Starting phenix.real_space_refine on Tue May 5 03:22:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t93_55715/05_2026/9t93_55715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t93_55715/05_2026/9t93_55715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t93_55715/05_2026/9t93_55715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t93_55715/05_2026/9t93_55715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t93_55715/05_2026/9t93_55715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t93_55715/05_2026/9t93_55715.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 7 5.49 5 S 159 5.16 5 C 16012 2.51 5 N 4430 2.21 5 O 4596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25205 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1573, 12757 Classifications: {'peptide': 1573} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 63, 'TRANS': 1509} Chain breaks: 6 Chain: "C" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2443 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 13, 'TRANS': 301} Chain: "E" Number of atoms: 8990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8990 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 37, 'TRANS': 1081} Chain breaks: 7 Chain: "G" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Unusual residues: {'ACE': 1} Classifications: {'peptide': 119, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23297 SG CYS E1520 117.067 85.531 28.767 1.00 85.52 S ATOM 23323 SG CYS E1523 116.644 87.812 25.833 1.00 87.28 S ATOM 23830 SG CYS E1651 114.610 84.458 26.025 1.00 76.22 S Time building chain proxies: 5.49, per 1000 atoms: 0.22 Number of scatterers: 25205 At special positions: 0 Unit cell: (181.45, 122.24, 153.755, 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 7 15.00 O 4596 8.00 N 4430 7.00 C 16012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E1801 " pdb="ZN ZN E1801 " - pdb=" NE2 HIS E1515 " pdb="ZN ZN E1801 " - pdb=" SG CYS E1520 " pdb="ZN ZN E1801 " - pdb=" SG CYS E1523 " pdb="ZN ZN E1801 " - pdb=" SG CYS E1651 " Number of angles added : 3 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 11 sheets defined 70.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 798 through 809 removed outlier: 3.802A pdb=" N ILE A 802 " --> pdb=" O VAL A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.787A pdb=" N LYS A 815 " --> pdb=" O GLU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 837 through 852 Processing helix chain 'A' and resid 855 through 861 removed outlier: 4.139A pdb=" N ARG A 859 " --> pdb=" O VAL A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 875 removed outlier: 4.081A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 892 Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.509A pdb=" N ASN A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 935 Processing helix chain 'A' and resid 942 through 960 removed outlier: 3.581A pdb=" N TYR A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Proline residue: A 948 - end of helix removed outlier: 3.653A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 965 Processing helix chain 'A' and resid 967 through 983 removed outlier: 3.660A pdb=" N GLY A 983 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 989 through 1004 Proline residue: A 995 - end of helix removed outlier: 3.558A pdb=" N ASN A 999 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1025 through 1029 Proline residue: A1029 - end of helix Processing helix chain 'A' and resid 1030 through 1042 Processing helix chain 'A' and resid 1048 through 1064 Processing helix chain 'A' and resid 1065 through 1069 removed outlier: 4.358A pdb=" N LYS A1068 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1084 removed outlier: 3.912A pdb=" N LEU A1074 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1101 Processing helix chain 'A' and resid 1102 through 1108 removed outlier: 5.970A pdb=" N ALA A1105 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1124 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1128 through 1143 Processing helix chain 'A' and resid 1151 through 1164 removed outlier: 3.850A pdb=" N HIS A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1186 through 1190 removed outlier: 4.412A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1202 removed outlier: 3.969A pdb=" N VAL A1198 " --> pdb=" O MET A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1219 removed outlier: 3.525A pdb=" N ARG A1215 " --> pdb=" O VAL A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1225 removed outlier: 3.581A pdb=" N GLU A1225 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1238 Processing helix chain 'A' and resid 1261 through 1270 removed outlier: 3.813A pdb=" N LEU A1265 " --> pdb=" O SER A1261 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS A1267 " --> pdb=" O ILE A1263 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A1268 " --> pdb=" O ASN A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1294 Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.543A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1317 Processing helix chain 'A' and resid 1317 through 1327 Processing helix chain 'A' and resid 1330 through 1348 removed outlier: 3.913A pdb=" N GLN A1348 " --> pdb=" O ALA A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1366 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1392 through 1407 removed outlier: 3.594A pdb=" N GLY A1407 " --> pdb=" O GLU A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1423 Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.682A pdb=" N GLY A1431 " --> pdb=" O GLU A1427 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1433 " --> pdb=" O ALA A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1445 removed outlier: 3.663A pdb=" N ILE A1445 " --> pdb=" O GLU A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 4.074A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1470 removed outlier: 4.046A pdb=" N VAL A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1488 removed outlier: 3.587A pdb=" N CYS A1483 " --> pdb=" O GLY A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1501 removed outlier: 3.615A pdb=" N LYS A1500 " --> pdb=" O GLN A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1523 removed outlier: 4.178A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A1513 " --> pdb=" O GLN A1509 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1534 removed outlier: 4.041A pdb=" N CYS A1534 " --> pdb=" O GLU A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 removed outlier: 4.656A pdb=" N ARG A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1571 Processing helix chain 'A' and resid 1571 through 1580 removed outlier: 3.933A pdb=" N ALA A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1608 removed outlier: 5.334A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A1592 " --> pdb=" O GLY A1588 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A1600 " --> pdb=" O LEU A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1624 removed outlier: 3.644A pdb=" N LEU A1623 " --> pdb=" O TRP A1619 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A1624 " --> pdb=" O TRP A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1641 Processing helix chain 'A' and resid 1649 through 1663 Processing helix chain 'A' and resid 1665 through 1678 Processing helix chain 'A' and resid 1693 through 1707 Processing helix chain 'A' and resid 1709 through 1728 removed outlier: 3.534A pdb=" N HIS A1719 " --> pdb=" O GLN A1715 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A1726 " --> pdb=" O GLN A1722 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A1727 " --> pdb=" O THR A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1763 removed outlier: 3.806A pdb=" N LYS A1753 " --> pdb=" O ARG A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1783 Processing helix chain 'A' and resid 1786 through 1814 Processing helix chain 'A' and resid 1874 through 1894 removed outlier: 3.527A pdb=" N TYR A1880 " --> pdb=" O THR A1876 " (cutoff:3.500A) Proline residue: A1883 - end of helix Processing helix chain 'A' and resid 1899 through 1914 Processing helix chain 'A' and resid 1916 through 1930 removed outlier: 3.670A pdb=" N ALA A1929 " --> pdb=" O GLU A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1931 through 1937 removed outlier: 3.888A pdb=" N LEU A1936 " --> pdb=" O ASP A1933 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A1937 " --> pdb=" O THR A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1944 Processing helix chain 'A' and resid 1950 through 1968 Processing helix chain 'A' and resid 1968 through 1981 removed outlier: 3.715A pdb=" N LEU A1972 " --> pdb=" O HIS A1968 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR A1974 " --> pdb=" O GLN A1970 " (cutoff:3.500A) Proline residue: A1975 - end of helix Processing helix chain 'A' and resid 1984 through 1999 Processing helix chain 'A' and resid 2002 through 2021 removed outlier: 3.731A pdb=" N VAL A2006 " --> pdb=" O SER A2002 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2040 Processing helix chain 'A' and resid 2043 through 2060 Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2092 removed outlier: 5.804A pdb=" N ARG A2076 " --> pdb=" O GLN A2072 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP A2077 " --> pdb=" O ALA A2073 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2115 removed outlier: 3.911A pdb=" N LEU A2097 " --> pdb=" O ASN A2093 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A2103 " --> pdb=" O GLN A2099 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A2106 " --> pdb=" O ASP A2102 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A2113 " --> pdb=" O ARG A2109 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A2114 " --> pdb=" O ARG A2110 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2118 No H-bonds generated for 'chain 'A' and resid 2116 through 2118' Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2127 through 2133 removed outlier: 3.569A pdb=" N LEU A2131 " --> pdb=" O SER A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2212 Processing helix chain 'A' and resid 2212 through 2218 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2279 through 2294 Processing helix chain 'A' and resid 2297 through 2306 Processing helix chain 'A' and resid 2309 through 2335 Processing helix chain 'A' and resid 2363 through 2368 removed outlier: 3.742A pdb=" N THR A2367 " --> pdb=" O GLU A2363 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A2368 " --> pdb=" O VAL