Starting phenix.real_space_refine on Thu Jan 18 18:52:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uak_8516/01_2024/5uak_8516.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uak_8516/01_2024/5uak_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uak_8516/01_2024/5uak_8516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uak_8516/01_2024/5uak_8516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uak_8516/01_2024/5uak_8516.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uak_8516/01_2024/5uak_8516.pdb" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 600": "NH1" <-> "NH2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A ARG 1239": "NH1" <-> "NH2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A ARG 1358": "NH1" <-> "NH2" Residue "A ARG 1386": "NH1" <-> "NH2" Residue "A ARG 1434": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/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: 5.25, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.09 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: 2.87 Time building geometry restraints manager: 3.65 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: 100.32 - 107.06: 183 107.06 - 113.80: 5163 113.80 - 120.55: 3899 120.55 - 127.29: 3413 127.29 - 134.03: 81 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 2.440 nonbonded pdb=" OG1 THR A 845 " pdb=" OG1 THR A 848 " model vdw 2.506 2.440 nonbonded pdb=" O THR A 940 " pdb=" OG1 THR A 943 " model vdw 2.517 2.440 nonbonded pdb=" O ILE A1117 " pdb=" OG1 THR A1121 " model vdw 2.517 2.440 nonbonded pdb=" O THR A 389 " pdb=" OG1 THR A 390 " model vdw 2.531 2.440 ... (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 ========== 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: 3.480 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: 11.880 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.280 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- 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= 0.483 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 356 HIS 0.005 0.001 HIS A1350 PHE 0.018 0.001 PHE A 587 TYR 0.010 0.001 TYR A 122 ARG 0.004 0.000 ARG A1066 *********************** 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 fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 1.083 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: 0.2452 time to fit residues: 125.4891 Evaluate side-chains 245 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN A1411 GLN A1423 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.3574 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= 0.188 Angle : 0.628 7.806 12739 Z= 0.328 Chirality : 0.040 0.155 1481 Planarity : 0.004 0.050 1565 Dihedral : 4.598 18.579 1245 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.89 % Allowed : 15.97 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1129 helix: 0.11 (0.18), residues: 741 sheet: -0.41 (0.58), residues: 60 loop : -1.99 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1274 HIS 0.003 0.001 HIS A 139 PHE 0.027 0.002 PHE A 490 TYR 0.021 0.002 TYR A 325 ARG 0.004 0.001 ARG A 170 *********************** 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 299 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 260 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7251 (mtt-85) cc_final: 0.6793 (tmm-80) REVERT: A 50 SER cc_start: 0.8049 (m) cc_final: 0.7842 (t) REVERT: A 89 TYR cc_start: 0.7752 (t80) cc_final: 0.7467 (t80) REVERT: A 104 ARG cc_start: 0.8064 (mmt90) cc_final: 0.7443 (mmm160) REVERT: A 152 MET cc_start: 0.8285 (mmp) cc_final: 0.7620 (tpp) REVERT: A 179 GLN cc_start: 0.8756 (tt0) cc_final: 0.8549 (mt0) REVERT: A 242 ARG cc_start: 0.7048 (tpt170) cc_final: 0.6431 (ttp-170) REVERT: A 294 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7564 (tptt) REVERT: A 476 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7644 (mp0) REVERT: A 493 GLN cc_start: 0.7305 (tt0) cc_final: 0.6937 (mt0) REVERT: A 498 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6402 (ppp) REVERT: A 516 ARG cc_start: 0.7506 (mtt180) cc_final: 0.7219 (ttt90) REVERT: A 518 ARG cc_start: 0.8399 (ttt180) cc_final: 0.7756 (tpp-160) REVERT: A 541 LEU cc_start: 0.7262 (mt) cc_final: 0.7054 (mp) REVERT: A 595 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7693 (tpt) REVERT: A 