Starting phenix.real_space_refine on Tue Nov 18 00:06:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uak_8516/11_2025/5uak_8516.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uak_8516/11_2025/5uak_8516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5uak_8516/11_2025/5uak_8516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uak_8516/11_2025/5uak_8516.map" model { file = "/net/cci-nas-00/data/ceres_data/5uak_8516/11_2025/5uak_8516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uak_8516/11_2025/5uak_8516.cif" } resolution = 3.87 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= 0.008 sd= 0.199 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 47 5.16 5 C 6029 2.51 5 N 1530 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9232 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 9137 Classifications: {'peptide': 1139} Link IDs: {'PTRANS': 28, 'TRANS': 1110} Chain breaks: 4 Chain: "R" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 2.06, per 1000 atoms: 0.22 Number of scatterers: 9232 At special positions: 0 Unit cell: (109.478, 120.099, 117.648, 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 47 16.00 O 1626 8.00 N 1530 7.00 C 6029 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: 0.78 Conformation dependent library (CDL) restraints added in 312.0 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 72.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.888A pdb=" N ILE A 23 " --> pdb=" O TRP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.545A pdb=" N GLU A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.526A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 4.467A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 88 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.546A pdb=" N GLY A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 166 removed outlier: 4.033A pdb=" N ALA A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.548A pdb=" N PHE A 143 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 151 " --> pdb=" O HIS A 147 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.923A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.690A pdb=" N ALA A 198 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS A 199 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.743A pdb=" N LEU A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 268 removed outlier: 3.892A pdb=" N VAL A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.521A pdb=" N VAL A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 323 removed outlier: 3.822A pdb=" N LYS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.710A pdb=" N ILE A 328 " --> pdb=" O TYR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 352 removed outlier: 4.152A pdb=" N PHE A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 352 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 removed outlier: 3.943A pdb=" N TRP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 removed outlier: 4.121A pdb=" N LEU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.778A pdb=" N ASN A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.725A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 removed outlier: 4.001A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 595 removed outlier: 3.695A pdb=" N CYS A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.845A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 845 through 854 removed outlier: 4.080A pdb=" N TYR A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 850 " --> pdb=" O TRP A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 883 removed outlier: 3.579A pdb=" N ILE A 869 " --> pdb=" O TRP A 865 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 878 " --> pdb=" O VAL A 874 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A 883 " --> pdb=" O VAL A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 922 removed outlier: 4.101A pdb=" N VAL A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 935 through 957 removed outlier: 4.100A pdb=" N HIS A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.669A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 986 removed outlier: 3.517A pdb=" N ILE A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1012 removed outlier: 3.661A pdb=" N THR A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1047 removed outlier: 3.522A pdb=" N ALA A1018 " --> pdb=" O TYR A1014 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.820A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.852A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 3.776A pdb=" N LYS A1080 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A1092 " --> pdb=" O ASN A1088 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A1094 " --> pdb=" O PHE A1090 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A1110 " --> pdb=" O ILE A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.622A pdb=" N GLY A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A1132 " --> pdb=" O ARG A1128 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A1138 " --> pdb=" O THR A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1169 removed outlier: 3.828A pdb=" N ILE A1151 " --> pdb=" O VAL A1147 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A1161 " --> pdb=" O MET A1157 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG A1162 " --> pdb=" O ARG A1158 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A1163 " --> pdb=" O SER A1159 