Starting phenix.real_space_refine on Wed Mar 4 23:11:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lhl_23345/03_2026/7lhl_23345.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lhl_23345/03_2026/7lhl_23345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lhl_23345/03_2026/7lhl_23345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lhl_23345/03_2026/7lhl_23345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lhl_23345/03_2026/7lhl_23345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lhl_23345/03_2026/7lhl_23345.map" } resolution = 3.6 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= 0.004 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 10751 2.51 5 N 3079 2.21 5 O 3224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17075 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4270 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 29, 'TRANS': 542} Chain breaks: 2 Chain: "B" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4249 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 30, 'TRANS': 538} Chain breaks: 2 Chain: "C" Number of atoms: 4254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4254 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 29, 'TRANS': 538} Chain breaks: 3 Chain: "D" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4302 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 31, 'TRANS': 544} Chain breaks: 2 Time building chain proxies: 3.88, per 1000 atoms: 0.23 Number of scatterers: 17075 At special positions: 0 Unit cell: (112.784, 124.488, 145.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 3224 8.00 N 3079 7.00 C 10751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 788.0 milliseconds 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 18 sheets defined 47.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.808A pdb=" N ALA A 899 " --> pdb=" O PRO A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 917 through 927 removed outlier: 4.108A pdb=" N ALA A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 923 " --> pdb=" O GLY A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 936 Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 944 through 954 Processing helix chain 'A' and resid 970 through 981 removed outlier: 3.572A pdb=" N ILE A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1012 removed outlier: 3.665A pdb=" N TYR A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1025 Processing helix chain 'A' and resid 1027 through 1037 removed outlier: 4.141A pdb=" N ASP A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A1034 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A1037 " --> pdb=" O ASP A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1076 removed outlier: 3.570A pdb=" N ILE A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1094 Proline residue: A1092 - end of helix Processing helix chain 'A' and resid 1103 through 1115 removed outlier: 3.662A pdb=" N GLU A1113 " --> pdb=" O ALA A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1149 removed outlier: 3.884A pdb=" N LEU A1142 " --> pdb=" O GLN A1138 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A1143 " --> pdb=" O PRO A1139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1200 removed outlier: 3.886A pdb=" N ILE A1193 " --> pdb=" O THR A1189 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS A1199 " --> pdb=" O GLU A1195 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY A1200 " --> pdb=" O THR A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1232 removed outlier: 3.767A pdb=" N LEU A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A1222 " --> pdb=" O GLY A1218 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A1223 " --> pdb=" O GLN A1219 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1248 removed outlier: 4.022A pdb=" N LEU A1246 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A1247 " --> pdb=" O ARG A1243 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A1248 " --> pdb=" O ALA A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1312 Processing helix chain 'A' and resid 1316 through 1324 removed outlier: 3.559A pdb=" N VAL A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1343 removed outlier: 3.872A pdb=" N LYS A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A1335 " --> pdb=" O THR A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 removed outlier: 3.628A pdb=" N VAL A1365 " --> pdb=" O VAL A1361 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A1366 " --> pdb=" O ALA A1362 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A1367 " --> pdb=" O SER A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1461 Processing helix chain 'A' and resid 1482 through 1494 removed outlier: 3.901A pdb=" N VAL A1487 " --> pdb=" O ALA A1483 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A1488 " --> pdb=" O GLU A1484 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 removed outlier: 3.787A pdb=" N ALA B 899 " --> pdb=" O PRO B 895 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 928 removed outlier: 3.576A pdb=" N VAL B 920 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 921 " --> pdb=" O ALA B 917 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 939 removed outlier: 3.918A pdb=" N GLN B 937 " --> pdb=" O ALA B 933 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 938 " --> pdb=" O ASP B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 954 Processing helix chain 'B' and resid 971 through 978 removed outlier: 3.814A pdb=" N GLY B 975 " --> pdb=" O VAL B 971 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1012 removed outlier: 3.605A pdb=" N LEU B1004 " --> pdb=" O PRO B1000 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B1011 " --> pdb=" O ARG B1007 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B1012 " --> pdb=" O TYR B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1025 removed outlier: 3.670A pdb=" N ALA B1021 " --> pdb=" O THR B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1037 Processing helix chain 'B' and resid 1061 through 1072 Processing helix chain 'B' and resid 1083 through 1094 Proline residue: B1092 - end of helix Processing helix chain 'B' and resid 1103 through 1115 removed outlier: 3.574A pdb=" N GLU B1113 " --> pdb=" O ALA B1109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B1114 " --> pdb=" O THR B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1134 removed outlier: 3.724A pdb=" N ARG B1133 " --> pdb=" O VAL B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1148 removed outlier: 4.106A pdb=" N LEU B1142 " --> pdb=" O GLN B1138 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B1143 " --> pdb=" O PRO B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1178 removed outlier: 3.763A pdb=" N THR B1177 " --> pdb=" O THR B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1197 Processing helix chain 'B' and resid 1205 through 1209 removed outlier: 