Starting phenix.real_space_refine on Thu Jun 26 13:25:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zr1_14881/06_2025/7zr1_14881.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr1_14881/06_2025/7zr1_14881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zr1_14881/06_2025/7zr1_14881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr1_14881/06_2025/7zr1_14881.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr1_14881/06_2025/7zr1_14881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr1_14881/06_2025/7zr1_14881.cif" } resolution = 4.0 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10626 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 6 5.49 5 Mg 2 5.21 5 S 93 5.16 5 C 13528 2.51 5 N 3941 2.21 5 O 4219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21793 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4284 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 29, 'TRANS': 499} Chain breaks: 1 Chain: "B" Number of atoms: 4168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4168 Classifications: {'peptide': 514} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 486} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 6282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6282 Classifications: {'peptide': 779} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 764} Chain breaks: 1 Chain: "D" Number of atoms: 6291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6291 Classifications: {'peptide': 780} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 765} Chain breaks: 1 Chain: "E" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 700 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.63, per 1000 atoms: 0.53 Number of scatterers: 21793 At special positions: 0 Unit cell: (109.797, 107.764, 398.523, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 93 16.00 P 6 15.00 Mg 2 11.99 O 4219 8.00 N 3941 7.00 C 13528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.95 Conformation dependent library (CDL) restraints added in 3.5 seconds 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5126 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 17 sheets defined 56.6% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 31 through 48 removed outlier: 3.950A pdb=" N THR A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.706A pdb=" N VAL A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 98 removed outlier: 4.166A pdb=" N VAL A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.584A pdb=" N ASP A 127 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 removed outlier: 3.977A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.704A pdb=" N VAL A 276 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 352 removed outlier: 3.563A pdb=" N THR A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.691A pdb=" N VAL A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 496 removed outlier: 4.194A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 521 removed outlier: 3.511A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.627A pdb=" N ARG A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.672A pdb=" N ARG B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 removed outlier: 3.528A pdb=" N GLN B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.860A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.603A pdb=" N ARG B 190 " --> pdb=" O HIS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.838A pdb=" N ALA B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 276' Processing helix chain 'B' and resid 325 through 352 removed outlier: 4.099A pdb=" N THR B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.875A pdb=" N ASP B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 393 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 458 through 472 removed outlier: 3.655A pdb=" N VAL B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.873A pdb=" N PHE B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 507 through 521 Processing helix chain 'B' and resid 525 through 532 removed outlier: 3.639A pdb=" N GLN B 529 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 548 through 556 Proline residue: B 553 - end of helix Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.870A pdb=" N GLY C 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.966A pdb=" N VAL C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 Processing helix chain 'C' and resid 147 through 154 removed outlier: 4.170A pdb=" N LEU C 151 " --> pdb=" O PRO C 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.860A pdb=" N ARG C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 293 removed outlier: 4.453A pdb=" N TYR C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 377 removed outlier: 4.078A pdb=" N ASN C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 413 removed outlier: 3.597A pdb=" N ARG C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 973 removed outlier: 3.809A pdb=" N ILE C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 