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.907A pdb=" N LEU A1253 " --> pdb=" O GLY A1249 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1283 removed outlier: 3.920A pdb=" N ARG A1283 " --> pdb=" O LEU A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1322 Processing helix chain 'A' and resid 1324 through 1330 Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 4.379A pdb=" N GLY A1342 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 3.571A pdb=" N SER A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1376 removed outlier: 4.566A pdb=" N HIS A1375 " --> pdb=" O GLU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1392 removed outlier: 3.808A pdb=" N THR A1387 " --> pdb=" O ILE A1383 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN A1390 " --> pdb=" O ARG A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 Processing helix chain 'A' and resid 1426 through 1436 removed outlier: 4.377A pdb=" N ASN A1432 " --> pdb=" O GLN A1428 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 18 removed outlier: 4.389A pdb=" N UNK R 9 " --> pdb=" O UNK R 5 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N UNK R 10 " --> pdb=" O UNK R 6 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N UNK R 15 " --> pdb=" O UNK R 11 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N UNK R 16 " --> pdb=" O UNK R 12 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N UNK R 17 " --> pdb=" O UNK R 13 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N UNK R 18 " --> pdb=" O UNK R 14 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 393 through 398 removed outlier: 4.155A pdb=" N VAL A 397 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 479 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.637A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASP A 572 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS A 491 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1225 through 1234 removed outlier: 7.194A pdb=" N ILE A1226 " --> pdb=" O LYS A1218 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LYS A1218 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A1228 " --> pdb=" O THR A1216 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR A1216 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL A1212 " --> pdb=" O GLN A1268 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN A1268 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP A1214 " --> pdb=" O GLU A1266 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A1266 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.764A pdb=" N GLY A1287 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP A1370 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A1289 " --> pdb=" O ASP A1370 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A1239 " --> pdb=" O GLN A1412 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU A1414 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY A1241 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE A1416 " --> pdb=" O GLY A1241 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A1243 " --> pdb=" O ILE A1416 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1491 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: 1.55 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2855 1.34 - 1.46: 1135 1.46 - 1.58: 5354 1.58 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 9423 Sorted by residual: bond pdb=" N GLY A1249 " pdb=" CA GLY A1249 " ideal model delta sigma weight residual 1.449 1.507 -0.057 1.45e-02 4.76e+03 1.57e+01 bond pdb=" CA VAL A1020 " pdb=" CB VAL A1020 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.23e+01 bond pdb=" C GLN A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.23e+00 bond pdb=" CA VAL A1020 " pdb=" C VAL A1020 " ideal model delta sigma weight residual 1.523 1.546 -0.023 9.20e-03 1.18e+04 6.08e+00 bond pdb=" CA PRO A 99 " pdb=" C PRO A 99 " ideal model delta sigma weight residual 1.520 1.544 -0.023 9.50e-03 1.11e+04 6.08e+00 ... (remaining 9418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 11076 1.59 - 3.18: 1523 3.18 - 4.78: 118 4.78 - 6.37: 21 6.37 - 7.96: 1 Bond angle restraints: 12739 Sorted by residual: angle pdb=" N VAL A 580 " pdb=" CA VAL A 580 " pdb=" C VAL A 580 " ideal model delta sigma weight residual 110.62 116.10 -5.48 1.14e+00 7.69e-01 2.31e+01 angle pdb=" N ALA A 399 " pdb=" CA ALA A 399 " pdb=" C ALA A 399 " ideal model delta sigma weight residual 108.74 114.99 -6.25 1.38e+00 5.25e-01 2.05e+01 angle pdb=" N LEU A 188 " pdb=" CA LEU A 188 " pdb=" C LEU A 188 " ideal model delta sigma weight residual 111.07 115.62 -4.55 1.07e+00 8.73e-01 1.81e+01 angle pdb=" CA VAL A1020 " pdb=" C VAL A1020 " pdb=" N PRO A1021 " ideal model delta sigma weight residual 120.83 118.29 2.54 6.10e-01 2.69e+00 1.74e+01 angle pdb=" N PHE A 931 " pdb=" CA PHE A 931 " pdb=" C PHE A 931 " ideal model delta sigma weight residual 111.33 116.11 -4.78 1.21e+00 6.83e-01 1.56e+01 ... (remaining 12734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.65: 4829 12.65 - 25.31: 538 25.31 - 37.96: 152 37.96 - 50.62: 72 50.62 - 63.27: 20 Dihedral angle restraints: 5611 sinusoidal: 2240 harmonic: 3371 Sorted by residual: dihedral pdb=" CA ILE A 70 " pdb=" CB ILE A 70 " pdb=" CG1 ILE A 70 " pdb=" CD1 ILE A 70 " ideal model delta sinusoidal sigma weight residual 60.00 113.50 -53.50 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA LEU A 167 " pdb=" C LEU A 167 " pdb=" N SER A 168 " pdb=" CA