3.604A pdb=" N LEU B1208 " --> pdb=" O PHE B1205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B1209 " --> pdb=" O ARG B1206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1205 through 1209' Processing helix chain 'B' and resid 1214 through 1232 removed outlier: 3.704A pdb=" N GLY B1218 " --> pdb=" O GLU B1214 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B1221 " --> pdb=" O ALA B1217 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B1228 " --> pdb=" O ALA B1224 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP B1230 " --> pdb=" O TRP B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1239 through 1246 removed outlier: 3.531A pdb=" N ARG B1243 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1312 removed outlier: 3.821A pdb=" N LEU B1309 " --> pdb=" O ALA B1305 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B1310 " --> pdb=" O GLU B1306 " (cutoff:3.500A) Processing helix chain 'B' and resid 1318 through 1323 removed outlier: 3.526A pdb=" N ALA B1322 " --> pdb=" O GLY B1318 " (cutoff:3.500A) Processing helix chain 'B' and resid 1327 through 1343 removed outlier: 3.718A pdb=" N THR B1331 " --> pdb=" O GLY B1327 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B1334 " --> pdb=" O ALA B1330 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B1335 " --> pdb=" O THR B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1370 removed outlier: 3.755A pdb=" N VAL B1365 " --> pdb=" O VAL B1361 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B1366 " --> pdb=" O ALA B1362 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B1367 " --> pdb=" O SER B1363 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B1370 " --> pdb=" O ASP B1366 " (cutoff:3.500A) Processing helix chain 'B' and resid 1445 through 1461 removed outlier: 4.557A pdb=" N ALA B1449 " --> pdb=" O ASP B1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 1485 through 1496 removed outlier: 3.546A pdb=" N GLN B1489 " --> pdb=" O ARG B1485 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B1490 " --> pdb=" O ALA B1486 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.664A pdb=" N GLN C 906 " --> pdb=" O SER C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 913 Processing helix chain 'C' and resid 917 through 927 removed outlier: 3.506A pdb=" N ALA C 921 " --> pdb=" O ALA C 917 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 923 " --> pdb=" O GLY C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 939 removed outlier: 3.980A pdb=" N GLN C 937 " --> pdb=" O ALA C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 954 removed outlier: 3.818A pdb=" N LEU C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 949 " --> pdb=" O GLY C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.869A pdb=" N LEU C 977 " --> pdb=" O ASP C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 999 through 1010 removed outlier: 3.630A pdb=" N LEU C1004 " --> pdb=" O PRO C1000 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1024 removed outlier: 3.505A pdb=" N THR C1020 " --> pdb=" O THR C1016 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C1021 " --> pdb=" O THR C1017 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C1022 " --> pdb=" O GLU C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1042 removed outlier: 3.597A pdb=" N LEU C1035 " --> pdb=" O ALA C1031 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C1039 " --> pdb=" O LEU C1035 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL C1040 " --> pdb=" O SER C1036 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP C1041 " --> pdb=" O ARG C1037 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C1042 " --> pdb=" O MET C1038 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1076 removed outlier: 3.568A pdb=" N ARG C1076 " --> pdb=" O LEU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1095 Proline residue: C1092 - end of helix Processing helix chain 'C' and resid 1104 through 1115 removed outlier: 3.522A pdb=" N LEU C1108 " --> pdb=" O GLY C1104 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1134 removed outlier: 3.954A pdb=" N ARG C1133 " --> pdb=" O VAL C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1149 removed outlier: 3.630A pdb=" N ASP C1143 " --> pdb=" O PRO C1139 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C1144 " --> pdb=" O ALA C1140 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C1145 " --> pdb=" O MET C1141 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1173 through 1178 removed outlier: 3.818A pdb=" N THR C1177 " --> pdb=" O THR C1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1194 Processing helix chain 'C' and resid 1205 through 1209 removed outlier: 3.739A pdb=" N THR C1209 " --> pdb=" O ARG C1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1230 removed outlier: 3.583A pdb=" N GLU C1220 " --> pdb=" O THR C1216 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C1227 " --> pdb=" O GLN C1223 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP C1230 " --> pdb=" O TRP C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1241 through 1246 Processing helix chain 'C' and resid 1297 through 1312 removed outlier: 3.539A pdb=" N ALA C1301 " --> pdb=" O SER C1297 " (cutoff:3.500A) Processing helix chain 'C' and resid 1318 through 1323 Processing helix chain 'C' and resid 1327 through 1343 removed outlier: 3.865A pdb=" N LEU C1332 " --> pdb=" O GLY C1328 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C1338 " --> pdb=" O LYS C1334 " (cutoff:3.500A) Processing helix chain 'C' and resid 1361 through 1369 removed outlier: 3.563A pdb=" N VAL C1365 " --> pdb=" O VAL C1361 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP C1366 " --> pdb=" O ALA C1362 " (cutoff:3.500A) Processing helix chain 'C' and resid 1445 through 1461 removed outlier: 3.911A pdb=" N ALA C1449 " --> pdb=" O ASP C1445 " (cutoff:3.500A) Processing helix chain 'C' and resid 1482 through 1495 removed outlier: 3.989A pdb=" N VAL C1488 " --> pdb=" O GLU C1484 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 906 removed outlier: 3.652A pdb=" N GLN D 906 " --> pdb=" O SER D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 927 removed outlier: 4.140A pdb=" N ALA D 921 " --> pdb=" O ALA D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 939 removed outlier: 4.162A pdb=" N GLN D 937 " --> pdb=" O ALA D 933 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 938 " --> pdb=" O ASP D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 954 removed outlier: 4.340A pdb=" N TRP D 947 " --> pdb=" O ASN D 943 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP D 949 " --> pdb=" O GLY D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 972 No H-bonds generated for 'chain 'D' and resid 970 through 972' Processing helix chain 'D' and resid 973 through 981 Processing helix chain 'D' and resid 1000 through 1012 removed outlier: 3.961A pdb=" N ILE D1005 " --> pdb=" O