A2364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2363 through 2368' Processing helix chain 'A' and resid 2380 through 2386 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2410 through 2423 Processing helix chain 'A' and resid 2427 through 2431 Processing helix chain 'A' and resid 2495 through 2508 Processing helix chain 'A' and resid 2520 through 2534 Processing helix chain 'A' and resid 2534 through 2540 removed outlier: 3.833A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.536A pdb=" N GLU C 267 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 47 Processing helix chain 'E' and resid 52 through 71 removed outlier: 3.646A pdb=" N THR E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 80 through 92 removed outlier: 3.872A pdb=" N CYS E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 113 through 122 Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.516A pdb=" N ARG E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 158 Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 162 through 176 removed outlier: 3.598A pdb=" N VAL E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.601A pdb=" N VAL E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 218 removed outlier: 3.525A pdb=" N THR E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 237 removed outlier: 3.569A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 234 " --> pdb=" O THR E 230 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS E 237 " --> pdb=" O HIS E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 removed outlier: 3.561A pdb=" N VAL E 244 " --> pdb=" O ARG E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 253 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 272 through 293 removed outlier: 3.546A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 302 Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 320 through 335 removed outlier: 3.502A pdb=" N GLY E 326 " --> pdb=" O GLU E 322 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 353 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 367 through 377 removed outlier: 3.544A pdb=" N THR E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 402 removed outlier: 3.635A pdb=" N ASN E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 414 Processing helix chain 'E' and resid 416 through 437 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 445 through 448 removed outlier: 3.511A pdb=" N CYS E 448 " --> pdb=" O HIS E 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 445 through 448' Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 462 through 486 Processing helix chain 'E' and resid 491 through 507 removed outlier: 3.685A pdb=" N LYS E 507 " --> pdb=" O ALA E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 536 removed outlier: 3.923A pdb=" N GLN E 536 " --> pdb=" O LEU E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 546 Processing helix chain 'E' and resid 547 through 557 Processing helix chain 'E' and resid 561 through 566 removed outlier: 3.614A pdb=" N LYS E 566 " --> pdb=" O LEU E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 582 Processing helix chain 'E' and resid 583 through 586 Processing helix chain 'E' and resid 587 through 591 Processing helix chain 'E' and resid 597 through 615 Processing helix chain 'E' and resid 616 through 618 No H-bonds generated for 'chain 'E' and resid 616 through 618' Processing helix chain 'E' and resid 619 through 639 Processing helix chain 'E' and resid 650 through 657 removed outlier: 3.856A pdb=" N THR E 653 " --> pdb=" O GLY E 650 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU E 655 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER E 656 " --> pdb=" O THR E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 658 through 668 removed outlier: 3.678A pdb=" N PHE E 662 " --> pdb=" O HIS E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 679 Processing helix chain 'E' and resid 680 through 689 removed outlier: 3.509A pdb=" N CYS E 684 " --> pdb=" O SER E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 705 Processing helix chain 'E' and resid 711 through 724 removed outlier: 3.735A pdb=" N ALA E 724 " --> pdb=" O ILE E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 742 removed outlier: 3.517A pdb=" N LEU E 736 " --> pdb=" O ALA E 732 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG E 737 " --> pdb=" O THR E 733 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL E 738 " --> pdb=" O LYS E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 759 removed outlier: 3.604A pdb=" N TRP E 750 " --> pdb=" O PHE E 746 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU E 753 " --> pdb=" O ASN E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 778 removed outlier: 3.566A pdb=" N SER E 767 " --> pdb=" O ASN E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 780 through 791 Processing helix chain 'E' and resid 794 through 796 No H-bonds generated for 'chain 'E' and resid 794 through 796' Processing helix chain 'E' and resid 797 through 806 removed outlier: 3.708A pdb=" N GLY E 801 " --> pdb=" O LEU E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 810 Processing helix chain 'E' and resid 811 through 820 Processing helix chain 'E' and resid 822 through 834 Processing helix chain 'E' and resid 834 through 852 removed outlier: 3.992A pdb=" N VAL E 840 " --> pdb=" O ASN E 836 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 887 Processing helix chain 'E' and resid 889 through 899 removed outlier: 3.661A pdb=" N LEU E 895 " --> pdb=" O THR E 891 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU E 896 " --> pdb=" O GLY E 892 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 911 removed outlier: 4.069A pdb=" N GLU E 904 " --> pdb=" O ASN E 900 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG E 907 " --> pdb=" O THR E 903 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN E 908 " --> pdb=" O GLU E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 934 Processing helix chain 'E' and resid 936 through 947 removed outlier: 3.514A pdb=" N ASN E 941 " --> pdb=" O ASN E 937 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 942 " --> pdb=" O TRP E 938 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU E 945 " --> pdb=" O ASN E 941 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 946 " --> pdb=" O LEU E 942 " (cutoff:3.500A) Processing helix chain 'E' and resid 948 through 959 Processing helix chain 'E' and resid 961 through 976 removed outlier: 3.769A pdb=" N ARG E 965 " --> pdb=" O VAL E 961 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY E 966 " --> pdb=" O LEU E 962 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 974 " --> pdb=" O TYR E 970 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 975 " --> pdb=" O VAL E 971 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 988 removed outlier: 3.618A pdb=" N CYS E 987 " --> pdb=" O ASP E 983 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS E 988 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 1432 through 1437 Processing helix chain 'E' and resid 1444 through 1448 Processing helix chain 'E' and resid 1481 through 1487 removed outlier: 3.800A pdb=" N GLN E1486 " --> pdb=" O LEU E1482 " (cutoff:3.500A) Processing helix chain 'E' and resid 1488 through 1494 Processing helix chain 'E' and resid 1523 through 1529 removed outlier: 4.257A pdb=" N GLU E1527 " --> pdb=" O CYS E1523 " (cutoff:3.500A) Processing helix chain 'E' and resid 1606 through 1624 removed outlier: 3.716A pdb=" N SER E1624 " --> pdb=" O VAL E1620 " (cutoff:3.500A) Processing helix chain 'E' and resid 1628 through 1643 removed outlier: 3.681A pdb=" N HIS E1632 " --> pdb=" O SER E1628 " (cutoff:3.500A) Processing helix chain 'E' and resid 1644 through 1647 Processing helix chain 'E' and resid 1649 through 1660 Processing helix chain 'E' and resid 1666 through 1677 removed outlier: 3.943A pdb=" N PHE E1677 " --> pdb=" O ILE E1673 " (cutoff:3.500A) Processing helix chain 'E' and resid 1682 through 1691 removed outlier: 3.662A pdb=" N GLU E1690 " --> pdb=" O HIS E1686 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E1691 " --> pdb=" O GLU E1687 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 32 through 37 removed outlier: 3.555A pdb=" N ASP G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 138 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 7.437A pdb=" N SER A2159 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N THR A2173 " --> pdb=" O SER A2159 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A2161 " --> pdb=" O LYS A2171 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR A2173 " --> pdb=" O ILE A2156 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE A2156 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 7.437A pdb=" N SER A2159 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N THR A2173 " --> pdb=" O SER A2159 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A2161 " --> pdb=" O LYS A2171 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A2234 " --> pdb=" O LEU A2230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id=AA4, first strand: chain 'C' and resid 34 through 39 removed outlier: 3.923A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.808A pdb=" N ALA C 47 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER C 80 " --> pdb=" O ILE G 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.849A pdb=" N GLY C 103 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL C 91 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR C 101 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE C 93 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TRP C 99 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 104 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 131 through 136 removed outlier: 6.952A pdb=" N GLY C 146 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 134 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C 144 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU C 136 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU C 142 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 178 removed outlier: 3.545A pdb=" N SER C 175 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN C 198 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 223 through 228 removed outlier: 3.800A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYS C 244 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU C 257 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 246 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 275 through 278 removed outlier: 3.673A pdb=" N GLY C 275 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 294 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 990 through 992 1464 hydrogen bonds defined for protein. 