1051 removed outlier: 3.913A pdb=" N ALA C1019 " --> pdb=" O ASP C1015 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C1051 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1106 removed outlier: 4.011A pdb=" N ASP C1055 " --> pdb=" O ASN C1051 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C1089 " --> pdb=" O SER C1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1160 removed outlier: 3.815A pdb=" N LYS C1115 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C1116 " --> pdb=" O THR C1112 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C1131 " --> pdb=" O GLY C1127 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C1143 " --> pdb=" O GLN C1139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C1145 " --> pdb=" O HIS C1141 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C1154 " --> pdb=" O ARG C1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 1208 through 1228 removed outlier: 3.672A pdb=" N LYS C1212 " --> pdb=" O SER C1208 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C1225 " --> pdb=" O LEU C1221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C1227 " --> pdb=" O LEU C1223 " (cutoff:3.500A) Processing helix chain 'C' and resid 1244 through 1266 removed outlier: 3.920A pdb=" N ARG C1249 " --> pdb=" O SER C1245 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C1264 " --> pdb=" O LYS C1260 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN C1265 " --> pdb=" O ALA C1261 " (cutoff:3.500A) Processing helix chain 'C' and resid 1276 through 1287 removed outlier: 3.650A pdb=" N LEU C1280 " --> pdb=" O ASP C1276 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C1281 " --> pdb=" O GLU C1277 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR C1282 " --> pdb=" O GLU C1278 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET C1283 " --> pdb=" O PHE C1279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C1284 " --> pdb=" O LEU C1280 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C1286 " --> pdb=" O TYR C1282 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C1287 " --> pdb=" O MET C1283 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.771A pdb=" N ILE D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 removed outlier: 3.631A pdb=" N VAL D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.686A pdb=" N ASP D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 159 through 167 removed outlier: 3.698A pdb=" N LEU D 163 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 181 through 208 removed outlier: 4.208A pdb=" N TYR D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 293 removed outlier: 4.168A pdb=" N GLN D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 220 " --> pdb=" O ASN D 216 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 378 removed outlier: 4.417A pdb=" N GLU D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLN D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG D 371 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 412 removed outlier: 3.733A pdb=" N GLU D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 973 removed outlier: 3.741A pdb=" N ILE D 967 " --> pdb=" O ILE D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 1051 removed outlier: 3.726A pdb=" N LEU D 979 " --> pdb=" O GLY D 975 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG D1022 " --> pdb=" O ASP D1018 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN D1051 " --> pdb=" O LEU D1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1106 removed outlier: 4.205A pdb=" N ASP D1055 " --> pdb=" O ASN D1051 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D1092 " --> pdb=" O ASP D1088 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG D1093 " --> pdb=" O GLU D1089 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D1094 " --> pdb=" O GLU D1090 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D1100 " --> pdb=" O GLU D1096 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D1104 " --> pdb=" O LEU D1100 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS D1106 " --> pdb=" O LEU D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1106 through 1159 removed outlier: 4.265A pdb=" N LYS D1110 " --> pdb=" O LYS D1106 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D1111 " --> pdb=" O ALA D1107 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D1114 " --> pdb=" O LYS D1110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D1124 " --> pdb=" O LYS D1120 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D1125 " --> pdb=" O ALA D1121 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D1127 " --> pdb=" O ILE D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1208 through 1228 Processing helix chain 'D' and resid 1244 through 1263 Processing helix chain 'D' and resid 1276 through 1286 removed outlier: 3.737A pdb=" N MET D1283 " --> pdb=" O PHE D1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 623 Processing helix chain 'E' and resid 641 through 649 