LEU D1001 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY D1006 " --> pdb=" O GLY D1002 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D1007 " --> pdb=" O ASP D1003 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR D1008 " --> pdb=" O LEU D1004 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D1012 " --> pdb=" O TYR D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1024 removed outlier: 4.097A pdb=" N THR D1020 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA D1021 " --> pdb=" O THR D1017 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D1022 " --> pdb=" O GLU D1018 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1041 removed outlier: 3.617A pdb=" N SER D1032 " --> pdb=" O VAL D1028 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL D1034 " --> pdb=" O VAL D1030 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D1040 " --> pdb=" O SER D1036 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP D1041 " --> pdb=" O ARG D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1076 removed outlier: 3.524A pdb=" N ARG D1076 " --> pdb=" O LEU D1072 " (cutoff:3.500A) Processing helix chain 'D' and resid 1083 through 1095 Proline residue: D1092 - end of helix Processing helix chain 'D' and resid 1104 through 1115 removed outlier: 3.780A pdb=" N THR D1110 " --> pdb=" O ASP D1106 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D1113 " --> pdb=" O ALA D1109 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1134 removed outlier: 4.257A pdb=" N ARG D1133 " --> pdb=" O VAL D1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1148 removed outlier: 4.138A pdb=" N LEU D1142 " --> pdb=" O GLN D1138 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D1148 " --> pdb=" O GLU D1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1178 removed outlier: 3.705A pdb=" N THR D1177 " --> pdb=" O THR D1173 " (cutoff:3.500A) Processing helix chain 'D' and resid 1187 through 1200 removed outlier: 3.557A pdb=" N GLY D1200 " --> pdb=" O THR D1196 " (cutoff:3.500A) Processing helix chain 'D' and resid 1215 through 1232 removed outlier: 3.783A pdb=" N GLN D1219 " --> pdb=" O GLY D1215 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D1220 " --> pdb=" O THR D1216 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D1227 " --> pdb=" O GLN D1223 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TRP D1230 " --> pdb=" O TRP D1226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY D1232 " --> pdb=" O LEU D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1246 removed outlier: 3.651A pdb=" N ARG D1243 " --> pdb=" O PHE D1239 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D1244 " --> pdb=" O ALA D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1297 through 1312 Processing helix chain 'D' and resid 1318 through 1324 Processing helix chain 'D' and resid 1328 through 1343 removed outlier: 4.055A pdb=" N LYS D1334 " --> pdb=" O ALA D1330 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D1335 " --> pdb=" O THR D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1369 removed outlier: 3.605A pdb=" N VAL D1365 " --> pdb=" O VAL D1361 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP D1366 " --> pdb=" O ALA D1362 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D1367 " --> pdb=" O SER D1363 " (cutoff:3.500A) Processing helix chain 'D' and resid 1432 through 1435 Processing helix chain 'D' and resid 1446 through 1460 removed outlier: 3.978A pdb=" N ALA D1450 " --> pdb=" O ALA D1446 " (cutoff:3.500A) Processing helix chain 'D' and resid 1482 through 1495 removed outlier: 4.551A pdb=" N VAL D1487 " --> pdb=" O ALA D1483 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL D1488 " --> pdb=" O GLU D1484 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D1489 " --> pdb=" O ARG D1485 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D1490 " --> pdb=" O ALA D1486 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D1495 " --> pdb=" O ALA D1491 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1234 through 1236 Processing sheet with id=AA2, first strand: chain 'A' and resid 1346 through 1348 Processing sheet with id=AA3, first strand: chain 'A' and resid 1384 through 1388 removed outlier: 3.566A pdb=" N VAL A1385 " --> pdb=" O LEU A1421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1430 through 1431 removed outlier: 3.974A pdb=" N SER A1436 " --> pdb=" O GLU A1431 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 957 through 960 removed outlier: 3.515A pdb=" N ALA B 969 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 4.608A pdb=" N GLY B1157 " --> pdb=" O TRP B1165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1151 through 1152 removed outlier: 3.531A pdb=" N HIS B1169 " --> pdb=" O MET B1152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1234 through 1236 Processing sheet with id=AA9, first strand: chain 'B' and resid 1385 through 1388 Processing sheet with id=AB1, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AB2, first strand: chain 'C' and resid 1151 through 1152 Processing sheet with id=AB3, first strand: chain 'C' and resid 1202 through 1203 Processing sheet with id=AB4, first strand: chain 'C' and resid 1384 through 1388 removed outlier: 3.646A pdb=" N LEU C1421 " --> pdb=" O VAL C1385 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 959 through 960 Processing sheet with id=AB6, first strand: chain 'D' and resid 1120 through 1121 Processing sheet with id=AB7, first strand: chain 'D' and resid 1202 through 1203 Processing sheet with id=AB8, first strand: chain 'D' and resid 1385 through 1388 Processing sheet with id=AB9, first strand: chain 'D' and resid 1429 through 1431 removed outlier: 4.065A pdb=" N PHE D1429 " --> pdb=" O LEU D1438 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1665 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: 2.32 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5780 1.34 - 1.45: 2435 1.45 - 1.57: 9187 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 17435 Sorted by residual: bond pdb=" N VAL C1361 " pdb=" CA VAL C1361 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.07e-02 8.73e+03 1.24e+01 bond pdb=" N CYS C1345 " pdb=" CA CYS C1345 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.26e-02 6.30e+03 1.24e+01 bond pdb=" N MET C1152 " pdb=" CA MET C1152 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N ASP A1163 " pdb=" CA ASP A1163 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 bond pdb=" N TRP C1153 " pdb=" CA TRP C1153 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.48e+00 ... (remaining 17430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 22829 2.04 - 4.08: 828 4.08 - 6.11: 115 6.11 - 8.15: 14 8.15 - 10.19: 1 Bond angle restraints: 23787 Sorted by residual: angle pdb=" C ARG C1347 " pdb=" N GLY C1348 " pdb=" CA GLY C1348 " ideal model delta sigma weight residual 122.18 128.42 -6.24 6.90e-01 2.10e+00 