4239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8329 1.34 - 1.46: 5307 1.46 - 1.58: 11826 1.58 - 1.70: 10 1.70 - 1.82: 248 Bond restraints: 25720 Sorted by residual: bond pdb=" C ACE G 1 " pdb=" O ACE G 1 " ideal model delta sigma weight residual 1.199 1.227 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" N VAL E 858 " pdb=" CA VAL E 858 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.90e-02 2.77e+03 7.83e-01 bond pdb=" CA VAL A 854 " pdb=" C VAL A 854 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.27e-02 6.20e+03 7.78e-01 bond pdb=" N PRO A1116 " pdb=" CA PRO A1116 " ideal model delta sigma weight residual 1.465 1.483 -0.018 2.03e-02 2.43e+03 7.59e-01 bond pdb=" CA ILE A1192 " pdb=" CB ILE A1192 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 7.59e-01 ... (remaining 25715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 33771 1.72 - 3.43: 976 3.43 - 5.15: 77 5.15 - 6.86: 10 6.86 - 8.58: 5 Bond angle restraints: 34839 Sorted by residual: angle pdb=" N ILE A2356 " pdb=" CA ILE A2356 " pdb=" C ILE A2356 " ideal model delta sigma weight residual 109.34 117.18 -7.84 2.08e+00 2.31e-01 1.42e+01 angle pdb=" N VAL A 854 " pdb=" CA VAL A 854 " pdb=" C VAL A 854 " ideal model delta sigma weight residual 109.34 116.13 -6.79 2.08e+00 2.31e-01 1.06e+01 angle pdb=" N ASN A2233 " pdb=" CA ASN A2233 " pdb=" C ASN A2233 " ideal model delta sigma weight residual 110.80 117.72 -6.92 2.13e+00 2.20e-01 1.06e+01 angle pdb=" CB ARG A1132 " pdb=" CG ARG A1132 " pdb=" CD ARG A1132 " ideal model delta sigma weight residual 111.30 103.84 7.46 2.30e+00 1.89e-01 1.05e+01 angle pdb=" C ASP C 291 " pdb=" N ASN C 292 " pdb=" CA ASN C 292 " ideal model delta sigma weight residual 122.40 126.52 -4.12 1.45e+00 4.76e-01 8.09e+00 ... (remaining 34834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 14561 17.73 - 35.47: 827 35.47 - 53.20: 153 53.20 - 70.93: 51 70.93 - 88.66: 25 Dihedral angle restraints: 15617 sinusoidal: 6448 harmonic: 9169 Sorted by residual: dihedral pdb=" CA VAL A1043 " pdb=" C VAL A1043 " pdb=" N MET A1044 " pdb=" CA MET A1044 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA TRP E 557 " pdb=" C TRP E 557 " pdb=" N PRO E 558 " pdb=" CA PRO E 558 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ARG A1896 " pdb=" C ARG A1896 " pdb=" N GLY A1897 " pdb=" CA GLY A1897 " ideal model delta harmonic sigma weight residual 180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 15614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2407 0.038 - 0.076: 1174 0.076 - 0.114: 296 0.114 - 0.151: 64 0.151 - 0.189: 5 Chirality restraints: 3946 Sorted by residual: chirality pdb=" CA PHE A1122 " pdb=" N PHE A1122 " pdb=" C PHE A1122 " pdb=" CB PHE A1122 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA ASN A2233 " pdb=" N ASN A2233 " pdb=" C ASN A2233 " pdb=" CB ASN A2233 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" C4 IHP A2601 " pdb=" C3 IHP A2601 " pdb=" C5 IHP A2601 " pdb=" O14 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 3943 not shown) Planarity restraints: 4425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1132 " -0.582 9.50e-02 1.11e+02 2.62e-01 4.61e+01 pdb=" NE ARG A1132 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A1132 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A1132 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A1132 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 32 " 0.295 9.50e-02 1.11e+02 1.33e-01 1.34e+01 pdb=" NE ARG E 32 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG E 32 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG E 32 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG E 32 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 111 " 0.240 9.50e-02 1.11e+02 1.09e-01 9.40e+00 pdb=" NE ARG G 111 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG G 111 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG G 111 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG G 111 " 0.000 2.00e-02 2.50e+03 ... (remaining 4422 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 10506 2.95 - 3.44: 24862 3.44 - 3.93: 40441 3.93 - 4.41: 45637 4.41 - 4.90: 75806 Nonbonded interactions: 197252 Sorted by model distance: nonbonded pdb=" O ASP A2506 " pdb=" O GLY A2510 " model vdw 2.464 3.040 nonbonded pdb=" O MET A1998 " pdb=" O HIS A2001 " model vdw 2.514 3.040 nonbonded pdb=" O ILE E 437 " pdb=" CA LEU E 438 " model vdw 2.551 2.776 nonbonded pdb=" O SER C 190 " pdb=" OG1 THR C 191 " model vdw 2.577 3.040 nonbonded pdb=" OG SER C 229 " pdb=" O ASP C 231 " model vdw 2.579 3.040 ... (remaining 197247 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: 13.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 29.550 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.003 0.036 25724 Z= 0.150 Angle : 0.695 8.576 34842 Z= 0.441 Chirality : 0.046 0.189 3946 Planarity : 0.010 0.262 4425 Dihedral : 12.886 88.664 9647 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.59 (0.14), residues: 3087 helix: -0.62 (0.10), residues: 1941 sheet: 0.33 (0.36), residues: 187 loop : 0.42 (0.22), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.003 ARG A1132 TYR 0.021 0.004 TYR A 853 PHE 0.038 0.002 PHE A1122 TRP 0.020 0.002 TRP G 108 HIS 0.007 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00281 (25720) covalent geometry : angle 0.69462 (34839) hydrogen bonds : bond 0.23272 ( 1461) hydrogen bonds : angle 6.69766 ( 4239) metal coordination : bond 0.00313 ( 4) metal coordination : angle 3.27623 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 813 MET cc_start: 0.7124 (mmm) cc_final: 0.6829 (mpp) REVERT: A 827 MET cc_start: 0.4140 (mmm) cc_final: 0.3909 (mmt) REVERT: A 842 TRP cc_start: 0.7006 (t-100) cc_final: 0.6526 (t60) REVERT: A 859 ARG cc_start: 0.7202 (ttp-110) cc_final: 0.6320 (mmt180) REVERT: A 886 ARG cc_start: 0.7232 (ttt-90) cc_final: 0.6550 (ttp-170) REVERT: A 1028 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7975 (mtp180) REVERT: A 1033 GLU cc_start: 0.7793 (tp30) cc_final: 0.7588 (tp30) REVERT: A 1078 MET cc_start: 0.8690 (mtt) cc_final: 0.8404 (mtt) REVERT: A 1083 MET cc_start: 0.7922 (mtp) cc_final: 0.7719 (mtm) REVERT: A 1274 ARG cc_start: 0.5944 (mmp-170) cc_final: 0.5663 (mmm160) REVERT: A 1279 ASP cc_start: 0.6184 (m-30) cc_final: 0.5517 (m-30) REVERT: A 1285 ARG cc_start: 0.7562 (ttm110) cc_final: 0.6996 (ttt-90) REVERT: A 1339 ARG cc_start: 0.7708 (mtt90) cc_final: 0.7429 (mtm110) REVERT: A 1391 ARG cc_start: 0.7420 (mtt180) cc_final: 0.7207 (mtt-85) REVERT: A 1481 MET cc_start: 0.7991 (mtt) cc_final: 0.7689 (mtt) REVERT: A 1509 GLN cc_start: 0.5101 (mm-40) cc_final: 0.4830 (mm110) REVERT: A 1535 MET cc_start: 0.6631 (mmp) cc_final: 0.6383 (mmp) REVERT: A 1545 PHE cc_start: 0.7358 (t80) cc_final: 0.6882 (t80) REVERT: A 1562 GLN cc_start: 0.7281 (mt0) cc_final: 0.6752 (mm-40) REVERT: A 1575 LEU cc_start: 0.8357 (tp) cc_final: 0.8017 (tm) REVERT: A 1758 GLN cc_start: 0.8193 (tt0) cc_final: 0.7781 (tt0) REVERT: A 1896 ARG cc_start: 0.7422 (mtt90) cc_final: 0.7006 (mtt-85) REVERT: A 2219 ASN cc_start: 0.8270 (m-40) cc_final: 0.8062 (m-40) REVERT: A 2262 ASN cc_start: 0.8081 (m-40) cc_final: 0.7693 (p0) REVERT: C 67 MET cc_start: 0.6910 (mtt) cc_final: 0.6599 (mtt) REVERT: C 82 ASP cc_start: 0.6293 (m-30) cc_final: 0.5827 (m-30) REVERT: C 179 ASP cc_start: 0.5765 (t0) cc_final: 0.5164 (p0) REVERT: C 184 TYR cc_start: 0.6458 (m-80) cc_final: 0.5218 (m-80) REVERT: C 197 TRP cc_start: 0.6324 (m-90) cc_final: 0.5816 (m100) REVERT: C 261 LYS cc_start: 0.6843 (mtmt) cc_final: 0.6589 (mmtt) REVERT: C 270 ARG cc_start: 0.6711 (ttm110) cc_final: 0.6210 (tpt-90) REVERT: C 283 GLN cc_start: 0.7071 (mt0) cc_final: 0.6542 (mt0) REVERT: C 286 VAL cc_start: 0.7922 (t) cc_final: 0.7570 (p) REVERT: E 75 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7629 (tm-30) REVERT: E 180 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7725 (mtp85) REVERT: E 274 LYS cc_start: 0.7901 (tptt) cc_final: 0.7575 (pmmt) REVERT: E 345 GLU cc_start: 0.8441 (tt0) cc_final: 0.7839 (tp30) REVERT: E 361 SER cc_start: 0.8453 (m) cc_final: 0.8162 (p) REVERT: E 382 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7393 (mmp-170) REVERT: E 417 ASP cc_start: 0.7544 (m-30) cc_final: 0.7059 (t0) REVERT: E 540 HIS cc_start: 0.6451 (m-70) cc_final: 0.6049 (m-70) REVERT: E 599 LYS cc_start: 0.8094 (tttt) cc_final: 0.7800 (tmmt) REVERT: E 617 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6599 (tm-30) REVERT: E 632 GLN cc_start: 0.7587 (mt0) cc_final: 0.7274 (mm-40) REVERT: E 675 MET cc_start: 0.7353 (tpp) cc_final: 0.7140 (tpp) REVERT: E 695 ASP cc_start: 0.8071 (t0) cc_final: 0.7723 (p0) REVERT: E 719 LYS cc_start: 0.8417 (tttt) cc_final: 0.7750 (mptt) REVERT: E 791 LYS cc_start: 0.8070 (mttt) cc_final: 0.7809 (mmtm) REVERT: E 813 LYS cc_start: 0.8210 (tttt) cc_final: 0.7875 (mtmm) REVERT: E 904 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7995 (tp30) REVERT: E 1607 MET cc_start: 0.5407 (mmm) cc_final: 0.4932 (mtt) REVERT: E 1631 CYS cc_start: 0.8347 (t) cc_final: 0.7627 (m) REVERT: E 1642 LYS cc_start: 0.7135 (tttt) cc_final: 0.6665 (mtmm) REVERT: E 1655 GLU cc_start: 0.8876 (tp30) cc_final: 0.8312 (tp30) REVERT: E 1687 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7358 (mm-30) REVERT: G 26 MET cc_start: 0.8435 (mmm) cc_final: 0.8201 (mmp) REVERT: G 83 ARG cc_start: 0.7089 (mtm180) cc_final: 0.6884 (mtm-85) REVERT: G 85 ASN cc_start: 0.8234 (t0) cc_final: 0.8025 (t0) REVERT: G 92 ARG cc_start: 0.7242 (ttm170) cc_final: 0.6812 (mmm-85) REVERT: G 95 LYS cc_start: 0.6860 (ttmm) cc_final: 0.6615 (ttpp) outliers start: 0 outliers final: 2 residues processed: 486 average time/residue: 0.7848 time to fit residues: 429.6189 Evaluate side-chains 301 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 691 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1026 HIS A1049 GLN A1684 GLN A1722 GLN A1808 ASN A1997 ASN A2093 ASN A2180 HIS C 64 HIS C 153 HIS C 164 GLN E 209 ASN E 559 ASN E 561 ASN E 620 GLN E1485 GLN E1494 ASN E1681 GLN G 88 GLN G 118 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101025 restraints weight = 35545.045| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.84 r_work: 0.3009 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25724 