SER A 168 " ideal model delta harmonic sigma weight residual 180.00 164.83 15.17 0 5.00e+00 4.00e-02 9.20e+00 dihedral pdb=" CA ASP A 36 " pdb=" CB ASP A 36 " pdb=" CG ASP A 36 " pdb=" OD1 ASP A 36 " ideal model delta sinusoidal sigma weight residual -30.00 -81.74 51.74 1 2.00e+01 2.50e-03 9.14e+00 ... (remaining 5608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 988 0.051 - 0.102: 352 0.102 - 0.153: 111 0.153 - 0.204: 23 0.204 - 0.254: 7 Chirality restraints: 1481 Sorted by residual: chirality pdb=" CA ILE A 40 " pdb=" N ILE A 40 " pdb=" C ILE A 40 " pdb=" CB ILE A 40 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA VAL A1212 " pdb=" N VAL A1212 " pdb=" C VAL A1212 " pdb=" CB VAL A1212 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA SER A1049 " pdb=" N SER A1049 " pdb=" C SER A1049 " pdb=" CB SER A1049 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1478 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 21 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 22 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 323 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO A 324 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 139 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 140 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " -0.024 5.00e-02 4.00e+02 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 3567 2.96 - 3.44: 9573 3.44 - 3.93: 14149 3.93 - 4.41: 14795 4.41 - 4.90: 25835 Nonbonded interactions: 67919 Sorted by model distance: nonbonded pdb=" O GLY A 91 " pdb=" OG1 THR A 94 " model vdw 2.474 3.040 nonbonded pdb=" OG1 THR A 845 " pdb=" OG1 THR A 848 " model vdw 2.506 3.040 nonbonded pdb=" O THR A 940 " pdb=" OG1 THR A 943 " model vdw 2.517 3.040 nonbonded pdb=" O ILE A1117 " pdb=" OG1 THR A1121 " model vdw 2.517 3.040 nonbonded pdb=" O THR A 389 " pdb=" OG1 THR A 390 " model vdw 2.531 3.040 ... (remaining 67914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.890 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 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 0.057 9423 Z= 0.542 Angle : 1.078 7.960 12739 Z= 0.751 Chirality : 0.059 0.254 1481 Planarity : 0.004 0.056 1565 Dihedral : 13.276 63.270 3429 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: -3.02 (0.20), residues: 1129 helix: -1.64 (0.16), residues: 684 sheet: -1.25 (0.56), residues: 71 loop : -2.56 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1066 TYR 0.010 0.001 TYR A 122 PHE 0.018 0.001 PHE A 587 TRP 0.010 0.001 TRP A 356 HIS 0.005 0.001 HIS A1350 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 9423) covalent geometry : angle 1.07812 (12739) hydrogen bonds : bond 0.24178 ( 507) hydrogen bonds : angle 8.52828 ( 1491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7332 (mtt-85) cc_final: 0.6644 (tmm-80) REVERT: A 32 LEU cc_start: 0.7721 (mt) cc_final: 0.7516 (mp) REVERT: A 39 GLN cc_start: 0.7774 (mt0) cc_final: 0.7216 (pt0) REVERT: A 66 ASN cc_start: 0.8861 (m110) cc_final: 0.8567 (m110) REVERT: A 68 LYS cc_start: 0.6865 (mttt) cc_final: 0.6609 (mmtt) REVERT: A 80 ARG cc_start: 0.6132 (mmt-90) cc_final: 0.5800 (ttt180) REVERT: A 89 TYR cc_start: 0.8047 (t80) cc_final: 0.7662 (t80) REVERT: A 104 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7348 (mmm160) REVERT: A 152 MET cc_start: 0.8321 (mmp) cc_final: 0.8079 (tpp) REVERT: A 172 LEU cc_start: 0.7425 (tt) cc_final: 0.7205 (mt) REVERT: A 179 GLN cc_start: 0.8866 (tt0) cc_final: 0.8636 (mt0) REVERT: A 242 ARG cc_start: 0.7178 (tpt170) cc_final: 0.6567 (ttp-170) REVERT: A 294 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7620 (tptt) REVERT: A 378 GLN cc_start: 0.7979 (mp-120) cc_final: 0.7766 (mm-40) REVERT: A 476 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7669 (mp0) REVERT: A 493 GLN cc_start: 0.7125 (tt0) cc_final: 0.6827 (mt0) REVERT: A 512 TYR cc_start: 0.6807 (t80) cc_final: 0.6530 (t80) REVERT: A 515 TYR cc_start: 0.8554 (t80) cc_final: 0.8266 (t80) REVERT: A 516 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7064 (ttt90) REVERT: A 518 ARG cc_start: 0.8364 (ttt180) cc_final: 0.7763 (tpp-160) REVERT: A 645 MET cc_start: 0.3561 (mtp) cc_final: 0.2813 (mmm) REVERT: A 1028 MET cc_start: 0.7397 (ttp) cc_final: 0.7041 (tmm) REVERT: A 1032 TYR cc_start: 0.8432 (t80) cc_final: 0.8149 (t80) REVERT: A 1118 SER cc_start: 0.8779 (p) cc_final: 0.8164 (p) REVERT: A 1140 MET cc_start: 0.7674 (ptp) cc_final: 0.7474 (tmm) REVERT: A 1145 TRP cc_start: 0.7753 (m-10) cc_final: 0.7464 (m-10) REVERT: A 1157 MET cc_start: 0.7682 (ttm) cc_final: 0.7441 (tpp) REVERT: A 1160 VAL cc_start: 0.7156 (t) cc_final: 0.6814 (p) REVERT: A 1209 GLN cc_start: 0.8883 (tt0) cc_final: 0.8660 (tp40) REVERT: A 1269 ILE cc_start: 0.8966 (mt) cc_final: 0.8740 (pt) REVERT: A 1330 GLN cc_start: 0.8402 (mm110) cc_final: 0.7984 (pt0) REVERT: A 1366 ILE cc_start: 0.8008 (mt) cc_final: 0.7678 (mt) REVERT: A 1418 GLU cc_start: 0.8444 (tp30) cc_final: 0.7407 (pm20) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1088 time to fit residues: 56.2995 Evaluate side-chains 245 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 207 GLN A 396 ASN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 HIS A1303 ASN A1411 GLN A1423 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.145736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.126919 restraints weight = 22414.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130099 restraints weight = 12074.