645 MET cc_start: 0.4543 (mtp) cc_final: 0.3574 (mmm) REVERT: A 849 TYR cc_start: 0.7690 (m-80) cc_final: 0.7324 (m-80) REVERT: A 929 MET cc_start: 0.1170 (mmm) cc_final: 0.0965 (mmm) REVERT: A 1209 GLN cc_start: 0.8928 (tt0) cc_final: 0.8565 (tp40) REVERT: A 1263 THR cc_start: 0.8602 (p) cc_final: 0.8283 (m) REVERT: A 1330 GLN cc_start: 0.8431 (mm110) cc_final: 0.8103 (pt0) outliers start: 39 outliers final: 13 residues processed: 274 average time/residue: 0.2242 time to fit residues: 83.7857 Evaluate side-chains 220 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 269 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 993 ASP 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 57 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 103 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 359 GLN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN A1352 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.4457 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= 0.187 Angle : 0.584 6.901 12739 Z= 0.302 Chirality : 0.039 0.159 1481 Planarity : 0.004 0.049 1565 Dihedral : 4.411 16.321 1245 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.49 % Allowed : 18.46 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1129 helix: 0.87 (0.19), residues: 733 sheet: -0.28 (0.57), residues: 80 loop : -1.56 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1274 HIS 0.004 0.001 HIS A 856 PHE 0.020 0.001 PHE A 490 TYR 0.018 0.001 TYR A 304 ARG 0.005 0.001 ARG A 334 *********************** 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 263 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.7680 (t80) cc_final: 0.7342 (t80) REVERT: A 104 ARG cc_start: 0.8047 (mmt90) cc_final: 0.7453 (mmm160) REVERT: A 152 MET cc_start: 0.8304 (mmp) cc_final: 0.7787 (mmm) REVERT: A 195 LEU cc_start: 0.6966 (tp) cc_final: 0.6587 (tt) REVERT: A 242 ARG cc_start: 0.7156 (tpt170) cc_final: 0.6501 (ttp-170) REVERT: A 294 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7420 (tptt) REVERT: A 446 PHE cc_start: 0.6662 (p90) cc_final: 0.6286 (p90) REVERT: A 476 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7697 (mp0) REVERT: A 493 GLN cc_start: 0.7398 (tt0) cc_final: 0.7032 (mt0) REVERT: A 498 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6664 (ppp) REVERT: A 516 ARG cc_start: 0.7486 (mtt180) cc_final: 0.7100 (ttt90) REVERT: A 518 ARG cc_start: 0.8356 (ttt180) cc_final: 0.7731 (tpp-160) REVERT: A 595 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7397 (tpt) REVERT: A 600 ARG cc_start: 0.6802 (mtp180) cc_final: 0.6533 (mtt-85) REVERT: A 607 MET cc_start: 0.6680 (mpt) cc_final: 0.6201 (mmt) REVERT: A 645 MET cc_start: 0.4553 (mtp) cc_final: 0.3522 (mmm) REVERT: A 1140 MET cc_start: 0.7273 (tmm) cc_final: 0.6936 (tmm) REVERT: A 1209 GLN cc_start: 0.8941 (tt0) cc_final: 0.8511 (tp40) REVERT: A 1263 THR cc_start: 0.8588 (p) cc_final: 0.8262 (m) REVERT: A 1330 GLN cc_start: 0.8449 (mm110) cc_final: 0.8101 (pt0) REVERT: A 1418 GLU cc_start: 0.8081 (tp30) cc_final: 0.7657 (tp30) outliers start: 35 outliers final: 16 residues processed: 247 average time/residue: 0.2206 time to fit residues: 75.8413 Evaluate side-chains 217 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1295 ILE Chi-restraints excluded: chain A residue 1335 LEU Chi-restraints excluded: chain A residue 1407 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 958 GLN A1079 HIS A1209 GLN ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9423 Z= 0.405 Angle : 0.789 7.271 12739 Z= 0.411 Chirality : 0.045 0.197 1481 Planarity : 0.005 0.045 1565 Dihedral : 5.247 22.485 1245 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.09 % Allowed : 19.36 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1129 helix: 0.53 (0.18), residues: 712 sheet: -0.18 (0.58), residues: 76 loop : -1.76 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 277 HIS 0.009 0.002 HIS A 146 PHE 0.024 0.003 PHE A 626 TYR 0.017 0.002 TYR A 569 ARG 0.006 0.001 ARG A 21 *********************** 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 259 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 208 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.7629 (t80) cc_final: 0.7302 (t80) REVERT: A 104 ARG cc_start: 0.7740 (mmt90) cc_final: 0.7107 (mmm160) REVERT: A 172 LEU cc_start: 