Z= 0.150 Angle : 0.608 8.601 34842 Z= 0.331 Chirality : 0.042 0.179 3946 Planarity : 0.004 0.079 4425 Dihedral : 5.840 87.890 3438 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.73 % Allowed : 6.05 % Favored : 92.22 % 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: 1.30 (0.15), residues: 3087 helix: 1.19 (0.11), residues: 1983 sheet: 0.52 (0.34), residues: 190 loop : 0.47 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1132 TYR 0.020 0.002 TYR E 817 PHE 0.036 0.002 PHE A1122 TRP 0.019 0.002 TRP E 750 HIS 0.007 0.001 HIS C 64 Details of bonding type rmsd covalent geometry : bond 0.00306 (25720) covalent geometry : angle 0.60755 (34839) hydrogen bonds : bond 0.06592 ( 1461) hydrogen bonds : angle 4.43755 ( 4239) metal coordination : bond 0.00820 ( 4) metal coordination : angle 3.64921 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 1.065 Fit side-chains REVERT: A 804 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6718 (mm-30) REVERT: A 813 MET cc_start: 0.7309 (mmm) cc_final: 0.6909 (mpp) REVERT: A 815 LYS cc_start: 0.6824 (ptmt) cc_final: 0.6523 (ptmt) REVERT: A 842 TRP cc_start: 0.6996 (t-100) cc_final: 0.6556 (t60) REVERT: A 882 ARG cc_start: 0.5952 (ttp80) cc_final: 0.5290 (ttp-110) REVERT: A 886 ARG cc_start: 0.7403 (ttt-90) cc_final: 0.6730 (ttp-170) REVERT: A 1028 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7909 (mtp180) REVERT: A 1033 GLU cc_start: 0.7720 (tp30) cc_final: 0.7515 (tp30) REVERT: A 1078 MET cc_start: 0.8644 (mtt) cc_final: 0.8344 (mtt) REVERT: A 1083 MET cc_start: 0.7824 (mtp) cc_final: 0.7577 (mtm) REVERT: A 1194 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8393 (tmm) REVERT: A 1274 ARG cc_start: 0.5860 (mmp-170) cc_final: 0.5640 (mmm160) REVERT: A 1279 ASP cc_start: 0.6037 (m-30) cc_final: 0.5675 (m-30) REVERT: A 1285 ARG cc_start: 0.7443 (ttm110) cc_final: 0.6862 (ttt-90) REVERT: A 1339 ARG cc_start: 0.7680 (mtt90) cc_final: 0.7396 (mtm110) REVERT: A 1343 LEU cc_start: 0.8023 (mt) cc_final: 0.7375 (tt) REVERT: A 1391 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7233 (mtt-85) REVERT: A 1535 MET cc_start: 0.6555 (mmp) cc_final: 0.6131 (mmp) REVERT: A 1545 PHE cc_start: 0.7142 (t80) cc_final: 0.6650 (t80) REVERT: A 1547 ARG cc_start: 0.7293 (mtm180) cc_final: 0.6800 (mtt-85) REVERT: A 1562 GLN cc_start: 0.6874 (mt0) cc_final: 0.6342 (mm-40) REVERT: A 1575 LEU cc_start: 0.8061 (tp) cc_final: 0.7799 (tm) REVERT: A 1632 ASP cc_start: 0.8156 (m-30) cc_final: 0.7924 (m-30) REVERT: A 1758 GLN cc_start: 0.8299 (tt0) cc_final: 0.7807 (tt0) REVERT: A 1774 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7856 (tp40) REVERT: A 1955 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.7671 (mtp85) REVERT: A 2262 ASN cc_start: 0.7995 (m-40) cc_final: 0.7580 (p0) REVERT: C 64 HIS cc_start: 0.6931 (m-70) cc_final: 0.6422 (p-80) REVERT: C 100 MET cc_start: 0.5665 (ttp) cc_final: 0.4706 (ttp) REVERT: C 117 ARG cc_start: 0.5883 (mtt-85) cc_final: 0.5630 (tpm170) REVERT: C 179 ASP cc_start: 0.5759 (t0) cc_final: 0.5205 (p0) REVERT: C 184 TYR cc_start: 0.6581 (m-80) cc_final: 0.5512 (m-80) REVERT: C 270 ARG cc_start: 0.6731 (ttm110) cc_final: 0.6330 (tpp-160) REVERT: C 283 GLN cc_start: 0.7192 (mt0) cc_final: 0.6787 (mt0) REVERT: C 286 VAL cc_start: 0.8082 (t) cc_final: 0.7730 (p) REVERT: C 292 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7252 (m110) REVERT: E 75 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7709 (tm-30) REVERT: E 180 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7807 (mtp85) REVERT: E 274 LYS cc_start: 0.7824 (tptt) cc_final: 0.7381 (pmmt) REVERT: E 275 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6731 (tm-30) REVERT: E 382 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7739 (mmt-90) REVERT: E 467 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8183 (mm) REVERT: E 599 LYS cc_start: 0.8044 (tttt) cc_final: 0.7779 (ttpt) REVERT: E 617 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6488 (tm-30) REVERT: E 719 LYS cc_start: 0.8308 (tttt) cc_final: 0.7700 (mptt) REVERT: E 856 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8287 (mtpp) REVERT: E 957 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8610 (mttm) REVERT: E 1607 MET cc_start: 0.5335 (mmm) cc_final: 0.4931 (mtt) REVERT: E 1631 CYS cc_start: 0.7984 (t) cc_final: 0.7699 (m) REVERT: E 1642 LYS cc_start: 0.6971 (tttt) cc_final: 0.6459 (mtmm) REVERT: E 1687 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7380 (mm-30) REVERT: G 92 ARG cc_start: 0.7035 (ttm170) cc_final: 0.6798 (mtp85) outliers start: 48 outliers final: 14 residues processed: 343 average time/residue: 0.7691 time to fit residues: 299.5121 Evaluate side-chains 280 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1194 MET Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1697 THR Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2281 MET Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2543 ILE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 856 LYS Chi-restraints excluded: chain E residue 1514 GLU Chi-restraints excluded: chain E residue 1692 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 270 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 271 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 0.0570 chunk 122 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1722 GLN A1744 HIS A1931 GLN ** E 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 571 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101758 restraints weight = 35921.993| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.00 r_work: 0.3003 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25724 Z= 0.129 Angle : 0.545 9.407 34842 Z= 0.290 Chirality : 0.041 0.161 3946 Planarity : 0.004 0.048 4425 Dihedral : 5.404 86.753 3436 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.95 % Allowed : 7.56 % Favored : 90.49 % 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: 1.74 (0.15), residues: 3087 helix: 1.69 (0.12), residues: 1965 sheet: 0.66 (0.34), residues: 190 loop : 0.26 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2042 TYR 0.020 0.002 TYR E1643 PHE 0.030 0.001 PHE A1122 TRP 0.020 0.001 TRP C 112 HIS 0.004 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00269 (25720) covalent geometry : angle 0.54473 (34839) hydrogen bonds : bond 0.05638 ( 1461) hydrogen bonds : angle 4.05064 ( 4239) metal coordination : bond 0.00855 ( 4) metal coordination : angle 2.84190 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 289 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 804 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6822 (mm-30) REVERT: A 807 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.5420 (tm-30) REVERT: A 813 MET cc_start: 0.7112 (mmm) cc_final: 0.6785 (mpp) REVERT: A 815 LYS cc_start: 0.6805 (ptmt) cc_final: 0.6594 (ptmt) REVERT: A 856 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6735 (mm-30) REVERT: A 886 ARG cc_start: 0.7406 (ttt-90) cc_final: 0.6757 (ttp-170) REVERT: A 1033 GLU cc_start: 0.7703 (tp30) cc_final: 0.7433 (tp30) REVERT: A 1078 MET cc_start: 0.8709 (mtt) cc_final: 0.8425 (mtt) REVERT: A 1083 MET cc_start: 0.7741 (mtp) cc_final: 0.7526 (mtm) REVERT: A 1274 ARG cc_start: 0.5859 (mmp-170) cc_final: 0.5633 (mmm160) REVERT: A 1279 ASP cc_start: 0.6010 (m-30) cc_final: 0.5663 (m-30) REVERT: A 1285 ARG cc_start: 0.7472 (ttm110) cc_final: 0.6798 (ttt-90) REVERT: A 1286 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7495 (mmm-85) REVERT: A 1339 ARG cc_start: 0.7663 (mtt90) cc_final: 0.7390 (mtm110) REVERT: A 1343 LEU cc_start: 0.8062 (mt) cc_final: 0.7409 (tt) REVERT: A 1391 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7338 (mtt-85) REVERT: A 1514 ARG cc_start: 0.6387 (tmm-80) cc_final: 0.6030 (mmm-85) REVERT: A 1535 MET cc_start: 0.6537 (mmp) cc_final: 0.6166 (mmp) REVERT: A 1562 GLN cc_start: 0.6864 (mt0) cc_final: 0.6326 (mm-40) REVERT: A 1575 LEU cc_start: 0.7938 (tp) cc_final: 0.7672 (tm) REVERT: A 1711 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7278 (mm) REVERT: A 1758 GLN cc_start: 0.8281 (tt0) cc_final: 0.7841 (tt0) REVERT: A 1774 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7932 (tp40) REVERT: A 1955 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7687 (mtp85) REVERT: A 1993 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8329 (tttm) REVERT: A 1997 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8089 (m110) REVERT: A 2029 GLU cc_start: 0.8803 (tt0) cc_final: 0.8514 (pt0) REVERT: A 2219 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8246 (t0) REVERT: A 2262 ASN cc_start: 0.8010 (m-40) cc_final: 0.7592 (p0) REVERT: C 64 HIS cc_start: 0.6888 (m-70) cc_final: 0.6553 (p-80) REVERT: C 100 MET cc_start: 0.5533 (ttp) cc_final: 0.4548 (ttp) REVERT: C 117 ARG cc_start: 0.5880 (mtt-85) cc_final: 0.5587 (tpm170) REVERT: C 142 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5724 (mp0) REVERT: C 179 ASP cc_start: 0.5830 (t0) cc_final: 0.5355 (p0) REVERT: C 184 TYR cc_start: 0.6672 (m-80) cc_final: 0.5680 (m-80) REVERT: C 197 TRP cc_start: 0.6266 (OUTLIER) cc_final: 0.4603 (m100) REVERT: C 270 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6189 (tpp80) REVERT: C 283 GLN cc_start: 0.7187 (mt0) cc_final: 0.6797 (mt0) REVERT: C 286 VAL cc_start: 0.8011 (t) cc_final: 0.7615 (p) REVERT: C 292 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7503 (m110) REVERT: E 75 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7723 (tm-30) REVERT: E 180 ARG cc_start: 0.8226 (mtt-85) cc_final: 0.7876 (mtp85) REVERT: E 274 LYS cc_start: 0.7667 (tptt) cc_final: 0.7200 (pmmt) REVERT: E 345 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: E 382 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7936 (mmt-90) REVERT: E 467 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8131 (mm) REVERT: E 617 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6583 (tm-30) REVERT: E 674 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.7081 (mtpt) REVERT: E 719 LYS cc_start: 0.8294 (tttt) cc_final: 0.7683 (mptt) REVERT: E 753 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7415 (mp0) REVERT: E 922 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8668 (tttp) REVERT: E 957 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8576 (mttm) REVERT: E 1607 MET cc_start: 0.5292 (mmm) cc_final: 0.4902 (mtt) REVERT: E 1631 CYS cc_start: 0.8088 (t) cc_final: 0.7777 (m) REVERT: E 1642 LYS cc_start: 0.6888 (tttt) cc_final: 0.6280 (mtmm) REVERT: E 1687 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7525 (mm-30) REVERT: G 71 ASP cc_start: 0.7379 (m-30) cc_final: 0.6910 (p0) REVERT: G 92 ARG cc_start: 0.7127 (ttm170) cc_final: 0.6661 (mtp85) REVERT: G 96 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6610 (mm-30) outliers start: 54 outliers final: 21 residues processed: 321 average time/residue: 0.7573 time to fit residues: 275.8378 Evaluate side-chains 299 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1286 ARG Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1997 ASN Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2281 MET Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2543 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 843 ILE Chi-restraints excluded: chain E residue 922 LYS Chi-restraints excluded: chain E residue 1514 GLU Chi-restraints excluded: chain E residue 1683 LEU Chi-restraints excluded: chain E residue 1692 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 210 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1722 GLN A1931 GLN C 28 GLN C 30 HIS C 76 ASN ** E 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 885 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108088 restraints weight = 35578.970| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.00 r_work: 0.2929 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25724 Z= 0.149 Angle : 0.561 9.603 34842 Z= 0.295 Chirality : 0.041 0.160 3946 Planarity : 0.004 0.051 4425 Dihedral : 5.351 87.010 3436 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.23 % Allowed : 8.39 % Favored : 89.37 % 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: 1.66 (0.15), residues: 3087 helix: 1.68 (0.12), residues: 1977 sheet: 0.63 (0.34), residues: 190 loop : 0.06 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 97 TYR 0.018 0.002 TYR E 817 PHE 0.029 0.002 PHE A1122 TRP 0.021 0.001 TRP A2429 HIS 0.004 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00331 (25720) covalent geometry : angle 0.56040 (34839) hydrogen bonds : bond 0.05879 ( 1461) hydrogen bonds : angle 4.00624 ( 4239) metal coordination : bond 0.01001 ( 4) metal coordination : angle 3.03956 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 804 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6743 (mm-30) REVERT: A 807 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.5496 (tm-30) REVERT: A 813 MET cc_start: 0.7194 (mmm) cc_final: 0.6896 (mmt) REVERT: A 815 LYS cc_start: 0.6945 (ptmt) cc_final: 0.6735 (ptmt) REVERT: A 886 ARG cc_start: 0.7411 (ttt-90) cc_final: 0.6748 (ttp-170) REVERT: A 1078 MET cc_start: 0.8678 (mtt) cc_final: 0.8356 (mtt) REVERT: A 1274 ARG cc_start: 0.5777 (mmp-170) cc_final: 0.5509 (mmm160) REVERT: A 1279 ASP cc_start: 0.6037 (m-30) cc_final: 0.5591 (m-30) REVERT: A 1285 ARG cc_start: 0.7347 (ttm110) cc_final: 0.6711 (ttt-90) REVERT: A 1339 ARG cc_start: 0.7666 (mtt90) cc_final: 0.7412 (mtm110) REVERT: A 1343 LEU cc_start: 0.8079 (mt) cc_final: 0.7406 (tt) REVERT: A 1514 ARG cc_start: 0.6346 (tmm-80) cc_final: 0.5887 (mmm-85) REVERT: A 1535 MET cc_start: 0.6571 (mmp) cc_final: 0.6227 (mmp) REVERT: A 1541 HIS cc_start: 0.6509 (t70) cc_final: 0.6203 (t-90) REVERT: A 1562 GLN cc_start: 0.6798 (mt0) cc_final: 0.6269 (mm-40) REVERT: A 1575 LEU cc_start: 0.7895 (tp) cc_final: 0.7641 (tm) REVERT: A 1758 GLN cc_start: 0.8172 (tt0) cc_final: 0.7646 (tp-100) REVERT: A 1774 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7836 (tp40) REVERT: A 1955 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7650 (mtp85) REVERT: A 1993 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8313 (tttm) REVERT: A 1997 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8037 (m110) REVERT: A 2029 GLU cc_start: 0.8675 (tt0) cc_final: 0.8431 (pt0) REVERT: C 64 HIS cc_start: 0.6787 (m-70) cc_final: 0.6578 (p-80) REVERT: C 100 MET cc_start: 0.5565 (ttp) cc_final: 0.4491 (ttp) REVERT: C 142 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5497 (pm20) REVERT: C 179 ASP cc_start: 0.5778 (t0) cc_final: 0.5430 (p0) REVERT: C 184 TYR cc_start: 0.6722 (m-80) cc_final: 0.5772 (m-80) REVERT: C 197 TRP cc_start: 0.6282 (OUTLIER) cc_final: 0.4517 (m100) REVERT: C 270 ARG cc_start: 0.6643 (ttm110) cc_final: 0.6201 (tpp80) REVERT: C 283 GLN cc_start: 0.7146 (mt0) cc_final: 0.6710 (mt0) REVERT: C 286 VAL cc_start: 0.7999 (t) cc_final: 0.7573 (p) REVERT: C 292 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7559 (m110) REVERT: E 75 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7763 (tm-30) REVERT: E 180 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7962 (mtp85) REVERT: E 274 LYS cc_start: 0.7637 (tptt) cc_final: 0.7280 (mtmm) REVERT: E 345 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: E 467 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8139 (mm) REVERT: E 617 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6488 (tm-30) REVERT: E 674 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6907 (mtpt) REVERT: E 709 ARG cc_start: 0.7394 (mtp85) cc_final: 0.7140 (mmm-85) REVERT: E 719 LYS cc_start: 0.8328 (tttt) cc_final: 0.7700 (mptt) REVERT: E 753 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7329 (mp0) REVERT: E 922 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8559 (tttp) REVERT: E 957 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8547 (mttm) REVERT: E 998 LYS cc_start: 0.8719 (tttt) cc_final: 0.8042 (tppt) REVERT: E 1607 MET cc_start: 0.5229 (mmm) cc_final: 0.4891 (mtt) REVERT: E 1631 CYS cc_start: 0.8077 (t) cc_final: 0.7781 (m) REVERT: E 1642 LYS cc_start: 0.6901 (tttt) cc_final: 0.6345 (mtmm) REVERT: G 70 VAL cc_start: 0.8139 (m) cc_final: 0.7819 (p) REVERT: G 71 ASP cc_start: 0.7288 (m-30) cc_final: 0.6776 (p0) REVERT: G 92 ARG cc_start: 0.7141 (ttm170) cc_final: 0.6767 (mtp85) REVERT: G 93 LEU cc_start: 0.7594 (tp) cc_final: 0.7354 (tt) outliers start: 62 outliers final: 30 residues processed: 313 average time/residue: 0.7790 time to fit residues: 277.1778 Evaluate side-chains 300 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1601 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1997 ASN Chi-restraints excluded: chain A residue 2045 LYS Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2281 MET Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2543 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 843 ILE Chi-restraints excluded: chain E residue 922 LYS Chi-restraints excluded: chain E residue 1514 GLU Chi-restraints excluded: chain E residue 1683 LEU Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain G residue 29 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 61 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 273 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1722 GLN A2410 HIS C 30 HIS ** E 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1684 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.144092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110153 restraints weight = 35648.221| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.97 r_work: 0.2973 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25724 Z= 0.111 Angle : 0.503 10.487 34842 Z= 0.264 Chirality : 0.039 0.156 3946 Planarity : 0.004 0.048 4425 Dihedral : 5.074 84.663 3436 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.80 % Allowed : 9.37 % Favored : 88.83 % 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: 1.90 (0.15), residues: 3087 helix: 1.93 (0.12), residues: 1974 sheet: 0.50 (0.34), residues: 196 loop : 0.03 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 97 TYR 0.017 0.001 TYR C 101 PHE 0.025 0.001 PHE A1122 TRP 0.027 0.001 TRP A2429 HIS 0.004 0.001 HIS A1988 Details of bonding type rmsd covalent geometry : bond 0.00225 (25720) covalent geometry : angle 0.50291 (34839) hydrogen bonds : bond 0.04683 ( 1461) hydrogen bonds : angle 3.81282 ( 4239) metal coordination : bond 0.00819 ( 4) metal coordination : angle 2.33866 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 804 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6841 (mm-30) REVERT: A 813 MET cc_start: 0.7166 (mmm) cc_final: 0.6753 (mpp) REVERT: A 886 ARG cc_start: 0.7367 (ttt-90) cc_final: 0.6702 (ttp-170) REVERT: A 1078 MET cc_start: 0.8725 (mtt) cc_final: 0.8475 (mtt) REVERT: A 1274 ARG cc_start: 0.5723 (mmp-170) cc_final: 0.5430 (mmm160) REVERT: A 1279 ASP cc_start: 0.5928 (m-30) cc_final: 0.5526 (m-30) REVERT: A 1285 ARG cc_start: 0.7351 (ttm110) cc_final: 0.6729 (ttt-90) REVERT: A 1339 ARG cc_start: 0.7602 (mtt90) cc_final: 0.7361 (mtm110) REVERT: A 1343 LEU cc_start: 0.8221 (mt) cc_final: 0.7536 (tt) REVERT: A 1514 ARG cc_start: 0.6479 (tmm-80) cc_final: 0.6185 (tmm160) REVERT: A 1535 MET cc_start: 0.6425 (mmp) cc_final: 0.6159 (mmp) REVERT: A 1541 HIS cc_start: 0.6400 (t70) cc_final: 0.6128 (t-90) REVERT: A 1743 LEU cc_start: 0.7566 (mt) cc_final: 0.7351 (mm) REVERT: A 1758 GLN cc_start: 0.8191 (tt0) cc_final: 0.7732 (tt0) REVERT: A 1774 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7852 (tp40) REVERT: A 1955 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7624 (mtp85) REVERT: A 1993 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8281 (tttm) REVERT: A 1997 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7941 (m110) REVERT: A 2029 GLU cc_start: 0.8615 (tt0) cc_final: 0.8370 (pt0) REVERT: A 2219 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8115 (t0) REVERT: A 2262 ASN cc_start: 0.7828 (m-40) cc_final: 0.7537 (p0) REVERT: C 100 MET cc_start: 0.5496 (ttp) cc_final: 0.4505 (ttp) REVERT: C 161 HIS cc_start: 0.6850 (m-70) cc_final: 0.6485 (t70) REVERT: C 179 ASP cc_start: 0.5748 (t0) cc_final: 0.5411 (p0) REVERT: C 184 TYR cc_start: 0.6730 (m-80) cc_final: 0.5764 (m-80) REVERT: C 270 ARG cc_start: 0.6565 (ttm110) cc_final: 0.6172 (tpp80) REVERT: C 283 GLN cc_start: 0.7135 (mt0) cc_final: 0.6693 (mt0) REVERT: C 286 VAL cc_start: 0.7983 (t) cc_final: 0.7552 (p) REVERT: C 292 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7601 (m110) REVERT: E 48 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8015 (tp) REVERT: E 75 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7786 (tm-30) REVERT: E 83 ASP cc_start: 0.7622 (m-30) cc_final: 0.7284 (m-30) REVERT: E 180 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7943 (mtp85) REVERT: E 274 LYS cc_start: 0.7504 (tptt) cc_final: 0.7149 (mtmm) REVERT: E 345 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: E 467 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8097 (mm) REVERT: E 617 