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132203 restraints weight = 7621.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133765 restraints weight = 5433.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.134795 restraints weight = 4146.344| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9423 Z= 0.194 Angle : 0.687 7.257 12739 Z= 0.361 Chirality : 0.042 0.152 1481 Planarity : 0.005 0.050 1565 Dihedral : 4.825 19.681 1245 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.29 % Allowed : 15.97 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1129 helix: 0.16 (0.18), residues: 732 sheet: -0.69 (0.56), residues: 72 loop : -1.90 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1386 TYR 0.020 0.002 TYR A 325 PHE 0.029 0.002 PHE A 490 TRP 0.023 0.002 TRP A 277 HIS 0.006 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9423) covalent geometry : angle 0.68741 (12739) hydrogen bonds : bond 0.05379 ( 507) hydrogen bonds : angle 4.97886 ( 1491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TRP cc_start: 0.8170 (p90) cc_final: 0.7903 (p90) REVERT: A 50 SER cc_start: 0.8688 (m) cc_final: 0.7736 (t) REVERT: A 89 TYR cc_start: 0.8625 (t80) cc_final: 0.8237 (t80) REVERT: A 136 LEU cc_start: 0.9354 (mt) cc_final: 0.8978 (mp) REVERT: A 152 MET cc_start: 0.8636 (mmp) cc_final: 0.8277 (mmm) REVERT: A 195 LEU cc_start: 0.8832 (tp) cc_final: 0.8435 (tt) REVERT: A 242 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7324 (ttp-170) REVERT: A 294 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8227 (tptt) REVERT: A 498 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7430 (ppp) REVERT: A 502 ILE cc_start: 0.8273 (pp) cc_final: 0.7847 (mt) REVERT: A 512 TYR cc_start: 0.7270 (t80) cc_final: 0.6813 (t80) REVERT: A 518 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7683 (tpp-160) REVERT: A 595 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.7007 (tpt) REVERT: A 645 MET cc_start: 0.4361 (mtp) cc_final: 0.2972 (mmm) REVERT: A 1038 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8437 (mm-40) REVERT: A 1413 PHE cc_start: 0.7848 (m-80) cc_final: 0.7623 (m-80) outliers start: 43 outliers final: 18 residues processed: 263 average time/residue: 0.0940 time to fit residues: 34.2652 Evaluate side-chains 217 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1324 LEU Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1407 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.0040 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128084 restraints weight = 22605.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131199 restraints weight = 12109.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133441 restraints weight = 7795.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134805 restraints weight = 5507.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135984 restraints weight = 4312.958| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9423 Z= 0.127 Angle : 0.590 7.182 12739 Z= 0.305 Chirality : 0.039 0.147 1481 Planarity : 0.004 0.051 1565 Dihedral : 4.463 17.821 1245 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.99 % Allowed : 19.26 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1129 helix: 0.75 (0.19), residues: 722 sheet: -0.40 (0.52), residues: 91 loop : -1.62 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 975 TYR 0.019 0.001 TYR A 627 PHE 0.026 0.001 PHE A 446 TRP 0.010 0.001 TRP A1274 HIS 0.004 0.001 HIS A 856 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9423) covalent geometry : angle 0.59025 (12739) hydrogen bonds : bond 0.04424 ( 507) hydrogen bonds : angle 4.57067 ( 1491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8790 (m) cc_final: 0.7996 (t) REVERT: A 52 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8728 (mmtm) REVERT: A 89 TYR cc_start: 0.8572 (t80) cc_final: 0.8179 (t80) REVERT: A 152 MET cc_start: 0.8549 (mmp) cc_final: 0.7963 (tpp) REVERT: A 195 LEU cc_start: 0.8800 (tp) cc_final: 0.8448 (tt) REVERT: A 242 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7297 (ttp-170) REVERT: A 294 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8188 (tptt) REVERT: A 446 PHE cc_start: 0.7139 (p90) cc_final: 0.6706 (p90) REVERT: A 498 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7656 (ppp) REVERT: A 502 ILE cc_start: 0.8228 (pp) cc_final: 0.7961 (mt) REVERT: A 512 TYR cc_start: 0.7186 (t80) cc_final: 0.6665 (t80) REVERT: A 518 ARG cc_start: 0.8038 (ttt180) cc_final: 0.7614 (tpp-160) REVERT: A 568 LEU cc_start: 0.8254 (tt) cc_final: 0.7955 (mm) REVERT: A 595 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6170 (tpt) REVERT: A 645 MET cc_start: 0.4462 (mtp) cc_final: 0.3062 (mmm) REVERT: A 974 ASN cc_start: 0.8783 (t0) cc_final: 0.8519 (t0) REVERT: A 1038 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8339 (mm-40) REVERT: A 1106 ILE cc_start: 0.8946 (mt) cc_final: 0.8716 (mt) REVERT: A 1140 MET cc_start: 0.8117 (tmm) cc_final: 0.7441 (tmm) REVERT: A 1413 PHE cc_start: 0.7825 (m-80) cc_final: 0.7624 (m-80) REVERT: A 1418 GLU cc_start: 0.7213 (tp30) cc_final: 0.6870 (tp30) outliers start: 30 outliers final: 15 residues processed: 245 average time/residue: 0.1003 time to fit residues: 34.0379 Evaluate side-chains 219 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1397 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.144137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125250 restraints weight = 22961.