Processing helix chain 'E' and resid 652 through 656 Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 148 removed outlier: 6.536A pdb=" N VAL A 118 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG A 11 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU A 53 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 13 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 281 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.560A pdb=" N MET A 177 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 208 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE A 238 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 210 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 237 " --> pdb=" O MET A 260 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 259 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP A 248 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 261 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.752A pdb=" N VAL A 160 " --> pdb=" O ARG A 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 309 removed outlier: 3.521A pdb=" N ARG A 369 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 306 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 371 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 308 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 373 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N HIS A 406 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A 370 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N TYR A 408 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 372 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.482A pdb=" N ARG A 533 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 148 removed outlier: 5.916A pdb=" N VAL B 118 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 52 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG B 11 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU B 53 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 13 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 281 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 293 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 90 removed outlier: 7.081A pdb=" N LYS B 171 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU B 209 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 173 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR B 211 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR B 175 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN B 208 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE B 238 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 210 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 237 " --> pdb=" O MET B 260 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN B 261 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP B 248 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'B' and resid 303 through 309 removed outlier: 3.542A pdb=" N ARG B 306 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS B 406 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 370 " --> pdb=" O HIS B 406 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR B 408 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 372 " --> pdb=" O TYR B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.736A pdb=" N LYS C 3 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER C 84 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 7 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS C 82 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE C 9 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN C 80 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 102 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.736A pdb=" N LYS C 3 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER C 84 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 7 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS C 82 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE C 9 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN C 80 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER C 92 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 121 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 117 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 118 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1233 through 1237 removed outlier: 6.361A pdb=" N ILE C1234 " --> pdb=" O ILE C1271 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ILE C1273 " --> pdb=" O ILE C1234 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU C1236 " --> pdb=" O ILE C1273 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N TYR C1293 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 31 " --> pdb=" O TYR C1293 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C1295 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C 33 " --> pdb=" O VAL C1295 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG C1297 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C1306 " --> pdb=" O ARG C1294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1167 through 1173 removed outlier: 3.536A pdb=" N ASN C1189 " --> pdb=" O ASP C1173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.815A pdb=" N SER D 84 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU D 7 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS D 82 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 9 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN D 80 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 110 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.815A pdb=" N SER D 84 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU D 7 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS D 82 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 9 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN D 80 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER D 92 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU D 118 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1235 through 1237 removed outlier: 8.509A pdb=" N TYR D1293 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU D 31 " --> pdb=" O TYR D1293 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL D1295 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL D 33 " --> pdb=" O VAL D1295 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ARG D1297 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1167 through 1170 1293 hydrogen bonds defined for protein. 3738 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: 10.02 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.30: 3859 1.30 - 1.46: 7892 1.46 - 1.62: 10219 1.62 - 1.79: 23 1.79 - 1.95: 137 Bond restraints: 22130 Sorted by residual: bond pdb=" C ASP A 506 " pdb=" O ASP A 506 " ideal model delta sigma weight residual 1.236 1.140 0.097 1.25e-02 6.40e+03 5.98e+01 bond pdb=" C LYS D 184 " pdb=" O LYS D 184 " ideal model delta sigma weight residual 1.237 1.321 -0.084 1.19e-02 7.06e+03 4.99e+01 bond pdb=" C PRO D 169 " pdb=" O PRO D 169 " ideal model delta sigma weight residual 1.235 1.146 0.089 1.30e-02 5.92e+03 4.69e+01 bond pdb=" C THR D 186 " pdb=" O THR D 186 " ideal model delta sigma weight residual 1.236 1.309 -0.073 1.26e-02 6.30e+03 3.34e+01 bond pdb=" C LYS C 184 " pdb=" O LYS C 184 " ideal model delta sigma weight residual 1.236 1.301 -0.065 1.15e-02 7.56e+03 3.21e+01 ... (remaining 22125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 28965 2.64 - 5.29: 703 5.29 - 7.93: 101 7.93 - 10.58: 15 10.58 - 13.22: 1 Bond angle restraints: 29785 Sorted by residual: angle pdb=" C LEU C 195 " pdb=" N LYS C 196 " pdb=" CA LYS C 196 " ideal model delta sigma weight residual 120.28 133.50 -13.22 1.34e+00 5.57e-01 9.74e+01 angle pdb=" N GLU C 181 " pdb=" CA GLU C 181 " pdb=" C GLU C 181 " ideal model delta sigma weight residual 112.58 102.11 10.47 1.22e+00 6.72e-01 7.37e+01 angle pdb=" N GLU D 181 " pdb=" CA GLU D 181 " pdb=" C GLU D 181 " ideal model delta sigma weight residual 113.23 102.85 10.38 1.22e+00 6.72e-01 7.23e+01 angle pdb=" CA ARG D 175 " pdb=" C ARG D 175 " pdb=" O ARG D 175 " ideal model delta sigma weight residual 120.70 112.49 8.21 1.03e+00 9.43e-01 6.35e+01 angle pdb=" C LYS D 199 " pdb=" N GLY D 200 " pdb=" CA GLY D 200 " ideal model delta sigma weight residual 119.98 128.48 -8.50 1.11e+00 8.12e-01 5.87e+01 ... (remaining 29780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.61: 12570 18.61 - 37.21: 1019 37.21 - 55.82: 170 55.82 - 74.43: 26 74.43 - 93.03: 4 Dihedral angle restraints: 13789 sinusoidal: 5924 harmonic: 7865 Sorted by residual: dihedral pdb=" N ILE D1123 " pdb=" C ILE D1123 " pdb=" CA ILE D1123 " pdb=" CB ILE D1123 " ideal model delta harmonic sigma weight residual 123.40 136.59 -13.19 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" C ILE D1123 " pdb=" N ILE D1123 " pdb=" CA ILE D1123 " pdb=" CB ILE D1123 " ideal model delta harmonic sigma weight residual -122.00 -134.32 12.32 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" C ARG D 175 " pdb=" N ARG D 175 " pdb=" CA ARG D 175 " pdb=" CB ARG D 175 " ideal model delta harmonic sigma weight residual -122.60 -134.37 11.77 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 13786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2906 0.083 - 0.166: 305 0.166 - 0.248: 38 0.248 - 0.331: 4 0.331 - 0.414: 6 Chirality restraints: 3259 Sorted by residual: chirality pdb=" CA ILE D1123 " pdb=" N ILE D1123 " pdb=" C ILE D1123 " pdb=" CB ILE D1123 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CB ILE D1123 " pdb=" CA ILE D1123 " pdb=" CG1 ILE D1123 " pdb=" CG2 ILE D1123 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA ARG D 175 " pdb=" N ARG D 175 " pdb=" C ARG D 175 " pdb=" CB ARG D 175 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 3256 not shown) Planarity restraints: 3932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C1147 " -0.026 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C GLN C1147 " 0.092 2.00e-02 2.50e+03 