MET cc_start: 0.8698 (ttt) cc_final: 0.8309 (ttt) REVERT: B 1955 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8320 (ttp80) REVERT: B 1996 LYS cc_start: 0.8694 (tmmt) cc_final: 0.8460 (tmtm) REVERT: B 2045 LYS cc_start: 0.8970 (mptt) cc_final: 0.8569 (mptt) REVERT: B 2143 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8353 (t) REVERT: B 2322 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8580 (mtm-85) REVERT: B 2429 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.7275 (p90) REVERT: B 2432 MET cc_start: 0.6415 (mtp) cc_final: 0.6110 (mpt) REVERT: D 44 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: D 67 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8335 (mmm) REVERT: D 135 CYS cc_start: 0.8160 (t) cc_final: 0.7522 (p) REVERT: D 155 TRP cc_start: 0.6530 (t60) cc_final: 0.6220 (t60) REVERT: D 181 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7531 (t70) REVERT: D 255 MET cc_start: 0.8537 (tpp) cc_final: 0.8206 (tpt) REVERT: D 273 MET cc_start: 0.8783 (mmt) cc_final: 0.8476 (tpt) REVERT: F 57 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7438 (tp) REVERT: F 79 PHE cc_start: 0.7699 (m-80) cc_final: 0.7388 (m-80) REVERT: F 137 GLN cc_start: 0.7520 (tm-30) cc_final: 0.7154 (tm-30) REVERT: F 254 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8206 (pp) REVERT: F 272 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: F 629 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7416 (t0) REVERT: F 954 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8423 (ptmm) REVERT: F 960 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: F 964 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7812 (pp) REVERT: F 998 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7508 (ttmt) REVERT: F 1516 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7846 (p) REVERT: F 1679 ASP cc_start: 0.8270 (t0) cc_final: 0.7627 (m-30) REVERT: H 29 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8282 (mpp) outliers start: 105 outliers final: 64 residues processed: 331 average time/residue: 0.6231 time to fit residues: 240.8825 Evaluate side-chains 313 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 231 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1141 ARG Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1571 LEU Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 1998 MET Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2281 MET Chi-restraints excluded: chain B residue 2322 ARG Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2413 SER Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain B residue 2548 PHE Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 297 TRP Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 535 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 802 LEU Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 960 GLU Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 998 LYS Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1516 THR Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1537 LEU Chi-restraints excluded: chain F residue 1620 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 220 optimal weight: 0.6980 chunk 264 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1719 HIS B1992 ASN B2499 GLN D 44 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099948 restraints weight = 35522.047| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.72 r_work: 0.3027 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25510 Z= 0.151 Angle : 0.574 11.950 34597 Z= 0.285 Chirality : 0.042 0.195 3935 Planarity : 0.004 0.059 4391 Dihedral : 7.770 147.704 3507 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.74 % Allowed : 19.93 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3096 helix: 0.71 (0.12), residues: 1925 sheet: -0.97 (0.37), residues: 181 loop : -1.60 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1955 TYR 0.022 0.001 TYR F1643 PHE 0.017 0.001 PHE B1122 TRP 0.022 0.001 TRP D 297 HIS 0.009 0.001 HIS B1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (25505) covalent geometry : angle 0.57369 / 0.29 (34594) hydrogen bonds : bond 0.03823 / 2.54 ( 1281) hydrogen bonds : angle 4.02179 / 2.94 ( 3795) metal coordination : bond 0.00490 / 0.25 ( 4) metal coordination : angle 1.37955 / 0.80 ( 3) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 238 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7397 (t80) REVERT: B 1141 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7646 (ttp-110) REVERT: B 1174 MET cc_start: 0.8898 (mmm) cc_final: 0.8581 (mmm) REVERT: B 1368 ASP cc_start: 0.7730 (p0) cc_final: 0.7510 (p0) REVERT: B 1495 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7751 (tp-100) REVERT: B 1996 LYS cc_start: 0.8679 (tmmt) cc_final: 0.8463 (tttp) REVERT: B 2045 LYS cc_start: 0.8956 (mptt) cc_final: 0.8666 (mmtt) REVERT: B 2322 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8550 (mtm-85) REVERT: B 2429 TRP cc_start: 0.7688 (OUTLIER) cc_final: 0.7225 (p90) REVERT: D 44 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: D 67 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8335 (mmm) REVERT: D 135 CYS cc_start: 0.8124 (t) cc_final: 0.7524 (p) REVERT: D 155 TRP cc_start: 0.6561 (t60) cc_final: 0.6227 (t60) REVERT: D 181 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7494 (t70) REVERT: D 255 MET cc_start: 0.8544 (tpp) cc_final: 0.8195 (tpt) REVERT: D 273 MET cc_start: 0.8773 (mmt) cc_final: 0.8466 (tpt) REVERT: F 79 PHE cc_start: 0.7802 (m-80) cc_final: 0.7537 (m-80) REVERT: F 137 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7138 (tm-30) REVERT: F 254 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8278 (pp) REVERT: F 272 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: F 629 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7401 (t0) REVERT: F 790 MET cc_start: 0.8662 (ptp) cc_final: 0.8363 (pmm) REVERT: F 922 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8108 (mmmt) REVERT: F 954 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8405 (ptmm) REVERT: F 960 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: F 964 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7867 (pp) REVERT: F 998 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7495 (ttmt) REVERT: F 1516 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7844 (p) REVERT: F 1679 ASP cc_start: 0.8160 (t0) cc_final: 0.7551 (m-30) REVERT: H 29 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8226 (mpp) outliers start: 101 outliers final: 67 residues processed: 318 average time/residue: 0.6168 time to fit residues: 228.9517 Evaluate side-chains 320 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 237 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1141 ARG Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1338 ILE Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1571 LEU Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1768 THR Chi-restraints excluded: chain B residue 1895 SER Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 1998 MET Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2010 MET Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2079 MET Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2281 MET Chi-restraints excluded: chain B residue 2322 ARG Chi-restraints excluded: chain B residue 2326 VAL Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2413 SER Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain B residue 2548 PHE Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 535 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 802 LEU Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 960 GLU Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 998 LYS Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1516 THR Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1537 LEU Chi-restraints excluded: chain F residue 1620 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 277 optimal weight: 0.3980 chunk 107 optimal weight: 0.0010 chunk 222 optimal weight: 0.0980 chunk 162 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 256 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 217 optimal weight: 0.9980 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1719 HIS B2117 GLN D 40 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 219 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN F 564 ASN F 827 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104358 restraints weight = 35234.268| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.81 r_work: 0.3064 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25510 Z= 0.098 Angle : 0.538 11.286 34597 Z= 0.266 Chirality : 0.039 0.174 3935 Planarity : 0.004 0.079 4391 Dihedral : 7.652 147.804 3507 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.82 % Allowed : 21.01 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 3096 helix: 0.94 (0.12), residues: 1931 sheet: -0.92 (0.37), residues: 181 loop : -1.50 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B1955 