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.128404 restraints weight = 12340.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.130576 restraints weight = 7876.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131982 restraints weight = 5600.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133125 restraints weight = 4367.787| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9423 Z= 0.138 Angle : 0.590 6.619 12739 Z= 0.303 Chirality : 0.039 0.166 1481 Planarity : 0.004 0.048 1565 Dihedral : 4.485 19.575 1245 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.69 % Allowed : 20.36 % Favored : 75.95 % 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: 0.25 (0.25), residues: 1129 helix: 0.95 (0.19), residues: 717 sheet: -0.02 (0.56), residues: 91 loop : -1.47 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 975 TYR 0.015 0.001 TYR A 304 PHE 0.034 0.002 PHE A 626 TRP 0.012 0.001 TRP A 19 HIS 0.004 0.001 HIS A 856 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9423) covalent geometry : angle 0.59037 (12739) hydrogen bonds : bond 0.04119 ( 507) hydrogen bonds : angle 4.40456 ( 1491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8845 (m) cc_final: 0.8113 (t) REVERT: A 89 TYR cc_start: 0.8613 (t80) cc_final: 0.8202 (t80) REVERT: A 105 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9073 (tt) REVERT: A 152 MET cc_start: 0.8560 (mmp) cc_final: 0.8277 (mmm) REVERT: A 195 LEU cc_start: 0.8834 (tp) cc_final: 0.8559 (tt) REVERT: A 294 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8310 (tptt) REVERT: A 352 ARG cc_start: 0.6959 (tpt170) cc_final: 0.6629 (tpp-160) REVERT: A 498 MET cc_start: 0.8069 (ppp) cc_final: 0.7785 (ppp) REVERT: A 502 ILE cc_start: 0.8309 (pp) cc_final: 0.8095 (mt) REVERT: A 518 ARG cc_start: 0.7989 (ttt180) cc_final: 0.7624 (tpp-160) REVERT: A 541 LEU cc_start: 0.7634 (mm) cc_final: 0.7419 (tp) REVERT: A 595 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6525 (tpt) REVERT: A 645 MET cc_start: 0.4462 (mtp) cc_final: 0.3092 (mmm) REVERT: A 914 TYR cc_start: 0.5538 (m-80) cc_final: 0.4258 (m-80) REVERT: A 974 ASN cc_start: 0.8724 (t0) cc_final: 0.8473 (t0) REVERT: A 980 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8566 (tt) REVERT: A 996 GLN cc_start: 0.8835 (tp40) cc_final: 0.8566 (tp40) REVERT: A 1038 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8130 (mm110) REVERT: A 1102 ARG cc_start: 0.5722 (tpt170) cc_final: 0.5480 (tpt170) REVERT: A 1106 ILE cc_start: 0.8929 (mt) cc_final: 0.8713 (mt) REVERT: A 1140 MET cc_start: 0.8158 (tmm) cc_final: 0.7473 (tmm) REVERT: A 1418 GLU cc_start: 0.7105 (tp30) cc_final: 0.6895 (tp30) outliers start: 37 outliers final: 22 residues processed: 238 average time/residue: 0.0862 time to fit residues: 29.2878 Evaluate side-chains 222 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1407 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.144236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125488 restraints weight = 23042.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.128704 restraints weight = 12353.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130863 restraints weight = 7838.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132050 restraints weight = 5563.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133242 restraints weight = 4409.447| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9423 Z= 0.128 Angle : 0.587 8.289 12739 Z= 0.299 Chirality : 0.039 0.148 1481 Planarity : 0.003 0.045 1565 Dihedral : 4.434 17.196 1245 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.69 % Allowed : 21.16 % Favored : 75.15 % 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: 0.44 (0.25), residues: 1129 helix: 1.09 (0.19), residues: 719 sheet: 0.00 (0.55), residues: 91 loop : -1.39 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.013 0.001 TYR A 304 PHE 0.035 0.001 PHE A1033 TRP 0.012 0.001 TRP A1089 HIS 0.003 0.001 HIS A1350 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9423) covalent geometry : angle 0.58724 (12739) hydrogen bonds : bond 0.03941 ( 507) hydrogen bonds : angle 4.28053 ( 1491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8847 (m) cc_final: 0.8152 (t) REVERT: A 89 TYR cc_start: 0.8588 (t80) cc_final: 0.8163 (t80) REVERT: A 152 MET cc_start: 0.8553 (mmp) cc_final: 0.8282 (mmm) REVERT: A 172 LEU cc_start: 0.7915 (tt) cc_final: 0.7691 (mt) REVERT: A 237 GLN cc_start: 0.8348 (tt0) cc_final: 0.8079 (tt0) REVERT: A 294 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8338 (tptt) REVERT: A 337 PHE cc_start: 0.8538 (m-80) cc_final: 0.8279 (t80) REVERT: A 454 LEU cc_start: 0.8759 (tp) cc_final: 0.8492 (tp) REVERT: A 518 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7582 (tpp-160) REVERT: A 595 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6269 (tpt) REVERT: A 600 ARG cc_start: 0.6939 (mtt-85) cc_final: 0.6146 (mtt-85) REVERT: A 645 MET cc_start: 0.4554 (mtp) cc_final: 0.3204 (mmm) REVERT: A 877 SER cc_start: 0.9303 (m) cc_final: 0.9062 (p) REVERT: A 914 TYR cc_start: 0.5564 (m-80) cc_final: 0.4247 (m-80) REVERT: A 974 ASN cc_start: 0.8707 (t0) cc_final: 0.8426 (t0) REVERT: A 980 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 996 GLN cc_start: 0.8824 (tp40) cc_final: 0.8509 (tp40) REVERT: A 1038 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8260 (mm-40) REVERT: A 1140 MET cc_start: 0.8128 (tmm) cc_final: 0.7574 (tmm) REVERT: A 1413 PHE cc_start: 0.7683 (m-80) cc_final: 0.7190 (m-80) outliers start: 37 outliers final: 24 residues processed: 237 average time/residue: 0.0877 time to fit residues: 29.2013 Evaluate side-chains 227 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1407 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126016 restraints weight = 23298.