8.18e+01 angle pdb=" C SER B1439 " pdb=" N PHE B1440 " pdb=" CA PHE B1440 " ideal model delta sigma weight residual 120.82 128.52 -7.70 1.50e+00 4.44e-01 2.64e+01 angle pdb=" CA SER C1154 " pdb=" C SER C1154 " pdb=" N GLY C1155 " ideal model delta sigma weight residual 114.92 121.33 -6.41 1.43e+00 4.89e-01 2.01e+01 angle pdb=" CA SER C1154 " pdb=" C SER C1154 " pdb=" O SER C1154 " ideal model delta sigma weight residual 122.14 116.70 5.44 1.24e+00 6.50e-01 1.92e+01 angle pdb=" C ALA C1444 " pdb=" N ASP C1445 " pdb=" CA ASP C1445 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 ... (remaining 23782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 9235 18.09 - 36.18: 808 36.18 - 54.26: 133 54.26 - 72.35: 30 72.35 - 90.44: 19 Dihedral angle restraints: 10225 sinusoidal: 3837 harmonic: 6388 Sorted by residual: dihedral pdb=" CA VAL C1474 " pdb=" C VAL C1474 " pdb=" N ALA C1475 " pdb=" CA ALA C1475 " ideal model delta harmonic sigma weight residual 180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA VAL A1422 " pdb=" C VAL A1422 " pdb=" N ASP A1423 " pdb=" CA ASP A1423 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA SER B1439 " pdb=" C SER B1439 " pdb=" N PHE B1440 " pdb=" CA PHE B1440 " ideal model delta harmonic sigma weight residual -180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 10222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2310 0.063 - 0.126: 362 0.126 - 0.189: 33 0.189 - 0.251: 5 0.251 - 0.314: 1 Chirality restraints: 2711 Sorted by residual: chirality pdb=" CA TRP C1153 " pdb=" N TRP C1153 " pdb=" C TRP C1153 " pdb=" CB TRP C1153 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ASP A1163 " pdb=" N ASP A1163 " pdb=" C ASP A1163 " pdb=" CB ASP A1163 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA SER C1154 " pdb=" N SER C1154 " pdb=" C SER C1154 " pdb=" CB SER C1154 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2708 not shown) Planarity restraints: 3143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 967 " 0.020 2.00e-02 2.50e+03 1.51e-02 5.69e+00 pdb=" CG TRP D 967 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 967 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP D 967 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 967 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 967 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 967 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 967 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 967 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 967 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B1118 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B1119 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B1119 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1119 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1080 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A1081 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1081 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1081 " -0.026 5.00e-02 4.00e+02 ... (remaining 3140 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 220 2.60 - 3.18: 16531 3.18 - 3.75: 24939 3.75 - 4.33: 33476 4.33 - 4.90: 53999 Nonbonded interactions: 129165 Sorted by model distance: nonbonded pdb=" OH TYR B1349 " pdb=" O GLU B1352 " model vdw 2.027 3.040 nonbonded pdb=" OG SER C1406 " pdb=" O HIS C1409 " model vdw 2.131 3.040 nonbonded pdb=" O VAL D 898 " pdb=" OG SER D 902 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASN A1472 " pdb=" N GLY A1473 " model vdw 2.169 3.120 nonbonded pdb=" O TRP D1153 " pdb=" OG1 THR D1235 " model vdw 2.174 3.040 ... (remaining 129160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 895 through 984 or resid 992 through 1045 or resid 1055 th \ rough 1056 or resid 1060 through 1250 or resid 1279 through 1499)) selection = (chain 'B' and (resid 895 through 984 or resid 992 through 1045 or resid 1047 th \ rough 1048 or resid 1060 through 1499)) selection = (chain 'C' and (resid 895 through 1045 or resid 1047 through 1048 or resid 1060 \ through 1499)) selection = (chain 'D' and (resid 895 through 984 or resid 992 through 1045 or resid 1047 th \ rough 1048 or resid 1060 through 1250 or resid 1279 through 1499)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.240 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 17435 Z= 0.363 Angle : 0.896 10.190 23787 Z= 0.535 Chirality : 0.047 0.314 2711 Planarity : 0.005 0.054 3143 Dihedral : 14.574 90.441 6149 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.65 % Allowed : 9.75 % Favored : 89.61 % Cbeta Deviations : 0.05 % 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: -4.21 (0.15), residues: 2259 helix: -2.82 (0.13), residues: 872 sheet: -3.60 (0.36), residues: 133 loop : -2.72 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1089 TYR 0.018 0.002 TYR C1349 PHE 0.016 0.002 PHE B1429 TRP 0.041 0.002 TRP D 967 HIS 0.009 0.001 HIS A1409 Details of bonding type rmsd covalent geometry : bond 0.00799 (17435) covalent geometry : angle 0.89580 (23787) hydrogen bonds : bond 0.25117 ( 576) hydrogen bonds : angle 9.26313 ( 1665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 923 LEU cc_start: 0.9324 (tp) cc_final: 0.8973 (tt) REVERT: A 972 GLU cc_start: 0.7989 (pt0) cc_final: 0.7570 (mp0) REVERT: A 973 ASP cc_start: 0.7623 (t70) cc_final: 0.7282 (t70) REVERT: C 1223 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7924 (tm-30) outliers start: 11 outliers final: 5 residues processed: 220 average time/residue: 0.1817 time to fit residues: 54.4421 Evaluate side-chains 143 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1163 ASP Chi-restraints excluded: chain C residue 1229 ILE Chi-restraints excluded: chain C residue 1347 ARG Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 GLN A1161 ASN ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1207 GLN A1346 GLN B 952 HIS B1019 GLN B1114 GLN B1158 GLN B1169 HIS B1180 HIS B1346 GLN B1394 ASN B1472 ASN B1489 GLN C 937 GLN C1114 GLN C1489 GLN D1114 GLN D1346 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.120608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.090665 restraints weight = 32816.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091596 restraints weight = 27347.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092747 restraints weight = 20891.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093143 restraints weight = 16047.