0.8017 (tt) cc_final: 0.7809 (mt) REVERT: A 294 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7567 (tptt) REVERT: A 476 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7640 (mp0) REVERT: A 498 MET cc_start: 0.6856 (ppp) cc_final: 0.6493 (ppp) REVERT: A 516 ARG cc_start: 0.7592 (mtt180) cc_final: 0.7205 (ttt90) REVERT: A 518 ARG cc_start: 0.8424 (ttt180) cc_final: 0.7872 (tpp-160) REVERT: A 645 MET cc_start: 0.4804 (mtp) cc_final: 0.3768 (mmm) REVERT: A 849 TYR cc_start: 0.7221 (m-80) cc_final: 0.7004 (m-80) REVERT: A 914 TYR cc_start: 0.5363 (m-80) cc_final: 0.4312 (m-80) REVERT: A 1209 GLN cc_start: 0.8903 (tt0) cc_final: 0.8544 (tp-100) REVERT: A 1330 GLN cc_start: 0.8520 (mm110) cc_final: 0.8088 (pt0) outliers start: 51 outliers final: 35 residues processed: 239 average time/residue: 0.2033 time to fit residues: 68.1374 Evaluate side-chains 221 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1304 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 91 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 A1054 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9423 Z= 0.177 Angle : 0.590 6.535 12739 Z= 0.303 Chirality : 0.039 0.166 1481 Planarity : 0.003 0.047 1565 Dihedral : 4.577 18.451 1245 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.19 % Allowed : 22.36 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1129 helix: 0.96 (0.19), residues: 726 sheet: 0.08 (0.54), residues: 91 loop : -1.54 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1089 HIS 0.013 0.001 HIS A1054 PHE 0.018 0.001 PHE A 587 TYR 0.013 0.001 TYR A 512 ARG 0.005 0.000 ARG A1403 *********************** 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 258 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8554 (mmtm) REVERT: A 89 TYR cc_start: 0.7691 (t80) cc_final: 0.7323 (t80) REVERT: A 104 ARG cc_start: 0.7663 (mmt90) cc_final: 0.6990 (mmm160) REVERT: A 195 LEU cc_start: 0.6827 (tp) cc_final: 0.6461 (tt) REVERT: A 236 PHE cc_start: 0.7588 (t80) cc_final: 0.7379 (t80) REVERT: A 237 GLN cc_start: 0.7547 (tt0) cc_final: 0.7319 (tt0) REVERT: A 294 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7431 (tptt) REVERT: A 476 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7644 (mp0) REVERT: A 494 PHE cc_start: 0.3790 (OUTLIER) cc_final: 0.3477 (m-80) REVERT: A 498 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6727 (ppp) REVERT: A 516 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7238 (ttt90) REVERT: A 518 ARG cc_start: 0.8350 (ttt180) cc_final: 0.7754 (tpp-160) REVERT: A 595 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7803 (tpt) REVERT: A 621 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7805 (mp0) REVERT: A 645 MET cc_start: 0.4665 (mtp) cc_final: 0.3694 (mmm) REVERT: A 849 TYR cc_start: 0.7156 (m-80) cc_final: 0.6913 (m-80) REVERT: A 931 PHE cc_start: 0.7380 (p90) cc_final: 0.7159 (p90) REVERT: A 1209 GLN cc_start: 0.8823 (tt0) cc_final: 0.8485 (tp40) REVERT: A 1210 MET cc_start: 0.4462 (tpp) cc_final: 0.4035 (tpp) REVERT: A 1281 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8272 (pp30) REVERT: A 1330 GLN cc_start: 0.8498 (mm110) cc_final: 0.8037 (pt0) REVERT: A 1413 PHE cc_start: 0.8189 (m-80) cc_final: 0.7774 (m-80) outliers start: 32 outliers final: 19 residues processed: 245 average time/residue: 0.1955 time to fit residues: 66.9780 Evaluate side-chains 219 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 SER 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 1281 GLN Chi-restraints excluded: chain A residue 1299 THR 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 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 110 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.5968 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= 0.177 Angle : 0.588 9.054 12739 Z= 0.298 Chirality : 0.039 0.164 1481 Planarity : 0.004 0.043 1565 Dihedral : 4.386 17.417 1245 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.89 % Allowed : 24.15 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1129 helix: 1.07 (0.19), residues: 726 sheet: 0.20 (0.54), residues: 91 loop : -1.42 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 19 HIS 0.004 0.001 HIS A1054 PHE 0.021 0.001 PHE A 587 TYR 0.015 0.001 TYR A 301 ARG 0.006 0.000 ARG A 975 *********************** 