pdb=" O GLN C1147 " -0.035 2.00e-02 2.50e+03 pdb=" N ILE C1148 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 181 " -0.026 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C GLU D 181 " 0.086 2.00e-02 2.50e+03 pdb=" O GLU D 181 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA D 182 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 178 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C GLU D 178 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU D 178 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE D 179 " 0.019 2.00e-02 2.50e+03 ... (remaining 3929 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 106 2.49 - 3.09: 17144 3.09 - 3.70: 34574 3.70 - 4.30: 48755 4.30 - 4.90: 76723 Nonbonded interactions: 177302 Sorted by model distance: nonbonded pdb=" OD2 ASP B 17 " pdb="MN MN B 801 " model vdw 1.888 2.320 nonbonded pdb=" NE2 HIS A 213 " pdb="MN MN A 802 " model vdw 1.899 2.400 nonbonded pdb=" OD1 ASP A 17 " pdb="MN MN A 801 " model vdw 1.988 2.320 nonbonded pdb=" ND1 HIS A 241 " pdb="MN MN A 802 " model vdw 2.006 2.400 nonbonded pdb="MG MG C1401 " pdb=" O2G AGS C1402 " model vdw 2.007 2.170 ... (remaining 177297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 126 or resid 133 through 179 or resid 185 throug \ h 219 or resid 223 through 358 or (resid 359 and (name N or name CA or name C or \ name O )) or resid 360 through 411 or resid 438 through 557 or resid 801 throug \ h 802)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 2 through 413 or resid 943 through 1309 or resid 1401 thro \ ugh 1402)) } 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: 28.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 53.550 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.006 0.104 22130 Z= 0.395 Angle : 0.907 13.222 29785 Z= 0.618 Chirality : 0.053 0.414 3259 Planarity : 0.005 0.056 3932 Dihedral : 13.258 93.035 8663 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.59 % Allowed : 6.67 % Favored : 92.74 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 2.22 % 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: 0.71 (0.16), residues: 2662 helix: 1.27 (0.14), residues: 1303 sheet: -0.04 (0.28), residues: 352 loop : -0.28 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D1156 HIS 0.015 0.001 HIS D1141 PHE 0.025 0.002 PHE D 176 TYR 0.019 0.002 TYR C 281 ARG 0.043 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.19248 ( 1260) hydrogen bonds : angle 6.93131 ( 3738) covalent geometry : bond 0.00594 (22130) covalent geometry : angle 0.90730 (29785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 365 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8168 (mt-10) REVERT: A 39 GLU cc_start: 0.8988 (tp30) cc_final: 0.8740 (tp30) REVERT: A 51 MET cc_start: 0.9000 (ppp) cc_final: 0.8624 (ppp) REVERT: A 61 ASP cc_start: 0.8781 (m-30) cc_final: 0.8042 (p0) REVERT: A 69 MET cc_start: 0.9293 (tpp) cc_final: 0.8713 (ttm) REVERT: A 107 TYR cc_start: 0.9544 (p90) cc_final: 0.9142 (p90) REVERT: A 125 HIS cc_start: 0.8982 (m90) cc_final: 0.8623 (m-70) REVERT: A 131 ASP cc_start: 0.9020 (m-30) cc_final: 0.8657 (t0) REVERT: A 229 MET cc_start: 0.9225 (mmm) cc_final: 0.8775 (mmm) REVERT: A 236 LEU cc_start: 0.9671 (tt) cc_final: 0.9452 (tt) REVERT: A 316 PHE cc_start: 0.9136 (m-80) cc_final: 0.8375 (m-80) REVERT: A 334 MET cc_start: 0.8600 (mmm) cc_final: 0.8396 (mmm) REVERT: A 340 MET cc_start: 0.8964 (mtp) cc_final: 0.8188 (mtp) REVERT: A 343 GLU cc_start: 0.8984 (tp30) cc_final: 0.8197 (tp30) REVERT: A 456 ILE cc_start: 0.7582 (pt) cc_final: 0.7166 (pt) REVERT: B 73 MET cc_start: 0.8696 (mtp) cc_final: 0.7851 (ttp) REVERT: B 83 MET cc_start: 0.8806 (mmp) cc_final: 0.8522 (mmp) REVERT: B 112 ILE cc_start: 0.9519 (mt) cc_final: 0.9271 (mm) REVERT: B 157 ASN cc_start: 0.8104 (t0) cc_final: 0.7879 (p0) REVERT: B 161 LYS cc_start: 0.9061 (mptt) cc_final: 0.8274 (mmtm) REVERT: B 164 LEU cc_start: 0.9283 (mt) cc_final: 0.8871 (mm) REVERT: B 210 LEU cc_start: 0.9328 (tp) cc_final: 0.8913 (tt) REVERT: B 217 TYR cc_start: 0.8392 (m-80) cc_final: 0.7900 (m-10) REVERT: B 317 LYS cc_start: 0.9329 (tptt) cc_final: 0.9118 (tmmt) REVERT: B 340 MET cc_start: 0.8060 (mmm) cc_final: 0.7766 (mmm) REVERT: B 445 VAL cc_start: 0.8893 (m) cc_final: 0.8460 (p) REVERT: C 3 LYS cc_start: 0.8744 (mttt) cc_final: 0.8414 (mmtt) REVERT: C 119 LEU cc_start: 0.9115 (mm) cc_final: 0.8576 (tt) REVERT: C 136 LEU cc_start: 0.9357 (mt) cc_final: 0.8987 (mt) REVERT: C 151 LEU cc_start: 0.9312 (mp) cc_final: 0.9069 (mp) REVERT: C 155 ILE cc_start: 0.9304 (mt) cc_final: 0.8990 (tt) REVERT: C 249 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: C 1144 MET cc_start: 0.8233 (mmm) cc_final: 0.7809 (mmm) REVERT: C 1168 ILE cc_start: 0.7321 (pt) cc_final: 0.6966 (mm) REVERT: C 1233 LEU cc_start: 0.9226 (tt) cc_final: 0.9017 (tp) REVERT: D 26 ASN cc_start: 0.9248 (t0) cc_final: 0.8914 (t0) REVERT: D 82 LYS cc_start: 0.9178 (ptpt) cc_final: 0.8968 (mppt) REVERT: D 136 LEU cc_start: 