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093570 restraints weight = 15331.104| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17435 Z= 0.156 Angle : 0.649 10.415 23787 Z= 0.329 Chirality : 0.042 0.195 2711 Planarity : 0.005 0.046 3143 Dihedral : 5.178 48.591 2499 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.00 % Allowed : 15.85 % Favored : 82.15 % 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: -2.78 (0.16), residues: 2259 helix: -1.09 (0.16), residues: 927 sheet: -3.32 (0.36), residues: 150 loop : -2.29 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1410 TYR 0.017 0.001 TYR C1349 PHE 0.013 0.001 PHE B1440 TRP 0.022 0.001 TRP B1226 HIS 0.005 0.001 HIS D1302 Details of bonding type rmsd covalent geometry : bond 0.00365 (17435) covalent geometry : angle 0.64884 (23787) hydrogen bonds : bond 0.04404 ( 576) hydrogen bonds : angle 5.40955 ( 1665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 GLU cc_start: 0.8153 (tp30) cc_final: 0.7885 (tp30) REVERT: A 1340 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 1317 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8577 (mtpp) REVERT: B 1493 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8214 (pp) REVERT: C 1065 LYS cc_start: 0.9207 (tppp) cc_final: 0.9005 (ttmm) REVERT: C 1381 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7320 (tm-30) REVERT: C 1426 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9014 (pt) REVERT: C 1474 VAL cc_start: 0.6628 (OUTLIER) cc_final: 0.6385 (t) REVERT: D 1334 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8539 (mmtt) outliers start: 34 outliers final: 14 residues processed: 202 average time/residue: 0.1485 time to fit residues: 43.5606 Evaluate side-chains 158 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1082 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1493 LEU Chi-restraints excluded: chain C residue 1229 ILE Chi-restraints excluded: chain C residue 1339 PHE Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain C residue 1474 VAL Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1101 ASN Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1409 HIS Chi-restraints excluded: chain D residue 1459 SER Chi-restraints excluded: chain D residue 1469 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 95 optimal weight: 0.0020 chunk 129 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 157 optimal weight: 0.0000 chunk 103 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1161 ASN ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092053 restraints weight = 33121.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093187 restraints weight = 26687.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094019 restraints weight = 20248.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096237 restraints weight = 16057.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096286 restraints weight = 13462.183| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17435 Z= 0.129 Angle : 0.601 11.690 23787 Z= 0.300 Chirality : 0.041 0.242 2711 Planarity : 0.004 0.040 3143 Dihedral : 4.694 31.506 2493 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.64 % Allowed : 17.91 % Favored : 79.45 % 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 (0.17), residues: 2259 helix: -0.31 (0.17), residues: 932 sheet: -3.15 (0.34), residues: 172 loop : -1.96 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 925 TYR 0.013 0.001 TYR C1349 PHE 0.012 0.001 PHE A1015 TRP 0.020 0.001 TRP B1226 HIS 0.004 0.001 HIS D1302 Details of bonding type rmsd covalent geometry : bond 0.00300 (17435) covalent geometry : angle 0.60115 (23787) hydrogen bonds : bond 0.03597 ( 576) hydrogen bonds : angle 4.79017 ( 1665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1003 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: A 1340 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8469 (tm-30) REVERT: B 1223 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 1317 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8606 (mtpp) REVERT: C 1426 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9018 (pt) outliers start: 45 outliers final: 25 residues processed: 197 average time/residue: 0.1239 time to fit residues: 37.6494 Evaluate side-chains 166 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1003 ASP Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1186 PHE Chi-restraints excluded: chain C residue 1339 PHE Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain D residue 904 GLN Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1238 THR Chi-restraints excluded: chain D residue 1245 VAL Chi-restraints excluded: chain D residue 1409 HIS Chi-restraints excluded: chain D residue 1459 SER Chi-restraints excluded: chain D residue 1469 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 130 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 151 optimal weight: 0.2980 chunk 164 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1161 ASN ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.122445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092274 restraints weight = 32951.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092503 restraints weight = 26259.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093261 restraints weight = 21715.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096120 restraints weight = 17300.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096166 restraints weight = 13454.117| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17435 Z= 0.118 Angle : 0.593 13.215 23787 Z= 0.292 Chirality : 0.041 0.254 2711 Planarity : 0.004 0.037 3143 Dihedral : 4.444 32.607 2491 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.41 % Allowed : 19.03 % Favored : 77.57 % 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: -1.69 (0.18), residues: 2259 helix: -0.03 (0.17), residues: 950 sheet: -2.90 (0.36), residues: 173 loop : -1.79 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 925 TYR 0.019 0.001 TYR A1008 PHE 0.013 0.001 PHE A1015 TRP 0.019 0.001 TRP B1226 HIS 0.004 0.001 HIS D1302 Details of bonding type rmsd covalent geometry : bond 0.00276 (17435) covalent geometry : angle 0.59303 (23787) hydrogen bonds : bond 0.03225 ( 576) hydrogen bonds : angle 4.53486 ( 1665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 155 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 972 GLU cc_start: 0.7958 (pt0) cc_final: 0.7618 (mp0) REVERT: A 1340 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 1223 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 1317 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8619 (mtpp) REVERT: B 1493 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8018 (pp) REVERT: C 1426 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9013 (pt) outliers start: 58 outliers final: 34 residues processed: 203 average time/residue: 0.1236 time to fit residues: 38.7174 Evaluate side-chains 175 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1493 LEU Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1186 PHE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain C residue 1463 ILE Chi-restraints excluded: chain D residue 897 VAL Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1020 THR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1146 LEU Chi-restraints excluded: chain D residue 1188 ASP Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1238 THR Chi-restraints excluded: chain D residue 1245 VAL Chi-restraints excluded: chain D residue 1409 HIS Chi-restraints excluded: chain D residue 1430 LEU Chi-restraints excluded: chain D residue 1459 SER Chi-restraints excluded: chain D residue 1469 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 172 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.091390 restraints weight = 32987.