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 249 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.7630 (t80) cc_final: 0.7189 (t80) REVERT: A 104 ARG cc_start: 0.7763 (mmt90) cc_final: 0.7103 (mmm160) REVERT: A 294 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7463 (tptt) REVERT: A 337 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6972 (t80) REVERT: A 476 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7738 (mp0) REVERT: A 487 ARG cc_start: 0.6669 (tpt170) cc_final: 0.6400 (ptt-90) REVERT: A 494 PHE cc_start: 0.3913 (OUTLIER) cc_final: 0.3565 (m-80) REVERT: A 498 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6778 (ppp) REVERT: A 516 ARG cc_start: 0.7582 (mtt180) cc_final: 0.7231 (ttt90) REVERT: A 518 ARG cc_start: 0.8330 (ttt180) cc_final: 0.7743 (tpp-160) REVERT: A 621 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7803 (mp0) REVERT: A 645 MET cc_start: 0.4656 (mtp) cc_final: 0.3695 (mmm) REVERT: A 849 TYR cc_start: 0.7094 (m-80) cc_final: 0.6882 (m-80) REVERT: A 1140 MET cc_start: 0.7504 (tmm) cc_final: 0.7265 (tmm) REVERT: A 1209 GLN cc_start: 0.8809 (tt0) cc_final: 0.8471 (tp40) REVERT: A 1210 MET cc_start: 0.4546 (tpp) cc_final: 0.4167 (tpp) REVERT: A 1281 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8260 (pp30) REVERT: A 1330 GLN cc_start: 0.8481 (mm110) cc_final: 0.8045 (pt0) REVERT: A 1413 PHE cc_start: 0.8314 (m-80) cc_final: 0.7912 (m-80) outliers start: 39 outliers final: 21 residues processed: 232 average time/residue: 0.2108 time to fit residues: 67.7054 Evaluate side-chains 217 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1281 GLN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1407 MET Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1423 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9423 Z= 0.235 Angle : 0.635 10.385 12739 Z= 0.323 Chirality : 0.040 0.168 1481 Planarity : 0.004 0.042 1565 Dihedral : 4.492 18.023 1245 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.69 % Allowed : 24.75 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1129 helix: 1.02 (0.19), residues: 721 sheet: 0.22 (0.58), residues: 84 loop : -1.41 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 19 HIS 0.004 0.001 HIS A1054 PHE 0.016 0.001 PHE A1392 TYR 0.022 0.001 TYR A 301 ARG 0.007 0.000 ARG A 975 *********************** 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 235 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.054 Fit side-chains REVERT: A 89 TYR cc_start: 0.7580 (t80) cc_final: 0.7131 (t80) REVERT: A 104 ARG cc_start: 0.7724 (mmt90) cc_final: 0.6861 (tpm170) REVERT: A 294 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7556 (tptt) REVERT: A 295 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6902 (tt) REVERT: A 476 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7612 (mp0) REVERT: A 494 PHE cc_start: 0.4002 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: A 498 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6726 (ppp) REVERT: A 516 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7306 (ttt90) REVERT: A 518 ARG cc_start: 0.8344 (ttt180) cc_final: 0.7759 (tpp-160) REVERT: A 595 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7671 (tpt) REVERT: A 621 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7781 (mp0) REVERT: A 645 MET cc_start: 0.4732 (mtp) cc_final: 0.3757 (mmm) REVERT: A 849 TYR cc_start: 0.7121 (m-80) cc_final: 0.6913 (m-80) REVERT: A 1140 MET cc_start: 0.7453 (tmm) cc_final: 0.7162 (tmm) REVERT: A 1209 GLN cc_start: 0.8838 (tt0) cc_final: 0.8517 (tp40) REVERT: A 1210 MET cc_start: 0.4563 (tpp) cc_final: 0.4202 (tpp) REVERT: A 1281 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8341 (pp30) REVERT: A 1330 GLN cc_start: 0.8487 (mm110) cc_final: 0.8057 (pt0) REVERT: A 1413 PHE cc_start: 0.8339 (m-80) cc_final: 0.7971 (m-80) outliers start: 37 outliers final: 25 residues processed: 217 average time/residue: 0.2208 time to fit residues: 67.0818 Evaluate side-chains 218 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1281 GLN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1407 MET Chi-restraints excluded: chain A residue 1415 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.0070 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 HIS ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.6324 