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6582 (tm-30) REVERT: E 674 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7160 (mtpt) REVERT: E 675 MET cc_start: 0.7271 (tpt) cc_final: 0.7060 (tpt) REVERT: E 709 ARG cc_start: 0.7283 (mtp85) cc_final: 0.7038 (mmm-85) REVERT: E 719 LYS cc_start: 0.8302 (tttt) cc_final: 0.7661 (mptt) REVERT: E 753 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7229 (mp0) REVERT: E 922 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8513 (tttp) REVERT: E 1535 ASN cc_start: 0.6986 (m110) cc_final: 0.6628 (t0) REVERT: E 1607 MET cc_start: 0.5239 (mmm) cc_final: 0.4917 (mtt) REVERT: E 1631 CYS cc_start: 0.8053 (t) cc_final: 0.7805 (m) REVERT: E 1642 LYS cc_start: 0.6720 (tttt) cc_final: 0.6140 (mtmm) REVERT: G 26 MET cc_start: 0.8314 (mmm) cc_final: 0.7867 (mmp) REVERT: G 70 VAL cc_start: 0.8173 (m) cc_final: 0.7857 (p) REVERT: G 71 ASP cc_start: 0.7270 (m-30) cc_final: 0.6739 (p0) REVERT: G 92 ARG cc_start: 0.7074 (ttm170) cc_final: 0.6736 (mtp85) REVERT: G 93 LEU cc_start: 0.7581 (tp) cc_final: 0.7361 (tt) outliers start: 50 outliers final: 20 residues processed: 309 average time/residue: 0.7277 time to fit residues: 255.1946 Evaluate side-chains 288 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1997 ASN Chi-restraints excluded: chain A residue 2045 LYS Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2530 LYS Chi-restraints excluded: chain A residue 2543 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 843 ILE Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 922 LYS Chi-restraints excluded: chain E residue 1514 GLU Chi-restraints excluded: chain E residue 1692 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 33 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 216 optimal weight: 0.0170 chunk 26 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1722 GLN C 30 HIS C 64 HIS C 122 GLN E 444 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100523 restraints weight = 35755.051| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.89 r_work: 0.3013 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25724 Z= 0.127 Angle : 0.524 10.216 34842 Z= 0.273 Chirality : 0.040 0.154 3946 Planarity : 0.004 0.049 4425 Dihedral : 5.058 84.991 3436 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.80 % Allowed : 10.01 % Favored : 88.18 % 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: 1.85 (0.15), residues: 3087 helix: 1.92 (0.12), residues: 1975 sheet: 0.52 (0.34), residues: 196 loop : -0.05 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 325 TYR 0.021 0.001 TYR E 817 PHE 0.027 0.001 PHE A1122 TRP 0.031 0.001 TRP A2429 HIS 0.004 0.001 HIS A2340 Details of bonding type rmsd covalent geometry : bond 0.00283 (25720) covalent geometry : angle 0.52388 (34839) hydrogen bonds : bond 0.05181 ( 1461) hydrogen bonds : angle 3.83051 ( 4239) metal coordination : bond 0.00821 ( 4) metal coordination : angle 2.60648 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 804 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6864 (mm-30) REVERT: A 807 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5575 (tm-30) REVERT: A 813 MET cc_start: 0.7178 (mmm) cc_final: 0.6753 (mpp) REVERT: A 856 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6997 (mm-30) REVERT: A 886 ARG cc_start: 0.7449 (ttt-90) cc_final: 0.6769 (ttp-170) REVERT: A 1032 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6928 (m-30) REVERT: A 1078 MET cc_start: 0.8807 (mtt) cc_final: 0.8544 (mtt) REVERT: A 1274 ARG cc_start: 0.5795 (mmp-170) cc_final: 0.5503 (mmm160) REVERT: A 1279 ASP cc_start: 0.5946 (m-30) cc_final: 0.5555 (m-30) REVERT: A 1285 ARG cc_start: 0.7456 (ttm110) cc_final: 0.6760 (ttt-90) REVERT: A 1339 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7472 (mtm110) REVERT: A 1343 LEU cc_start: 0.8280 (mt) cc_final: 0.7565 (tt) REVERT: A 1514 ARG cc_start: 0.6523 (tmm-80) cc_final: 0.6284 (tmm160) REVERT: A 1535 MET cc_start: 0.6411 (mmp) cc_final: 0.6148 (mmp) REVERT: A 1541 HIS cc_start: 0.6526 (t70) cc_final: 0.6246 (t-90) REVERT: A 1711 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7277 (mm) REVERT: A 1743 LEU cc_start: 0.7581 (mt) cc_final: 0.7350 (mm) REVERT: A 1758 GLN cc_start: 0.8259 (tt0) cc_final: 0.8005 (tt0) REVERT: A 1774 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7901 (tp40) REVERT: A 1955 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7792 (mtp85) REVERT: A 1993 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8329 (tttm) REVERT: A 1997 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.8109 (m110) REVERT: A 2029 GLU cc_start: 0.8762 (tt0) cc_final: 0.8543 (pt0) REVERT: A 2219 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8270 (t0) REVERT: C 100 MET cc_start: 0.5291 (ttp) cc_final: 0.4270 (ttp) REVERT: C 184 TYR cc_start: 0.6789 (m-80) cc_final: 0.5848 (m-80) REVERT: C 185 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.5599 (tmm) REVERT: C 270 ARG cc_start: 0.6664 (ttm110) cc_final: 0.6231 (tpp80) REVERT: C 283 GLN cc_start: 0.7166 (mt0) cc_final: 0.6743 (mt0) REVERT: C 286 VAL cc_start: 0.8067 (t) cc_final: 0.7629 (p) REVERT: C 292 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7641 (m110) REVERT: E 48 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8017 (tp) REVERT: E 75 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7832 (tm-30) REVERT: E 83 ASP cc_start: 0.7743 (m-30) cc_final: 0.7390 (m-30) REVERT: E 180 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.7986 (mtp85) REVERT: E 274 LYS cc_start: 0.7522 (tptt) cc_final: 0.7130 (pmtt) REVERT: E 345 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: E 467 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8236 (mm) REVERT: E 617 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6532 (tm-30) REVERT: E 674 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7267 (mtpt) REVERT: E 709 ARG cc_start: 0.7349 (mtp85) cc_final: 0.7090 (mmm-85) REVERT: E 719 LYS cc_start: 0.8381 (tttt) cc_final: 0.7732 (mptt) REVERT: E 753 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7425 (mp0) REVERT: E 817 TYR cc_start: 0.7952 (t80) cc_final: 0.7695 (t80) REVERT: E 922 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8594 (tttp) REVERT: E 1607 MET cc_start: 0.5284 (mmm) cc_final: 0.4936 (mtt) REVERT: E 1631 CYS cc_start: 0.8152 (t) cc_final: 0.7868 (m) REVERT: E 1642 LYS cc_start: 0.6811 (tttt) cc_final: 0.6201 (mtmm) REVERT: G 26 MET cc_start: 0.8329 (mmm) cc_final: 0.7880 (mmp) REVERT: G 70 VAL cc_start: 0.8175 (m) cc_final: 0.7839 (p) REVERT: G 71 ASP cc_start: 0.7399 (m-30) cc_final: 0.6905 (p0) REVERT: G 92 ARG cc_start: 0.7225 (ttm170) cc_final: 0.6860 (mtp85) REVERT: G 93 LEU cc_start: 0.7660 (tp) cc_final: 0.7406 (tt) outliers start: 50 outliers final: 23 residues processed: 297 average time/residue: 0.7550 time to fit residues: 254.6866 Evaluate side-chains 286 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1601 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1997 ASN Chi-restraints excluded: chain A residue 2045 LYS Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2543 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 843 ILE Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 922 LYS Chi-restraints excluded: chain E residue 1514 GLU Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain G residue 29 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 210 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 266 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 19 optimal weight: 0.0060 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 GLN A1722 GLN A2093 ASN A2515 HIS C 30 HIS ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103437 restraints weight = 35797.093| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.89 r_work: 0.3058 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25724 Z= 0.103 Angle : 0.489 10.767 34842 Z= 0.254 Chirality : 0.038 0.153 3946 Planarity : 0.004 0.048 4425 Dihedral : 4.867 83.325 3436 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.98 % Allowed : 9.98 % Favored : 88.04 % 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: 2.03 (0.15), residues: 3087 helix: 2.08 (0.12), residues: 1977 sheet: 0.51 (0.34), residues: 198 loop : -0.05 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 325 TYR 0.022 0.001 TYR E 817 PHE 0.024 0.001 PHE A1122 TRP 0.037 0.001 TRP A2429 HIS 0.004 0.001 HIS A1988 Details of bonding type rmsd covalent geometry : bond 0.00207 (25720) covalent geometry : angle 0.48821 (34839) hydrogen bonds : bond 0.04321 ( 1461) hydrogen bonds : angle 3.71179 ( 4239) metal coordination : bond 0.00742 ( 4) metal coordination : angle 2.03882 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 804 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6849 (mm-30) REVERT: A 813 MET cc_start: 0.7158 (mmm) cc_final: 0.6762 (mpp) REVERT: A 856 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6948 (mm-30) REVERT: A 886 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.6753 (ttp-170) REVERT: A 1078 MET cc_start: 0.8788 (mtt) cc_final: 0.8435 (mtt) REVERT: A 1274 ARG cc_start: 0.5821 (mmp-170) cc_final: 0.5479 (mmm160) REVERT: A 1279 ASP cc_start: 0.5961 (m-30) cc_final: 0.5519 (m-30) REVERT: A 1285 ARG cc_start: 0.7389 (ttm110) cc_final: 0.6767 (ttt-90) REVERT: A 1336 GLU cc_start: 0.7159 (tp30) cc_final: 0.6902 (tp30) REVERT: A 1339 ARG cc_start: 0.7667 (mtt90) cc_final: 0.7444 (mtm110) REVERT: A 1343 LEU cc_start: 0.8349 (mt) cc_final: 0.7658 (tt) REVERT: A 1514 ARG cc_start: 0.6517 (tmm-80) cc_final: 0.6260 (tmm160) REVERT: A 1541 HIS cc_start: 0.6482 (t70) cc_final: 0.6214 (t-90) REVERT: A 1650 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6389 (pmt) REVERT: A 1711 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7298 (mm) REVERT: A 1743 LEU cc_start: 0.7522 (mt) cc_final: 0.7303 (mm) REVERT: A 1758 GLN cc_start: 0.8208 (tt0) cc_final: 0.7969 (tt0) REVERT: A 1774 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7880 (tp40) REVERT: A 1955 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7832 (mtp85) REVERT: A 1993 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8363 (tttm) REVERT: A 2029 GLU cc_start: 0.8701 (tt0) cc_final: 0.8476 (pt0) REVERT: A 2089 MET cc_start: 0.8530 (tpt) cc_final: 0.8314 (mmm) REVERT: A 2219 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8246 (t0) REVERT: A 2262 ASN cc_start: 0.7874 (m-40) cc_final: 0.7571 (p0) REVERT: A 2515 HIS cc_start: 0.7114 (t-90) cc_final: 0.6884 (m-70) REVERT: C 49 GLU cc_start: 