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129249 restraints weight = 12631.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.131275 restraints weight = 8041.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.132882 restraints weight = 5849.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.133695 restraints weight = 4454.046| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9423 Z= 0.123 Angle : 0.590 9.795 12739 Z= 0.301 Chirality : 0.038 0.148 1481 Planarity : 0.004 0.042 1565 Dihedral : 4.364 16.468 1245 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.99 % Allowed : 22.06 % Favored : 73.95 % 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: 0.56 (0.25), residues: 1129 helix: 1.16 (0.19), residues: 719 sheet: 0.09 (0.55), residues: 91 loop : -1.28 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 975 TYR 0.016 0.001 TYR A 301 PHE 0.025 0.001 PHE A1033 TRP 0.010 0.001 TRP A 19 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9423) covalent geometry : angle 0.59001 (12739) hydrogen bonds : bond 0.03785 ( 507) hydrogen bonds : angle 4.26598 ( 1491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.8808 (m) cc_final: 0.8257 (t) REVERT: A 89 TYR cc_start: 0.8552 (t80) cc_final: 0.8112 (t80) REVERT: A 152 MET cc_start: 0.8561 (mmp) cc_final: 0.8289 (mmm) REVERT: A 237 GLN cc_start: 0.8208 (tt0) cc_final: 0.7967 (tt0) REVERT: A 294 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8353 (tptt) REVERT: A 337 PHE cc_start: 0.8548 (m-80) cc_final: 0.8312 (t80) REVERT: A 454 LEU cc_start: 0.8743 (tp) cc_final: 0.8509 (tp) REVERT: A 492 SER cc_start: 0.7973 (t) cc_final: 0.7616 (p) REVERT: A 498 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7539 (ppp) REVERT: A 518 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7660 (tpp-160) REVERT: A 595 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6033 (tpt) REVERT: A 645 MET cc_start: 0.4561 (mtp) cc_final: 0.3186 (mmm) REVERT: A 877 SER cc_start: 0.9330 (m) cc_final: 0.9114 (p) REVERT: A 914 TYR cc_start: 0.5613 (m-80) cc_final: 0.4249 (m-80) REVERT: A 974 ASN cc_start: 0.8714 (t0) cc_final: 0.8489 (t0) REVERT: A 980 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 996 GLN cc_start: 0.8824 (tp40) cc_final: 0.8438 (tp40) REVERT: A 1038 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8213 (mm-40) REVERT: A 1102 ARG cc_start: 0.5692 (tpt170) cc_final: 0.5402 (tpt170) REVERT: A 1105 MET cc_start: 0.8892 (mtt) cc_final: 0.8669 (mtt) REVERT: A 1140 MET cc_start: 0.8070 (tmm) cc_final: 0.7527 (tmm) REVERT: A 1413 PHE cc_start: 0.7679 (m-80) cc_final: 0.7153 (m-80) outliers start: 40 outliers final: 24 residues processed: 240 average time/residue: 0.0920 time to fit residues: 30.7878 Evaluate side-chains 225 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1407 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 109 optimal weight: 0.0170 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A1330 GLN ** 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 = 0.3961 r_free = 0.3961 target = 0.145417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.126768 restraints weight = 23165.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129948 restraints weight = 12490.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132131 restraints weight = 7923.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133611 restraints weight = 5623.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134767 restraints weight = 4351.175| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9423 Z= 0.119 Angle : 0.602 8.632 12739 Z= 0.304 Chirality : 0.039 0.146 1481 Planarity : 0.004 0.051 1565 Dihedral : 4.316 17.372 1245 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.99 % Allowed : 23.85 % Favored : 73.15 % 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: 0.59 (0.25), residues: 1129 helix: 1.17 (0.19), residues: 723 sheet: 0.16 (0.56), residues: 90 loop : -1.30 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 975 TYR 0.015 0.001 TYR A 919 PHE 0.034 0.001 PHE A1033 TRP 0.008 0.001 TRP A 19 HIS 0.011 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9423) covalent geometry : angle 0.60211 (12739) hydrogen bonds : bond 0.03646 ( 507) hydrogen bonds : angle 4.14724 ( 1491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8875 (m) cc_final: 0.8497 (t) REVERT: A 89 TYR cc_start: 0.8560 (t80) cc_final: 0.8082 (t80) REVERT: A 152 MET cc_start: 0.8543 (mmp) cc_final: 0.8288 (mmm) REVERT: A 237 GLN cc_start: 0.8139 (tt0) cc_final: 0.7874 (tt0) REVERT: A 294 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8330 (tptt) REVERT: A 454 LEU cc_start: 0.8750 (tp) cc_final: 0.8506 (tp) REVERT: A 498 MET cc_start: 0.7844 (ppp) cc_final: 0.7539 (ppp) REVERT: A 518 ARG cc_start: 0.7883 (ttt180) cc_final: 0.7602 (tpp-160) REVERT: A 595 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.5024 (tmm) REVERT: A 645 MET cc_start: 0.4508 (mtp) cc_final: 0.3195 (mmm) REVERT: A 849 TYR cc_start: 0.8981 (m-80) cc_final: 0.8696 (m-80) REVERT: A 914 TYR cc_start: 0.5591 (m-80) cc_final: 0.4226 (m-80) REVERT: A 974 ASN cc_start: 0.8722 (t0) cc_final: 0.8446 (t0) REVERT: A 980 