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= 0.182 Angle : 0.607 9.068 12739 Z= 0.305 Chirality : 0.039 0.161 1481 Planarity : 0.004 0.040 1565 Dihedral : 4.355 18.917 1245 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.19 % Allowed : 25.55 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1129 helix: 1.10 (0.19), residues: 724 sheet: 0.23 (0.57), residues: 84 loop : -1.23 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 19 HIS 0.004 0.001 HIS A1054 PHE 0.024 0.001 PHE A 236 TYR 0.030 0.001 TYR A 301 ARG 0.008 0.000 ARG A 975 *********************** 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 236 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.7620 (t80) cc_final: 0.7179 (t80) REVERT: A 104 ARG cc_start: 0.7630 (mmt90) cc_final: 0.6761 (tpm170) REVERT: A 294 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7549 (tptt) REVERT: A 295 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6894 (tt) REVERT: A 476 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7453 (mp0) REVERT: A 494 PHE cc_start: 0.4061 (OUTLIER) cc_final: 0.3722 (m-80) REVERT: A 498 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6747 (ppp) REVERT: A 516 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7314 (ttt90) REVERT: A 518 ARG cc_start: 0.8315 (ttt180) cc_final: 0.7788 (tpp-160) REVERT: A 595 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7581 (tpt) REVERT: A 621 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7764 (mp0) REVERT: A 645 MET cc_start: 0.4666 (mtp) cc_final: 0.3714 (mmm) REVERT: A 849 TYR cc_start: 0.7046 (m-80) cc_final: 0.6805 (m-80) REVERT: A 1209 GLN cc_start: 0.8713 (tt0) cc_final: 0.8396 (tp40) REVERT: A 1210 MET cc_start: 0.4612 (tpp) cc_final: 0.4294 (tpp) REVERT: A 1280 GLN cc_start: 0.8821 (tt0) cc_final: 0.8303 (tm-30) REVERT: A 1281 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8042 (pp30) REVERT: A 1330 GLN cc_start: 0.8483 (mm110) cc_final: 0.8065 (pt0) REVERT: A 1413 PHE cc_start: 0.8335 (m-80) cc_final: 0.7913 (m-80) outliers start: 32 outliers final: 20 residues processed: 223 average time/residue: 0.2328 time to fit residues: 72.5746 Evaluate side-chains 216 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1281 GLN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1423 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 67 optimal weight: 0.0050 chunk 108 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.6450 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= 0.195 Angle : 0.637 10.026 12739 Z= 0.319 Chirality : 0.039 0.193 1481 Planarity : 0.004 0.039 1565 Dihedral : 4.325 17.787 1245 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.79 % Allowed : 26.05 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1129 helix: 1.09 (0.19), residues: 726 sheet: 0.13 (0.55), residues: 90 loop : -1.21 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 19 HIS 0.003 0.001 HIS A1054 PHE 0.023 0.001 PHE A 587 TYR 0.026 0.001 TYR A 301 ARG 0.009 0.000 ARG A 975 *********************** 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 223 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.7620 (t80) cc_final: 0.7179 (t80) REVERT: A 104 ARG cc_start: 0.7666 (mmt90) cc_final: 0.6800 (tpm170) REVERT: A 294 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7549 (tptt) REVERT: A 295 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6871 (tt) REVERT: A 476 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7469 (mp0) REVERT: A 494 PHE cc_start: 0.4038 (OUTLIER) cc_final: 0.3676 (m-80) REVERT: A 498 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6765 (ppp) REVERT: A 516 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7332 (ttt90) REVERT: A 518 ARG cc_start: 0.8371 (ttt180) cc_final: 0.7783 (tpp-160) REVERT: A 595 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7741 (tmm) REVERT: A 621 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7754 (mp0) REVERT: A 645 MET cc_start: 0.4559 (mtp) cc_final: 0.3649 (mmm) REVERT: A 1209 GLN cc_start: 0.8719 (tt0) cc_final: 0.8402 (tp40) REVERT: A 1210 MET cc_start: 0.4635 (tpp) cc_final: 0.4295 (tpp) REVERT: A 1281 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8300 (pp30) REVERT: A 1330 GLN cc_start: 0.8475 (mm110) cc_final: 0.8074 (pt0) REVERT: A 1413 PHE cc_start: 