0.6650 (tp30) cc_final: 0.6438 (tp30) REVERT: C 100 MET cc_start: 0.5170 (ttp) cc_final: 0.4296 (ttp) REVERT: C 185 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6586 (tmm) REVERT: C 270 ARG cc_start: 0.6619 (ttm110) cc_final: 0.6221 (tpp80) REVERT: C 283 GLN cc_start: 0.7165 (mt0) cc_final: 0.6754 (mt0) REVERT: C 286 VAL cc_start: 0.8048 (t) cc_final: 0.7609 (p) REVERT: C 292 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7642 (m110) REVERT: C 305 LYS cc_start: 0.7003 (mmmt) cc_final: 0.6732 (mmmm) REVERT: E 48 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7997 (tp) REVERT: E 75 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7850 (tm-30) REVERT: E 83 ASP cc_start: 0.7782 (m-30) cc_final: 0.7378 (m-30) REVERT: E 180 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.7974 (mtp85) REVERT: E 274 LYS cc_start: 0.7458 (tptt) cc_final: 0.7141 (pmtt) REVERT: E 321 MET cc_start: 0.7663 (mmt) cc_final: 0.7261 (mmt) REVERT: E 345 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: E 467 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8151 (mm) REVERT: E 617 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6598 (tm-30) REVERT: E 674 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7274 (mtpt) REVERT: E 709 ARG cc_start: 0.7366 (mtp85) cc_final: 0.7120 (mmm-85) REVERT: E 719 LYS cc_start: 0.8366 (tttt) cc_final: 0.7712 (mptt) REVERT: E 753 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7382 (mp0) REVERT: E 817 TYR cc_start: 0.8106 (t80) cc_final: 0.7882 (t80) REVERT: E 821 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7090 (mtp180) REVERT: E 922 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8576 (tttp) REVERT: E 1535 ASN cc_start: 0.7081 (m110) cc_final: 0.6625 (t0) REVERT: E 1607 MET cc_start: 0.5357 (mmm) cc_final: 0.4907 (mtt) REVERT: E 1631 CYS cc_start: 0.8122 (t) cc_final: 0.7869 (m) REVERT: E 1642 LYS cc_start: 0.6749 (tttt) cc_final: 0.6134 (mtmm) REVERT: G 26 MET cc_start: 0.8297 (mmm) cc_final: 0.7829 (mmp) REVERT: G 70 VAL cc_start: 0.8174 (m) cc_final: 0.7829 (p) REVERT: G 71 ASP cc_start: 0.7377 (m-30) cc_final: 0.6904 (p0) REVERT: G 92 ARG cc_start: 0.7227 (ttm170) cc_final: 0.6892 (mtp85) REVERT: G 93 LEU cc_start: 0.7645 (tp) cc_final: 0.7384 (tt) outliers start: 55 outliers final: 22 residues processed: 308 average time/residue: 0.7709 time to fit residues: 270.9984 Evaluate side-chains 291 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1601 GLU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 2045 LYS Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2543 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 821 ARG Chi-restraints excluded: chain E residue 843 ILE Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 922 LYS Chi-restraints excluded: chain E residue 1514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 232 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 300 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 79 optimal weight: 0.0020 chunk 101 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1509 GLN A1722 GLN A1807 GLN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** 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 = 0.3800 r_free = 0.3800 target = 0.144204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102396 restraints weight = 35831.455| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.86 r_work: 0.3045 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25724 Z= 0.110 Angle : 0.498 10.500 34842 Z= 0.258 Chirality : 0.039 0.187 3946 Planarity : 0.004 0.048 4425 Dihedral : 4.827 83.400 3436 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.55 % Allowed : 10.73 % Favored : 87.72 % 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: 2.04 (0.15), residues: 3087 helix: 2.10 (0.12), residues: 1976 sheet: 0.56 (0.35), residues: 196 loop : -0.06 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 325 TYR 0.016 0.001 TYR E 817 PHE 0.025 0.001 PHE A1122 TRP 0.036 0.001 TRP A2429 HIS 0.004 0.001 HIS A1988 Details of bonding type rmsd covalent geometry : bond 0.00233 (25720) covalent geometry : angle 0.49740 (34839) hydrogen bonds : bond 0.04533 ( 1461) hydrogen bonds : angle 3.71195 ( 4239) metal coordination : bond 0.00719 ( 4) metal coordination : angle 2.20409 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 804 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6895 (mm-30) REVERT: A 813 MET cc_start: 0.7119 (mmm) cc_final: 0.6717 (mpp) REVERT: A 856 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 886 ARG cc_start: 0.7473 (ttt-90) cc_final: 0.6796 (ttp-170) REVERT: A 1078 MET cc_start: 0.8794 (mtt) cc_final: 0.8526 (mtt) REVERT: A 1274 ARG cc_start: 0.5845 (mmp-170) cc_final: 0.5512 (mmm160) REVERT: A 1279 ASP cc_start: 0.5948 (m-30) cc_final: 0.5513 (m-30) REVERT: A 1285 ARG cc_start: 0.7412 (ttm110) cc_final: 0.6790 (ttt-90) REVERT: A 1336 GLU cc_start: 0.7154 (tp30) cc_final: 0.6896 (tp30) REVERT: A 1339 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7478 (mtm110) REVERT: A 1343 LEU cc_start: 0.8542 (mt) cc_final: 0.7832 (tt) REVERT: A 1541 HIS cc_start: 0.6490 (t70) cc_final: 0.6227 (t-90) REVERT: A 1650 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6393 (pmt) REVERT: A 1711 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7317 (mm) REVERT: A 1758 GLN cc_start: 0.8193 (tt0) cc_final: 0.7940 (tt0) REVERT: A 1774 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7910 (tp40) REVERT: A 1955 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7864 (mtp85) REVERT: A 1993 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8390 (tttm) REVERT: A 2029 GLU cc_start: 0.8698 (tt0) cc_final: 0.8471 (pt0) REVERT: A 2219 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8305 (t0) REVERT: A 2262 ASN cc_start: 0.7895 (m-40) cc_final: 0.7630 (p0) REVERT: C 100 MET cc_start: 0.5192 (ttp) cc_final: 0.4277 (ttp) REVERT: C 185 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.5749 (tmm) REVERT: C 270 ARG cc_start: 0.6665 (ttm110) cc_final: 0.6254 (tpp80) REVERT: C 283 GLN cc_start: 0.7163 (mt0) cc_final: 0.6751 (mt0) REVERT: C 286 VAL cc_start: 0.8172 (t) cc_final: 0.7794 (p) REVERT: C 292 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7663 (m110) REVERT: E 48 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7959 (tp) REVERT: E 75 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7847 (tm-30) REVERT: E 83 ASP cc_start: 0.7768 (m-30) cc_final: 0.7428 (m-30) REVERT: E 180 ARG cc_start: 0.8347 (mtt-85) cc_final: 0.8006 (mtp85) REVERT: E 274 LYS cc_start: 0.7473 (tptt) cc_final: 0.7162 (pmtt) REVERT: E 321 MET cc_start: 0.7655 (mmt) cc_final: 0.7205 (mmt) REVERT: E 345 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: E 467 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8191 (mm) REVERT: E 617 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6611 (tm-30) REVERT: E 709 ARG cc_start: 0.7383 (mtp85) cc_final: 0.7136 (mmm-85) REVERT: E 719 LYS cc_start: 0.8398 (tttt) cc_final: 0.7743 (mptt) REVERT: E 753 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7436 (mp0) REVERT: E 817 TYR cc_start: 0.8067 (t80) cc_final: 0.7801 (t80) REVERT: E 821 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7316 (mtp180) REVERT: E 922 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8577 (tttp) REVERT: E 1535 ASN cc_start: 0.7068 (m110) cc_final: 0.6633 (t0) REVERT: E 1607 MET cc_start: 0.5409 (mmm) cc_final: 0.4931 (mtt) REVERT: E 1631 CYS cc_start: 0.8181 (t) cc_final: 0.7911 (m) REVERT: E 1642 LYS cc_start: 0.6789 (tttt) cc_final: 0.6154 (mtmm) REVERT: G 26 MET cc_start: 0.8311 (mmm) cc_final: 0.7860 (mmp) REVERT: G 70 VAL cc_start: 0.8229 (m) cc_final: 0.7891 (p) REVERT: G 71 ASP cc_start: 0.7349 (m-30) cc_final: 0.6962 (p0) REVERT: G 92 ARG cc_start: 0.7268 (ttm170) cc_final: 0.6932 (mtp85) REVERT: G 93 LEU cc_start: 0.7657 (tp) cc_final: 0.7392 (tt) outliers start: 43 outliers final: 23 residues processed: 293 average time/residue: 0.7745 time to fit residues: 258.3788 Evaluate side-chains 292 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1601 GLU Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 2045 LYS Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2543 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 843 ILE Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 922 LYS Chi-restraints excluded: chain E residue 1514 GLU Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain G residue 29 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 284 optimal weight: 0.0270 chunk 263 optimal weight: 0.0470 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1509 GLN A1722 GLN ** A1807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104322 restraints weight = 35959.865| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.99 r_work: 0.3068 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25724 Z= 0.097 Angle : 0.486 10.736 34842 Z= 0.249 Chirality : 0.038 0.207 3946 Planarity : 0.004 0.047 4425 Dihedral : 4.661 82.098 3436 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.33 % Allowed : 11.13 % Favored : 87.54 % 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: 2.16 (0.15), residues: 3087 helix: 2.20 (0.12), residues: 1980 sheet: 0.49 (0.35), residues: 191 loop : -0.02 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 97 TYR 0.017 0.001 TYR E 588 PHE 0.023 0.001 PHE A1122 TRP 0.041 0.001 TRP A2429 HIS 0.004 0.001 HIS A1988 Details of bonding type rmsd covalent geometry : bond 0.00192 (25720) covalent geometry : angle 0.48534 (34839) hydrogen bonds : bond 0.03894 ( 1461) hydrogen bonds : angle 3.62660 ( 4239) metal coordination : bond 0.00702 ( 4) metal coordination : angle 1.73563 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 813 MET cc_start: 0.6925 (mmm) cc_final: 0.6623 (mpp) REVERT: A 856 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 886 ARG cc_start: 0.7407 (ttt-90) cc_final: 0.6755 (ttp-170) REVERT: A 1032 ASP cc_start: 0.6991 (m-30) cc_final: 0.6719 (m-30) REVERT: A 1078 MET cc_start: 0.8774 (mtt) cc_final: 0.8430 (mtt) REVERT: A 1274 ARG cc_start: 0.5825 (mmp-170) cc_final: 0.5429 (mmm160) REVERT: A 1279 ASP cc_start: 0.6066 (m-30) cc_final: 0.5578 (m-30) REVERT: A 1285 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6683 (ttt-90) REVERT: A 1336 GLU cc_start: 0.7159 (tp30) cc_final: 0.6890 (tp30) REVERT: A 1339 ARG cc_start: 0.7660 (mtt90) cc_final: 0.7379 (mtm110) REVERT: A 1343 LEU cc_start: 0.8498 (mt) cc_final: 0.7803 (tt) REVERT: A 1514 ARG cc_start: 0.6492 (tmm-80) cc_final: 