TYR 0.013 0.001 TYR B1700 PHE 0.013 0.001 PHE B1011 TRP 0.015 0.001 TRP D 297 HIS 0.012 0.001 HIS B1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (25505) covalent geometry : angle 0.53808 / 0.27 (34594) hydrogen bonds : bond 0.03019 / 1.99 ( 1281) hydrogen bonds : angle 3.84432 / 2.81 ( 3795) metal coordination : bond 0.00445 / 0.23 ( 4) metal coordination : angle 1.20821 / 0.96 ( 3) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 267 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 886 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7608 (ttm170) REVERT: B 960 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8366 (mtt90) REVERT: B 994 MET cc_start: 0.8729 (tpp) cc_final: 0.8500 (mmm) REVERT: B 1141 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7619 (ttp-110) REVERT: B 1174 MET cc_start: 0.8864 (mmm) cc_final: 0.8643 (mmm) REVERT: B 1368 ASP cc_start: 0.7885 (p0) cc_final: 0.7614 (p0) REVERT: B 1495 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7792 (tp-100) REVERT: B 1595 MET cc_start: 0.8561 (ttm) cc_final: 0.8249 (ttm) REVERT: B 1955 ARG cc_start: 0.8725 (ttm110) cc_final: 0.8303 (ttp80) REVERT: B 1996 LYS cc_start: 0.8644 (tmmt) cc_final: 0.8403 (tmtm) REVERT: B 2016 LEU cc_start: 0.8692 (pp) cc_final: 0.8385 (pt) REVERT: B 2045 LYS cc_start: 0.8943 (mptt) cc_final: 0.8593 (mptt) REVERT: B 2059 GLU cc_start: 0.8157 (tt0) cc_final: 0.7821 (mt-10) REVERT: B 2429 TRP cc_start: 0.7704 (OUTLIER) cc_final: 0.7264 (p90) REVERT: D 135 CYS cc_start: 0.8131 (t) cc_final: 0.7528 (p) REVERT: D 155 TRP cc_start: 0.6442 (t60) cc_final: 0.6159 (t60) REVERT: D 181 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7552 (t70) REVERT: D 255 MET cc_start: 0.8416 (tpp) cc_final: 0.8196 (tpt) REVERT: D 273 MET cc_start: 0.8747 (mmt) cc_final: 0.8413 (tpt) REVERT: F 79 PHE cc_start: 0.7820 (m-80) cc_final: 0.7574 (m-80) REVERT: F 137 GLN cc_start: 0.7455 (tm-30) cc_final: 0.7089 (tm-30) REVERT: F 254 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8072 (pp) REVERT: F 597 LYS cc_start: 0.8098 (ptpp) cc_final: 0.7836 (pttm) REVERT: F 629 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7403 (t0) REVERT: F 709 ARG cc_start: 0.7553 (ptm-80) cc_final: 0.7298 (ptm-80) REVERT: F 954 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8389 (ptmm) REVERT: F 964 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7780 (pp) REVERT: F 998 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7508 (ttmt) REVERT: F 1516 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7825 (p) REVERT: F 1679 ASP cc_start: 0.8213 (t0) cc_final: 0.7895 (t70) outliers start: 76 outliers final: 45 residues processed: 325 average time/residue: 0.6114 time to fit residues: 233.0137 Evaluate side-chains 303 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1141 ARG Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1571 LEU Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 998 LYS Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1516 THR Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 170 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 199 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 80 optimal weight: 0.0370 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1719 HIS B2499 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103425 restraints weight = 35273.040| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.72 r_work: 0.3058 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25510 Z= 0.121 Angle : 0.560 11.804 34597 Z= 0.278 Chirality : 0.041 0.176 3935 Planarity : 0.004 0.077 4391 Dihedral : 7.632 147.207 3506 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.59 % Allowed : 21.60 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 3096 helix: 0.96 (0.12), residues: 1939 sheet: -0.85 (0.38), residues: 179 loop : -1.50 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B1955 TYR 0.021 0.001 TYR F1643 PHE 0.017 0.001 PHE D 320 TRP 0.019 0.001 TRP D 297 HIS 0.014 0.001 HIS B1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (25505) covalent geometry : angle 0.56024 / 0.28 (34594) hydrogen bonds : bond 0.03353 / 2.22 ( 1281) hydrogen bonds : angle 3.88522 / 2.84 ( 3795) metal coordination : bond 0.00410 / 0.21 ( 4) metal coordination : angle 1.13054 / 0.74 ( 3) Misc. bond : bond 0.00030 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 242 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: B 853 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7180 (t80) REVERT: B 960 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8355 (mtt90) REVERT: B 994 MET cc_start: 0.8688 (tpp) cc_final: 0.8407 (mmm) REVERT: B 1141 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7606 (ttp-110) REVERT: B 1174 MET cc_start: 0.8840 (mmm) cc_final: 0.8548 (mmm) REVERT: B 1368 ASP cc_start: 0.7854 (p0) cc_final: 0.7591 (p0) REVERT: B 1495 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7808 (tp-100) REVERT: B 1529 MET cc_start: 0.8551 (ttt) cc_final: 0.8335 (ttt) REVERT: B 1595 MET cc_start: 0.8600 (ttm) cc_final: 0.8265 (ttm) REVERT: B 1996 LYS cc_start: 0.8666 (tmmt) cc_final: 0.8445 (tmtm) REVERT: B 2045 LYS cc_start: 0.8929 (mptt) cc_final: 0.8582 (mptt) REVERT: B 2059 GLU cc_start: 0.8117 (tt0) cc_final: 0.7730 (mt-10) REVERT: B 2429 TRP cc_start: 0.7546 (OUTLIER) cc_final: 0.7145 (p90) REVERT: D 67 MET cc_start: 0.8499 (mpt) cc_final: 0.8287 (mmm) REVERT: D 135 CYS cc_start: 0.8079 (t) cc_final: 0.7552 (p) REVERT: D 181 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7544 (t70) REVERT: D 273 MET cc_start: 0.8720 (mmt) cc_final: 0.8381 (tpt) REVERT: F 79 PHE cc_start: 0.7793 (m-80) cc_final: 0.7569 (m-80) REVERT: F 83 ASP cc_start: 0.8051 (m-30) cc_final: 0.7822 (m-30) REVERT: F 137 GLN cc_start: 0.7477 (tm-30) cc_final: 0.7119 (tm-30) REVERT: F 254 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8168 (pp) REVERT: F 629 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7412 (t0) REVERT: F 709 ARG cc_start: 0.7549 (ptm-80) cc_final: 0.7282 (ptm-80) REVERT: F 954 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8401 (ptmm) REVERT: F 964 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7849 (pp) REVERT: F 998 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7479 (ttmt) REVERT: F 1516 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7842 (p) REVERT: F 1679 ASP cc_start: 0.8168 (t0) cc_final: 0.7862 (t70) outliers start: 70 outliers final: 51 residues processed: 300 average time/residue: 0.6261 time to fit residues: 220.5296 Evaluate side-chains 299 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 237 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1141 ARG Chi-restraints excluded: chain B residue 1172 THR Chi-restraints excluded: chain B residue 1372 LEU Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1572 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2057 MET Chi-restraints excluded: chain B residue 2164 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2228 ILE Chi-restraints excluded: chain B residue 2263 ILE Chi-restraints excluded: chain B residue 2327 MET Chi-restraints excluded: chain B residue 2429 TRP Chi-restraints excluded: chain B residue 2509 THR Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 702 VAL Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 802 LEU Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 893 CYS Chi-restraints excluded: chain F residue 954 LYS Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 998 LYS Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1514 GLU Chi-restraints excluded: chain F residue 1516 THR Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 166 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 307 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1334 GLN B1719 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102247 restraints weight = 35456.206| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.82 r_work: 0.3029 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 25510 Z= 0.189 Angle : 0.709 59.169 34597 Z= 0.395 Chirality : 0.043 0.335 3935 Planarity : 0.004 0.073 4391 Dihedral : 7.646 147.153 3506 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.70 % Allowed : 21.79 % Favored : 75.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 3096 helix: 0.92 (0.12), residues: 1939 sheet: -0.85 (0.38), residues: 179 loop : -1.52 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 39 TYR 0.011 0.002 TYR F1643 PHE 0.016 0.001 PHE D 320 TRP 0.019 0.001 TRP D 297 HIS 0.013 0.001 HIS B1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (25505) covalent geometry : angle 0.70895 / 0.39 (34594) hydrogen bonds : bond 0.03503 / 2.32 ( 1281) hydrogen bonds : angle 3.88982 / 2.85 ( 3795) metal coordination : bond 0.00483 / 0.25 ( 4) metal coordination : angle 1.18910 / 0.77 ( 3) Misc. bond : bond 0.00109 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8987.51 seconds wall clock time: 153 minutes 45.26 seconds (9225.26 seconds total)