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091216 restraints weight = 27069.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091577 restraints weight = 32645.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093140 restraints weight = 19701.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093559 restraints weight = 15650.723| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17435 Z= 0.168 Angle : 0.619 13.750 23787 Z= 0.305 Chirality : 0.042 0.202 2711 Planarity : 0.004 0.040 3143 Dihedral : 4.513 31.762 2491 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.88 % Allowed : 19.96 % Favored : 76.16 % 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: -1.56 (0.18), residues: 2259 helix: 0.12 (0.17), residues: 952 sheet: -2.97 (0.36), residues: 177 loop : -1.72 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1135 TYR 0.017 0.001 TYR A1008 PHE 0.014 0.001 PHE B1303 TRP 0.021 0.001 TRP B1226 HIS 0.004 0.001 HIS D1302 Details of bonding type rmsd covalent geometry : bond 0.00401 (17435) covalent geometry : angle 0.61854 (23787) hydrogen bonds : bond 0.03401 ( 576) hydrogen bonds : angle 4.59718 ( 1665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 915 ARG cc_start: 0.7736 (mpp80) cc_final: 0.7482 (mtm180) REVERT: A 1165 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.8269 (m-10) REVERT: A 1340 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8558 (tm-30) REVERT: B 1223 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7793 (tm-30) REVERT: B 1306 GLU cc_start: 0.8464 (tp30) cc_final: 0.8046 (tp30) REVERT: B 1317 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8620 (mtpp) REVERT: B 1493 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7999 (pp) REVERT: C 1038 MET cc_start: 0.7601 (mtt) cc_final: 0.7191 (mtt) REVERT: C 1410 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7767 (mmm160) REVERT: C 1426 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9072 (pt) REVERT: D 1484 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7121 (pp20) outliers start: 66 outliers final: 42 residues processed: 203 average time/residue: 0.1302 time to fit residues: 40.2930 Evaluate side-chains 182 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1165 TRP Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1353 SER Chi-restraints excluded: chain B residue 1390 THR Chi-restraints excluded: chain B residue 1493 LEU Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 931 THR Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1298 THR Chi-restraints excluded: chain C residue 1339 PHE Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain C residue 1463 ILE Chi-restraints excluded: chain D residue 897 VAL Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1020 THR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1146 LEU Chi-restraints excluded: chain D residue 1188 ASP Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1237 ASP Chi-restraints excluded: chain D residue 1238 THR Chi-restraints excluded: chain D residue 1245 VAL Chi-restraints excluded: chain D residue 1298 THR Chi-restraints excluded: chain D residue 1409 HIS Chi-restraints excluded: chain D residue 1430 LEU Chi-restraints excluded: chain D residue 1459 SER Chi-restraints excluded: chain D residue 1484 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 158 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 44 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.085804 restraints weight = 32703.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088143 restraints weight = 20934.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089656 restraints weight = 15898.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090583 restraints weight = 13408.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091215 restraints weight = 12092.837| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17435 Z= 0.138 Angle : 0.602 13.989 23787 Z= 0.296 Chirality : 0.041 0.247 2711 Planarity : 0.004 0.040 3143 Dihedral : 4.412 32.674 2491 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.70 % Allowed : 20.85 % Favored : 75.46 % 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: -1.44 (0.18), residues: 2259 helix: 0.26 (0.17), residues: 950 sheet: -2.97 (0.35), residues: 182 loop : -1.67 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1069 TYR 0.021 0.001 TYR D1008 PHE 0.014 0.001 PHE B1440 TRP 0.019 0.001 TRP D 967 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd covalent geometry : bond 0.00328 (17435) covalent geometry : angle 0.60205 (23787) hydrogen bonds : bond 0.03171 ( 576) hydrogen bonds : angle 4.47528 ( 1665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 ARG cc_start: 0.7753 (mpp80) cc_final: 0.7474 (mtm180) REVERT: A 1340 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8553 (tm-30) REVERT: B 1223 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 1306 GLU cc_start: 0.8481 (tp30) cc_final: 0.8027 (tp30) REVERT: B 1317 LYS cc_start: 0.8877 (ttmt) cc_final: 0.8659 (mtpp) REVERT: C 1038 MET cc_start: 0.7676 (mtt) cc_final: 0.7354 (mtt) REVERT: C 1426 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9047 (pt) REVERT: D 1484 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7060 (pp20) outliers start: 63 outliers final: 41 residues processed: 200 average time/residue: 0.1255 time to fit residues: 38.7471 Evaluate side-chains 184 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1353 SER Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 931 THR Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1298 THR Chi-restraints excluded: chain C residue 1339 PHE Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain C residue 1463 ILE Chi-restraints excluded: chain D residue 897 VAL Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1020 THR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1146 LEU Chi-restraints excluded: chain D residue 1188 ASP Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1237 ASP Chi-restraints excluded: chain D residue 1238 THR Chi-restraints excluded: chain D residue 1245 VAL Chi-restraints excluded: chain D residue 1298 THR Chi-restraints excluded: chain D residue 1409 HIS Chi-restraints excluded: chain D residue 1430 LEU Chi-restraints excluded: chain D residue 1459 SER Chi-restraints excluded: chain D residue 1484 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 143 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 122 optimal weight: 0.0170 chunk 212 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 182 optimal weight: 20.0000 chunk 225 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.123147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093117 restraints weight = 32587.