0.5914 (mmm-85) REVERT: A 1541 HIS cc_start: 0.6451 (t70) cc_final: 0.6172 (t-90) REVERT: A 1650 MET cc_start: 0.6847 (ttp) cc_final: 0.6313 (pmt) REVERT: A 1758 GLN cc_start: 0.8181 (tt0) cc_final: 0.7936 (tt0) REVERT: A 1774 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7849 (tp40) REVERT: A 1955 ARG cc_start: 0.8103 (ttp-170) cc_final: 0.7850 (mtp85) REVERT: A 1993 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8361 (tttm) REVERT: A 2029 GLU cc_start: 0.8626 (tt0) cc_final: 0.8413 (pt0) REVERT: A 2262 ASN cc_start: 0.7866 (m-40) cc_final: 0.7545 (p0) REVERT: C 100 MET cc_start: 0.5150 (ttp) cc_final: 0.4320 (ttp) REVERT: C 185 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6761 (tmm) REVERT: C 229 SER cc_start: 0.6365 (OUTLIER) cc_final: 0.5956 (t) REVERT: C 270 ARG cc_start: 0.6581 (ttm110) cc_final: 0.6153 (tpp80) REVERT: C 283 GLN cc_start: 0.7140 (mt0) cc_final: 0.6674 (mt0) REVERT: C 286 VAL cc_start: 0.8148 (t) cc_final: 0.7782 (p) REVERT: C 292 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7610 (m110) REVERT: E 48 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7894 (tp) REVERT: E 75 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7810 (tm-30) REVERT: E 83 ASP cc_start: 0.7774 (m-30) cc_final: 0.7380 (m-30) REVERT: E 180 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.7965 (mtp85) REVERT: E 274 LYS cc_start: 0.7430 (tptt) cc_final: 0.7104 (mtmm) REVERT: E 345 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: E 467 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8030 (mm) REVERT: E 525 GLU cc_start: 0.6735 (mp0) cc_final: 0.6461 (mt-10) REVERT: E 617 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6622 (tm-30) REVERT: E 673 VAL cc_start: 0.8940 (t) cc_final: 0.8593 (m) REVERT: E 675 MET cc_start: 0.7440 (tpt) cc_final: 0.7065 (tpt) REVERT: E 709 ARG cc_start: 0.7314 (mtp85) cc_final: 0.7073 (mmm-85) REVERT: E 719 LYS cc_start: 0.8333 (tttt) cc_final: 0.7685 (mptt) REVERT: E 753 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7358 (mp0) REVERT: E 817 TYR cc_start: 0.7979 (t80) cc_final: 0.7759 (t80) REVERT: E 821 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.7302 (mtp180) REVERT: E 922 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8555 (tttp) REVERT: E 1535 ASN cc_start: 0.6912 (m110) cc_final: 0.6518 (t0) REVERT: E 1607 MET cc_start: 0.5342 (mmm) cc_final: 0.4884 (mtt) REVERT: E 1631 CYS cc_start: 0.8103 (t) cc_final: 0.7854 (m) REVERT: E 1642 LYS cc_start: 0.6716 (tttt) cc_final: 0.6080 (mtmm) REVERT: G 26 MET cc_start: 0.8272 (mmm) cc_final: 0.7830 (mmp) REVERT: G 70 VAL cc_start: 0.8182 (m) cc_final: 0.7845 (p) REVERT: G 71 ASP cc_start: 0.7318 (m-30) cc_final: 0.6902 (p0) REVERT: G 92 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6875 (mtp85) REVERT: G 93 LEU cc_start: 0.7605 (tp) cc_final: 0.7329 (tt) outliers start: 37 outliers final: 18 residues processed: 302 average time/residue: 0.7237 time to fit residues: 248.7603 Evaluate side-chains 287 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1597 SER Chi-restraints excluded: chain A residue 1601 GLU Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 2045 LYS Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain E residue 843 ILE Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 922 LYS Chi-restraints excluded: chain E residue 1692 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 204 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 269 optimal weight: 0.0980 chunk 115 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1509 GLN A1722 GLN A1807 GLN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102491 restraints weight = 35881.241| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.01 r_work: 0.3045 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25724 Z= 0.109 Angle : 0.503 10.502 34842 Z= 0.258 Chirality : 0.039 0.173 3946 Planarity : 0.004 0.047 4425 Dihedral : 4.619 82.799 3434 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.19 % Allowed : 12.07 % Favored : 86.74 % 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: 2.15 (0.15), residues: 3087 helix: 2.18 (0.12), residues: 1978 sheet: 0.59 (0.36), residues: 186 loop : -0.02 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1391 TYR 0.018 0.001 TYR E 588 PHE 0.025 0.001 PHE A1122 TRP 0.041 0.001 TRP A2429 HIS 0.005 0.001 HIS A1988 Details of bonding type rmsd covalent geometry : bond 0.00231 (25720) covalent geometry : angle 0.50294 (34839) hydrogen bonds : bond 0.04350 ( 1461) hydrogen bonds : angle 3.67128 ( 4239) metal coordination : bond 0.00632 ( 4) metal coordination : angle 1.91524 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6174 Ramachandran restraints generated. 3087 Oldfield, 0 Emsley, 3087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 267 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 813 MET cc_start: 0.6954 (mmm) cc_final: 0.6619 (mpp) REVERT: A 856 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 886 ARG cc_start: 0.7433 (ttt-90) cc_final: 0.6751 (ttp-170) REVERT: A 1032 ASP cc_start: 0.7185 (m-30) cc_final: 0.6927 (m-30) REVERT: A 1078 MET cc_start: 0.8779 (mtt) cc_final: 0.8429 (mtt) REVERT: A 1274 ARG cc_start: 0.5839 (mmp-170) cc_final: 0.5428 (mmm160) REVERT: A 1279 ASP cc_start: 0.5973 (m-30) cc_final: 0.5514 (m-30) REVERT: A 1285 ARG cc_start: 0.7283 (ttm110) cc_final: 0.6633 (ttt-90) REVERT: A 1336 GLU cc_start: 0.7171 (tp30) cc_final: 0.6890 (tp30) REVERT: A 1339 ARG cc_start: 0.7690 (mtt90) cc_final: 0.7438 (mtm110) REVERT: A 1343 LEU cc_start: 0.8488 (mt) cc_final: 0.7822 (tt) REVERT: A 1477 MET cc_start: 0.7097 (mmt) cc_final: 0.6786 (tpp) REVERT: A 1514 ARG cc_start: 0.6492 (tmm-80) cc_final: 0.5903 (mmm-85) REVERT: A 1541 HIS cc_start: 0.6412 (t70) cc_final: 0.6148 (t-90) REVERT: A 1650 MET cc_start: 0.6848 (ttp) cc_final: 0.6260 (pmt) REVERT: A 1758 GLN cc_start: 0.8205 (tt0) cc_final: 0.7957 (tt0) REVERT: A 1774 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7878 (tp40) REVERT: A 1955 ARG cc_start: 0.8113 (ttp-170) cc_final: 0.7863 (mtp85) REVERT: A 1993 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8268 (tttm) REVERT: A 2029 GLU cc_start: 0.8681 (tt0) cc_final: 0.8454 (pt0) REVERT: A 2262 ASN cc_start: 0.7906 (m-40) cc_final: 0.7588 (p0) REVERT: C 100 MET cc_start: 0.5227 (ttp) cc_final: 0.4378 (ttp) REVERT: C 117 ARG cc_start: 0.6081 (mtt-85) cc_final: 0.5458 (tpp-160) REVERT: C 185 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6800 (tmm) REVERT: C 229 SER cc_start: 0.6382 (OUTLIER) cc_final: 0.5945 (t) REVERT: C 270 ARG cc_start: 0.6636 (ttm110) cc_final: 0.6208 (tpp80) REVERT: C 283 GLN cc_start: 0.7173 (mt0) cc_final: 0.6692 (mt0) REVERT: C 286 VAL cc_start: 0.8174 (t) cc_final: 0.7802 (p) REVERT: E 48 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7885 (tp) REVERT: E 75 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7802 (tm-30) REVERT: E 83 ASP cc_start: 0.7734 (m-30) cc_final: 0.7398 (m-30) REVERT: E 180 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.7957 (mtp85) REVERT: E 274 LYS cc_start: 0.7352 (tptt) cc_final: 0.7040 (mppt) REVERT: E 345 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7646 (mm-30) REVERT: E 467 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8139 (mm) REVERT: E 525 GLU cc_start: 0.6760 (mp0) cc_final: 0.6491 (mt-10) REVERT: E 617 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6621 (tm-30) REVERT: E 675 MET cc_start: 0.7387 (tpt) cc_final: 0.7060 (tpt) REVERT: E 709 ARG cc_start: 0.7335 (mtp85) cc_final: 0.7093 (mmm-85) REVERT: E 719 LYS cc_start: 0.8356 (tttt) cc_final: 0.7686 (mptt) REVERT: E 753 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7423 (mp0) REVERT: E 817 TYR cc_start: 0.7960 (t80) cc_final: 0.7735 (t80) REVERT: E 821 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7301 (mtp180) REVERT: E 922 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8593 (tttp) REVERT: E 1535 ASN cc_start: 0.6894 (m110) cc_final: 0.6517 (t0) REVERT: E 1607 MET cc_start: 0.5344 (mmm) cc_final: 0.4888 (mtt) REVERT: E 1631 CYS cc_start: 0.8158 (t) cc_final: 0.7875 (m) REVERT: E 1642 LYS cc_start: 0.6689 (tttt) cc_final: 0.6047 (mtmm) REVERT: G 26 MET cc_start: 0.8289 (mmm) cc_final: 0.7836 (mmp) REVERT: G 70 VAL cc_start: 0.8181 (m) cc_final: 0.7859 (p) REVERT: G 92 ARG cc_start: 0.7249 (ttm170) cc_final: 0.6882 (mtp85) REVERT: G 93 LEU cc_start: 0.7624 (tp) cc_final: 0.7347 (tt) outliers start: 33 outliers final: 19 residues processed: 289 average time/residue: 0.7536 time to fit residues: 247.7283 Evaluate side-chains 286 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1597 SER Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 2045 LYS Chi-restraints excluded: chain A residue 2244 ASP Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 678 LYS Chi-restraints excluded: chain E residue 843 ILE Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 922 LYS Chi-restraints excluded: chain E residue 1692 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 289 optimal weight: 7.9990 chunk 176 optimal weight: 0.0060 chunk 223 optimal weight: 0.0170 chunk 74 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 overall best weight: 2.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1722 GLN ** A1807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS E 418 HIS G 88 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099658 restraints weight = 35500.138| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.87 r_work: 0.2993 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25724 Z= 0.158 Angle : 0.570 9.570 34842 Z= 0.295 Chirality : 0.042 0.169 3946 Planarity : 0.004 0.050 4425 Dihedral : 4.889 85.558 3434 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.04 % Allowed : 12.18 % Favored : 86.78 % 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: 1.86 (0.15), residues: 3087 helix: 1.96 (0.12), residues: 1974 sheet: 0.60 (0.36), residues: 182 loop : -0.15 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1391 TYR 0.018 0.002 TYR E 588 PHE 0.029 0.002 PHE A1122 TRP 0.043 0.002 TRP A2429 HIS 0.005 0.001 HIS E 379 Details of bonding type rmsd covalent geometry : bond 0.00368 (25720) covalent geometry : angle 0.56928 (34839) hydrogen bonds : bond 0.05740 ( 1461) hydrogen bonds : angle 3.85010 ( 4239) metal coordination : bond 0.00672 ( 4) metal coordination : angle 2.59390 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9838.59 seconds wall clock time: 167 minutes 54.89 seconds (10074.89 seconds total)