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8523 (tt) REVERT: A 996 GLN cc_start: 0.8804 (tp40) cc_final: 0.8354 (tp40) REVERT: A 1038 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8280 (mm-40) REVERT: A 1102 ARG cc_start: 0.5593 (tpt170) cc_final: 0.5179 (tpt170) REVERT: A 1140 MET cc_start: 0.8082 (tmm) cc_final: 0.7787 (tmm) REVERT: A 1413 PHE cc_start: 0.7693 (m-80) cc_final: 0.7167 (m-80) outliers start: 30 outliers final: 20 residues processed: 234 average time/residue: 0.0917 time to fit residues: 30.0243 Evaluate side-chains 224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1407 MET Chi-restraints excluded: chain A residue 1419 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 GLN ** 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 = 0.3927 r_free = 0.3927 target = 0.142576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123755 restraints weight = 23127.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126809 restraints weight = 12578.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128979 restraints weight = 8053.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130513 restraints weight = 5752.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131489 restraints weight = 4444.861| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9423 Z= 0.141 Angle : 0.644 9.946 12739 Z= 0.324 Chirality : 0.040 0.181 1481 Planarity : 0.004 0.041 1565 Dihedral : 4.415 17.870 1245 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.29 % Allowed : 23.55 % Favored : 73.15 % 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: 0.59 (0.25), residues: 1129 helix: 1.17 (0.19), residues: 726 sheet: 0.33 (0.61), residues: 74 loop : -1.31 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 975 TYR 0.016 0.001 TYR A 301 PHE 0.058 0.002 PHE A1033 TRP 0.013 0.001 TRP A 19 HIS 0.008 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9423) covalent geometry : angle 0.64448 (12739) hydrogen bonds : bond 0.03916 ( 507) hydrogen bonds : angle 4.25749 ( 1491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8882 (m) cc_final: 0.8547 (t) REVERT: A 89 TYR cc_start: 0.8646 (t80) cc_final: 0.8138 (t80) REVERT: A 104 ARG cc_start: 0.7364 (mmm160) cc_final: 0.6789 (tpm170) REVERT: A 152 MET cc_start: 0.8579 (mmp) cc_final: 0.8296 (mmm) REVERT: A 237 GLN cc_start: 0.8175 (tt0) cc_final: 0.7898 (tt0) REVERT: A 294 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8368 (tptt) REVERT: A 454 LEU cc_start: 0.8703 (tp) cc_final: 0.8500 (tp) REVERT: A 498 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7566 (ppp) REVERT: A 518 ARG cc_start: 0.7869 (ttt180) cc_final: 0.7627 (tpp-160) REVERT: A 595 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.4835 (tmm) REVERT: A 645 MET cc_start: 0.4451 (mtp) cc_final: 0.3090 (mmm) REVERT: A 849 TYR cc_start: 0.9001 (m-80) cc_final: 0.8717 (m-80) REVERT: A 914 TYR cc_start: 0.5659 (m-80) cc_final: 0.4305 (m-80) REVERT: A 974 ASN cc_start: 0.8732 (t0) cc_final: 0.8492 (t0) REVERT: A 980 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 996 GLN cc_start: 0.8820 (tp40) cc_final: 0.8471 (tp40) REVERT: A 1038 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8413 (mm-40) REVERT: A 1102 ARG cc_start: 0.5571 (tpt170) cc_final: 0.4986 (tpt170) REVERT: A 1140 MET cc_start: 0.8055 (tmm) cc_final: 0.7703 (tmm) REVERT: A 1280 GLN cc_start: 0.8686 (tt0) cc_final: 0.8328 (tm-30) outliers start: 33 outliers final: 22 residues processed: 231 average time/residue: 0.0834 time to fit residues: 27.7545 Evaluate side-chains 226 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1407 MET Chi-restraints excluded: chain A residue 1419 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.144115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125394 restraints weight = 23173.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128430 restraints weight = 12618.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130571 restraints weight = 8123.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132159 restraints weight = 5822.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133153 restraints weight = 4456.353| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9423 Z= 0.126 Angle : 0.645 11.461 12739 Z= 0.322 Chirality : 0.040 0.184 1481 Planarity : 0.004 0.038 1565 Dihedral : 4.333 19.225 1245 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.69 % Allowed : 25.25 % Favored : 72.06 % 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: 0.56 (0.25), residues: 1129 helix: 1.19 (0.19), residues: 718 sheet: 0.20 (0.60), residues: 74 loop : -1.33 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 975 TYR 0.023 0.001 TYR A 301 PHE 0.051 0.001 PHE A1033 TRP 0.012 0.001 TRP A 19 HIS 0.006 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9423) covalent geometry : angle 0.64501 (12739) hydrogen bonds : bond 0.03789 ( 507) hydrogen bonds : angle 4.20295 ( 1491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8874 (m) cc_final: 0.8612 (t) REVERT: A 56 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8149 (mp0) REVERT: A 73 LEU cc_start: 0.8595 (tp) cc_final: 0.8384 (tp) REVERT: A 89 TYR cc_start: 0.8607 (t80) cc_final: 0.8083 (t80) REVERT: A 104 ARG cc_start: 0.7293 (mmm160) cc_final: 0.6723 (tpm170) REVERT: A 237 GLN cc_start: 0.8140 (tt0) cc_final: 0.7893 (tt0) REVERT: A 294 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8345 (tptt) REVERT: A 454 LEU cc_start: 0.8719 (tp) cc_final: 0.8501 (tp) REVERT: A 498 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7590 (ppp) REVERT: A 518 ARG cc_start: 0.7909 (ttt180) cc_final: 0.7644 (tpp-160) REVERT: A 645 MET cc_start: 0.4508 (mtp) cc_final: 0.3202 (mmm) REVERT: A 849 TYR cc_start: 0.8982 (m-80) cc_final: 0.8714 (m-80) REVERT: A 914 TYR cc_start: 0.5607 (m-80) cc_final: 0.4266 (m-80) REVERT: A 974 ASN cc_start: 0.8700 (t0) cc_final: 0.8435 (t0) REVERT: A 980 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 996 GLN cc_start: 0.8827 (tp40) cc_final: 0.8501 (tp40) REVERT: A 1038 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8392 (mm-40) REVERT: A 1102 ARG cc_start: 0.5486 (tpt170) cc_final: 0.5089 (tpt170) REVERT: A 1140 MET cc_start: 0.8006 (tmm) cc_final: 0.7740 (tmm) REVERT: A 1280 GLN cc_start: 0.8688 (tt0) cc_final: 0.8240 (tm-30) outliers start: 27 outliers final: 25 residues processed: 224 average time/residue: 0.0839 time to fit residues: 27.1048 Evaluate side-chains 224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1407 MET Chi-restraints excluded: chain A residue 1419 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 111 optimal weight: 0.0970 chunk 27 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.146321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128024 restraints weight = 23119.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131108 restraints weight = 12482.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133163 restraints weight = 7957.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.134686 restraints weight = 5827.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135719 restraints weight = 4417.957| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9423 Z= 0.124 Angle : 0.666 11.264 12739 Z= 0.330 Chirality : 0.040 0.218 1481 Planarity : 0.004 0.037 1565 Dihedral : 4.195 18.086 1245 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.79 % Allowed : 25.85 % Favored : 71.36 % 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: 0.57 (0.25), residues: 1129 helix: 1.17 (0.19), residues: 725 sheet: 0.43 (0.57), residues: 77 loop : -1.39 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 975 TYR 0.023 0.001 TYR A 301 PHE 0.044 0.001 PHE A1033 TRP 0.009 0.001 TRP A 19 HIS 0.006 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9423) covalent geometry : angle 0.66645 (12739) hydrogen bonds : bond 0.03624 ( 507) hydrogen bonds : angle 4.18404 ( 1491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8816 (m) cc_final: 0.8613 (t) REVERT: A 52 LYS cc_start: 0.9165 (mmtp) cc_final: 0.8632 (mmtp) REVERT: A 56 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8129 (mp0) REVERT: A 89 TYR cc_start: 0.8590 (t80) cc_final: 0.8054 (t80) REVERT: A 104 ARG cc_start: 0.7235 (mmm160) cc_final: 0.6677 (tpm170) REVERT: A 237 GLN cc_start: 0.8122 (tt0) cc_final: 0.7875 (tt0) REVERT: A 294 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8324 (tptt) REVERT: A 454 LEU cc_start: 0.8693 (tp) cc_final: 0.8480 (tp) REVERT: A 498 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7547 (ppp) REVERT: A 518 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7612 (tpp-160) REVERT: A 645 MET cc_start: 0.4514 (mtp) cc_final: 0.3257 (mmm) REVERT: A 849 TYR cc_start: 0.8965 (m-80) cc_final: 0.8705 (m-80) REVERT: A 914 TYR cc_start: 0.5665 (m-80) cc_final: 0.4248 (m-80) REVERT: A 974 ASN cc_start: 0.8700 (t0) cc_final: 0.8443 (t0) REVERT: A 980 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8480 (tt) REVERT: A 996 GLN cc_start: 0.8820 (tp40) cc_final: 0.8519 (tp40) REVERT: A 1102 ARG cc_start: 0.5355 (tpt170) cc_final: 0.5035 (tpt170) REVERT: A 1280 GLN cc_start: 0.8692 (tt0) cc_final: 0.8201 (tm-30) REVERT: A 1413 PHE cc_start: 0.7564 (m-80) cc_final: 0.7061 (m-80) outliers start: 28 outliers final: 22 residues processed: 234 average time/residue: 0.0842 time to fit residues: 28.0623 Evaluate side-chains 225 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1419 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 0.0050 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 0.0170 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.144301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125732 restraints weight = 23255.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.128965 restraints weight = 12618.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131022 restraints weight = 8032.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132593 restraints weight = 5738.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133686 restraints weight = 4377.921| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9423 Z= 0.129 Angle : 0.679 14.163 12739 Z= 0.332 Chirality : 0.040 0.204 1481 Planarity : 0.004 0.037 1565 Dihedral : 4.200 16.560 1245 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.69 % Allowed : 26.35 % Favored : 70.96 % 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: 0.65 (0.25), residues: 1129 helix: 1.20 (0.19), residues: 722 sheet: 0.25 (0.55), residues: 90 loop : -1.25 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1066 TYR 0.023 0.001 TYR A 301 PHE 0.044 0.001 PHE A1033 TRP 0.010 0.001 TRP A 19 HIS 0.006 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9423) covalent geometry : angle 0.67902 (12739) hydrogen bonds : bond 0.03638 ( 507) hydrogen bonds : angle 4.20199 ( 1491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1571.59 seconds wall clock time: 27 minutes 52.95 seconds (1672.95 seconds total)