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093085 restraints weight = 26522.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.093444 restraints weight = 31152.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094872 restraints weight = 19344.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095214 restraints weight = 15905.246| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17435 Z= 0.112 Angle : 0.583 14.419 23787 Z= 0.285 Chirality : 0.040 0.168 2711 Planarity : 0.004 0.040 3143 Dihedral : 4.233 34.339 2491 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.52 % Allowed : 21.61 % Favored : 74.87 % 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: -1.26 (0.18), residues: 2259 helix: 0.41 (0.17), residues: 955 sheet: -2.98 (0.35), residues: 182 loop : -1.57 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1347 TYR 0.019 0.001 TYR D1008 PHE 0.015 0.001 PHE B1440 TRP 0.018 0.001 TRP B1226 HIS 0.003 0.001 HIS C1096 Details of bonding type rmsd covalent geometry : bond 0.00261 (17435) covalent geometry : angle 0.58296 (23787) hydrogen bonds : bond 0.02897 ( 576) hydrogen bonds : angle 4.26917 ( 1665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 ARG cc_start: 0.7720 (mpp80) cc_final: 0.7454 (mtm180) REVERT: A 1136 ASP cc_start: 0.8441 (t70) cc_final: 0.7872 (p0) REVERT: A 1340 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 1223 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 1306 GLU cc_start: 0.8425 (tp30) cc_final: 0.7953 (tp30) REVERT: B 1317 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8629 (mtpp) REVERT: C 1038 MET cc_start: 0.7652 (mtt) cc_final: 0.7362 (mtt) REVERT: C 1426 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9036 (pt) REVERT: D 1469 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7727 (tp30) REVERT: D 1484 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6922 (pp20) outliers start: 60 outliers final: 40 residues processed: 203 average time/residue: 0.1261 time to fit residues: 39.3906 Evaluate side-chains 182 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1165 TRP Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1353 SER Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 931 THR Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1298 THR Chi-restraints excluded: chain C residue 1339 PHE Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain C residue 1463 ILE Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1020 THR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1237 ASP Chi-restraints excluded: chain D residue 1245 VAL Chi-restraints excluded: chain D residue 1298 THR Chi-restraints excluded: chain D residue 1409 HIS Chi-restraints excluded: chain D residue 1454 LEU Chi-restraints excluded: chain D residue 1459 SER Chi-restraints excluded: chain D residue 1484 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 153 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 191 optimal weight: 0.0770 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN D1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095094 restraints weight = 32779.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095111 restraints weight = 26722.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095657 restraints weight = 29553.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096794 restraints weight = 19381.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097180 restraints weight = 16617.952| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17435 Z= 0.100 Angle : 0.585 14.084 23787 Z= 0.285 Chirality : 0.040 0.188 2711 Planarity : 0.004 0.042 3143 Dihedral : 4.020 35.233 2491 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.88 % Allowed : 22.14 % Favored : 74.99 % 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: -1.08 (0.18), residues: 2259 helix: 0.55 (0.18), residues: 959 sheet: -2.79 (0.37), residues: 172 loop : -1.50 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1413 TYR 0.019 0.001 TYR D1008 PHE 0.013 0.001 PHE B1440 TRP 0.017 0.001 TRP B1226 HIS 0.005 0.001 HIS A1409 Details of bonding type rmsd covalent geometry : bond 0.00226 (17435) covalent geometry : angle 0.58482 (23787) hydrogen bonds : bond 0.02618 ( 576) hydrogen bonds : angle 4.12769 ( 1665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1136 ASP cc_start: 0.8377 (t70) cc_final: 0.7885 (p0) REVERT: A 1340 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 918 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8158 (tp30) REVERT: B 1223 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7705 (tm-30) REVERT: B 1306 GLU cc_start: 0.8379 (tp30) cc_final: 0.7901 (tp30) REVERT: B 1317 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8630 (mtpp) REVERT: C 1012 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7650 (ttm-80) REVERT: C 1426 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8963 (pt) REVERT: D 1469 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7583 (tp30) REVERT: D 1484 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7056 (pp20) outliers start: 49 outliers final: 34 residues processed: 209 average time/residue: 0.1336 time to fit residues: 42.0383 Evaluate side-chains 186 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1339 PHE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 931 THR Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1298 THR Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain C residue 1463 ILE Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1020 THR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1146 LEU Chi-restraints excluded: chain D residue 1188 ASP Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1245 VAL Chi-restraints excluded: chain D residue 1298 THR Chi-restraints excluded: chain D residue 1454 LEU Chi-restraints excluded: chain D residue 1484 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093788 restraints weight = 32823.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.093818 restraints weight = 27105.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094063 restraints weight = 33002.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095747 restraints weight = 19758.