0.8348 (m-80) cc_final: 0.7970 (m-80) outliers start: 28 outliers final: 22 residues processed: 211 average time/residue: 0.2059 time to fit residues: 60.9884 Evaluate side-chains 217 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 150 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 259 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 371 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1281 GLN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1423 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.0470 chunk 113 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.0000 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.6547 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= 0.174 Angle : 0.650 11.118 12739 Z= 0.317 Chirality : 0.039 0.222 1481 Planarity : 0.003 0.038 1565 Dihedral : 4.225 17.334 1245 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.59 % Allowed : 26.55 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1129 helix: 1.14 (0.20), residues: 727 sheet: 0.24 (0.56), residues: 90 loop : -1.11 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 19 HIS 0.003 0.001 HIS A1054 PHE 0.028 0.001 PHE A 490 TYR 0.025 0.001 TYR A 301 ARG 0.008 0.000 ARG A 975 ********************** 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 232 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 206 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8576 (mmtm) cc_final: 0.8296 (mmtm) REVERT: A 56 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8144 (mp0) REVERT: A 89 TYR cc_start: 0.7623 (t80) cc_final: 0.7180 (t80) REVERT: A 104 ARG cc_start: 0.7687 (mmt90) cc_final: 0.6806 (tpm170) REVERT: A 287 ASN cc_start: 0.8240 (m-40) cc_final: 0.7748 (t0) REVERT: A 294 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7463 (tptt) REVERT: A 295 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6830 (tt) REVERT: A 476 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7460 (mp0) REVERT: A 487 ARG cc_start: 0.6868 (tpt170) cc_final: 0.6370 (ptt-90) REVERT: A 494 PHE cc_start: 0.4068 (OUTLIER) cc_final: 0.3709 (m-80) REVERT: A 498 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6771 (ppp) REVERT: A 516 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7341 (ttt90) REVERT: A 518 ARG cc_start: 0.8362 (ttt180) cc_final: 0.7771 (tpp-160) REVERT: A 579 ASP cc_start: 0.8199 (m-30) cc_final: 0.7954 (t70) REVERT: A 595 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7584 (tpt) REVERT: A 621 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7762 (mp0) REVERT: A 645 MET cc_start: 0.4520 (mtp) cc_final: 0.3615 (mmm) REVERT: A 1209 GLN cc_start: 0.8683 (tt0) cc_final: 0.8347 (tp40) REVERT: A 1210 MET cc_start: 0.4709 (tpp) cc_final: 0.4391 (tpp) REVERT: A 1281 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8255 (pp30) REVERT: A 1330 GLN cc_start: 0.8501 (mm110) cc_final: 0.8103 (pt0) REVERT: A 1413 PHE cc_start: 0.8277 (m-80) cc_final: 0.7896 (m-80) outliers start: 26 outliers final: 20 residues processed: 221 average time/residue: 0.2316 time to fit residues: 72.3915 Evaluate side-chains 216 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1281 GLN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1423 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3926 r_free = 0.3926 target = 0.142768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124475 restraints weight = 23044.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127522 restraints weight = 12435.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129638 restraints weight = 7987.063| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6656 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= 0.182 Angle : 0.651 12.025 12739 Z= 0.318 Chirality : 0.039 0.244 1481 Planarity : 0.004 0.038 1565 Dihedral : 4.147 17.466 1245 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.89 % Allowed : 27.64 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1129 helix: 1.13 (0.19), residues: 729 sheet: 0.33 (0.56), residues: 90 loop : -1.05 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 19 HIS 0.003 0.001 HIS A1054 PHE 0.028 0.001 PHE A 490 TYR 0.024 0.001 TYR A 301 ARG 0.005 0.000 ARG A 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.47 seconds wall clock time: 43 minutes 35.05 seconds (2615.05 seconds total)