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096271 restraints weight = 15582.705| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17435 Z= 0.126 Angle : 0.614 15.437 23787 Z= 0.295 Chirality : 0.041 0.261 2711 Planarity : 0.004 0.046 3143 Dihedral : 4.087 34.593 2491 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.70 % Allowed : 22.72 % Favored : 74.57 % 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: -1.08 (0.18), residues: 2259 helix: 0.55 (0.18), residues: 959 sheet: -2.87 (0.36), residues: 181 loop : -1.47 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1069 TYR 0.017 0.001 TYR D1008 PHE 0.018 0.001 PHE B1440 TRP 0.018 0.001 TRP B1226 HIS 0.003 0.001 HIS D1302 Details of bonding type rmsd covalent geometry : bond 0.00301 (17435) covalent geometry : angle 0.61392 (23787) hydrogen bonds : bond 0.02794 ( 576) hydrogen bonds : angle 4.25700 ( 1665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 915 ARG cc_start: 0.7722 (mpp80) cc_final: 0.7477 (mtm180) REVERT: A 972 GLU cc_start: 0.8006 (pt0) cc_final: 0.7668 (mp0) REVERT: A 1136 ASP cc_start: 0.8442 (t70) cc_final: 0.7871 (p0) REVERT: A 1340 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8486 (tm-30) REVERT: B 918 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8181 (tp30) REVERT: B 1223 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 1306 GLU cc_start: 0.8421 (tp30) cc_final: 0.7931 (tp30) REVERT: B 1317 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8655 (mtpp) REVERT: C 1426 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9019 (pt) REVERT: D 1484 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7103 (pp20) outliers start: 46 outliers final: 37 residues processed: 191 average time/residue: 0.1254 time to fit residues: 36.8254 Evaluate side-chains 183 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1151 VAL Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 931 THR Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1298 THR Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain C residue 1463 ILE Chi-restraints excluded: chain D residue 904 GLN Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1020 THR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1146 LEU Chi-restraints excluded: chain D residue 1188 ASP Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1237 ASP Chi-restraints excluded: chain D residue 1238 THR Chi-restraints excluded: chain D residue 1298 THR Chi-restraints excluded: chain D residue 1484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 146 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 160 optimal weight: 0.0470 chunk 159 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.095711 restraints weight = 32385.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096777 restraints weight = 26570.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097602 restraints weight = 20293.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098200 restraints weight = 16097.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099149 restraints weight = 14911.364| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17435 Z= 0.101 Angle : 0.605 13.934 23787 Z= 0.290 Chirality : 0.041 0.276 2711 Planarity : 0.004 0.043 3143 Dihedral : 3.983 35.420 2491 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.58 % Allowed : 22.72 % Favored : 74.69 % 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: -1.03 (0.18), residues: 2259 helix: 0.60 (0.18), residues: 959 sheet: -2.81 (0.36), residues: 181 loop : -1.44 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1012 TYR 0.018 0.001 TYR D1008 PHE 0.020 0.001 PHE B1440 TRP 0.017 0.001 TRP B1226 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd covalent geometry : bond 0.00228 (17435) covalent geometry : angle 0.60475 (23787) hydrogen bonds : bond 0.02569 ( 576) hydrogen bonds : angle 4.15994 ( 1665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 972 GLU cc_start: 0.7972 (pt0) cc_final: 0.7710 (mp0) REVERT: A 1136 ASP cc_start: 0.8413 (t70) cc_final: 0.7882 (p0) REVERT: A 1340 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8501 (tm-30) REVERT: B 918 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8123 (tp30) REVERT: B 1223 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7698 (tm-30) REVERT: B 1306 GLU cc_start: 0.8433 (tp30) cc_final: 0.7952 (tp30) REVERT: B 1317 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8621 (mtpp) REVERT: C 1426 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8965 (pt) REVERT: D 1484 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7136 (pp20) outliers start: 44 outliers final: 37 residues processed: 189 average time/residue: 0.1300 time to fit residues: 37.2306 Evaluate side-chains 189 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1084 THR Chi-restraints excluded: chain A residue 1106 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1161 ASN Chi-restraints excluded: chain A residue 1165 TRP Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1351 VAL Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 931 THR Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1120 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain C residue 1298 THR Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1426 LEU Chi-restraints excluded: chain C residue 1463 ILE Chi-restraints excluded: chain D residue 904 GLN Chi-restraints excluded: chain D residue 967 TRP Chi-restraints excluded: chain D residue 1020 THR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1120 ILE Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1146 LEU Chi-restraints excluded: chain D residue 1188 ASP Chi-restraints excluded: chain D residue 1194 LEU Chi-restraints excluded: chain D residue 1238 THR Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1298 THR Chi-restraints excluded: chain D residue 1454 LEU Chi-restraints excluded: chain D residue 1484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 144 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 223 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.125547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095493 restraints weight = 32547.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094800 restraints weight = 26552.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095640 restraints weight = 27171.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097198 restraints weight = 18803.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097410 restraints weight = 16046.778| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17435 Z= 0.102 Angle : 0.603 13.985 23787 Z= 0.290 Chirality : 0.041 0.270 2711 Planarity : 0.004 0.050 3143 Dihedral : 3.955 35.550 2491 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.47 % Allowed : 23.02 % Favored : 74.52 % 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: -0.98 (0.18), residues: 2259 helix: 0.64 (0.18), residues: 957 sheet: -2.73 (0.36), residues: 181 loop : -1.43 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1191 TYR 0.016 0.001 TYR A1349 PHE 0.019 0.001 PHE B1440 TRP 0.017 0.001 TRP B1226 HIS 0.003 0.001 HIS D1302 Details of bonding type rmsd covalent geometry : bond 0.00233 (17435) covalent geometry : angle 0.60267 (23787) hydrogen bonds : bond 0.02557 ( 576) hydrogen bonds : angle 4.15849 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2385.79 seconds wall clock time: 42 minutes 1.42 seconds (2521.42 seconds total)