0.9375 (mt) cc_final: 0.9083 (mt) REVERT: D 151 LEU cc_start: 0.9255 (mt) cc_final: 0.8891 (mt) REVERT: D 172 LEU cc_start: 0.7256 (tp) cc_final: 0.6811 (tp) REVERT: D 1144 MET cc_start: 0.8639 (mmp) cc_final: 0.8326 (mmm) REVERT: D 1145 MET cc_start: 0.8326 (mmp) cc_final: 0.8072 (mmp) REVERT: D 1194 MET cc_start: 0.8236 (ptt) cc_final: 0.6792 (ptp) REVERT: D 1199 THR cc_start: 0.8897 (m) cc_final: 0.8630 (t) REVERT: D 1217 ILE cc_start: 0.8559 (mt) cc_final: 0.8310 (mt) REVERT: D 1254 SER cc_start: 0.8406 (t) cc_final: 0.7934 (m) REVERT: D 1255 LEU cc_start: 0.9524 (mt) cc_final: 0.9283 (mt) REVERT: D 1281 LYS cc_start: 0.8952 (ptmm) cc_final: 0.8522 (mmmt) REVERT: E 645 ASP cc_start: 0.9301 (m-30) cc_final: 0.8274 (m-30) outliers start: 14 outliers final: 2 residues processed: 375 average time/residue: 0.6024 time to fit residues: 331.3581 Evaluate side-chains 239 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 5.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 249 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 186 HIS ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 529 GLN B 79 ASN B 157 ASN B 159 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 446 GLN ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN C1284 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D1074 ASN E 623 HIS E 677 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.113135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.083856 restraints weight = 87933.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087158 restraints weight = 51403.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.087932 restraints weight = 27755.602| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22130 Z= 0.248 Angle : 0.739 10.098 29785 Z= 0.396 Chirality : 0.046 0.220 3259 Planarity : 0.005 0.087 3932 Dihedral : 6.117 107.987 2987 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.27 % Allowed : 10.24 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.00 (0.16), residues: 2662 helix: 1.47 (0.13), residues: 1344 sheet: 0.01 (0.27), residues: 377 loop : -0.09 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 655 HIS 0.010 0.001 HIS A 508 PHE 0.023 0.002 PHE A 119 TYR 0.037 0.003 TYR D1065 ARG 0.010 0.001 ARG D 175 Details of bonding type rmsd hydrogen bonds : bond 0.06195 ( 1260) hydrogen bonds : angle 5.33802 ( 3738) covalent geometry : bond 0.00506 (22130) covalent geometry : angle 0.73891 (29785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8704 (m-30) cc_final: 0.8329 (p0) REVERT: A 69 MET cc_start: 0.9442 (tpp) cc_final: 0.9111 (ttm) REVERT: A 125 HIS cc_start: 0.8914 (m90) cc_final: 0.8424 (m-70) REVERT: A 131 ASP cc_start: 0.9169 (m-30) cc_final: 0.8647 (t0) REVERT: A 177 MET cc_start: 0.8206 (tmm) cc_final: 0.7236 (tmm) REVERT: A 185 ILE cc_start: 0.9553 (tt) cc_final: 0.9247 (tp) REVERT: A 189 PHE cc_start: 0.9214 (m-10) cc_final: 0.8865 (m-10) REVERT: A 229 MET cc_start: 0.8889 (mmm) cc_final: 0.8363 (mmm) REVERT: A 230 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8892 (mm) REVERT: A 260 MET cc_start: 0.8006 (tmm) cc_final: 0.7768 (tmm) REVERT: A 316 PHE cc_start: 0.9170 (m-80) cc_final: 0.8920 (m-10) REVERT: A 334 MET cc_start: 0.9006 (mmm) cc_final: 0.8709 (mmm) REVERT: A 339 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8889 (tp30) REVERT: A 340 MET cc_start: 0.9158 (mtp) cc_final: 0.8074 (mtp) REVERT: A 347 MET cc_start: 0.8858 (mmm) cc_final: 0.8410 (mmm) REVERT: A 456 ILE cc_start: 0.8562 (pt) cc_final: 0.8300 (pt) REVERT: A 480 MET cc_start: 0.9343 (mpp) cc_final: 0.9013 (mpp) REVERT: B 51 MET cc_start: 0.6690 (tmm) cc_final: 0.6489 (tmm) REVERT: B 73 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8240 (ttm) REVERT: B 80 CYS cc_start: 0.8161 (m) cc_final: 0.7645 (p) REVERT: B 83 MET cc_start: 0.8731 (mmp) cc_final: 0.8513 (mpp) REVERT: B 112 ILE cc_start: 0.9517 (mt) cc_final: 0.9282 (mm) REVERT: B 161 LYS cc_start: 0.9185 (mptt) cc_final: 0.8547 (mmtm) REVERT: B 217 TYR cc_start: 0.8267 (m-80) cc_final: 0.7886 (m-80) REVERT: B 374 TYR cc_start: 0.8698 (p90) cc_final: 0.8388 (p90) REVERT: B 445 VAL cc_start: 0.9503 (m) cc_final: 0.8806 (m) REVERT: B 483 MET cc_start: 0.9061 (ppp) cc_final: 0.8803 (ppp) REVERT: C 10 LEU cc_start: 0.8606 (mt) cc_final: 0.8317 (mt) REVERT: C 82 LYS cc_start: 0.8950 (mmtp) cc_final: 0.8395 (mmmt) REVERT: C 85 PHE cc_start: 0.9030 (p90) cc_final: 0.8369 (p90) REVERT: C 119 LEU cc_start: 0.9111 (mm) cc_final: 0.8630 (tt) REVERT: C 151 LEU cc_start: 0.9570 (mp) cc_final: 0.9282 (mp) REVERT: C 156 PHE cc_start: 0.8325 (m-10) cc_final: 0.8119 (m-10) REVERT: C 183 GLN cc_start: 0.9405 (mp10) cc_final: 0.8815 (pm20) REVERT: C 192 ILE cc_start: 0.9747 (mp) cc_final: 0.9455 (tp) REVERT: C 201 ASP cc_start: 0.9643 (t70) cc_final: 0.9345 (t0) REVERT: C 204 LYS cc_start: 0.9303 (pptt) cc_final: 0.9069 (pptt) REVERT: C 209 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8411 (ttp80) REVERT: C 1081 MET cc_start: 0.4024 (mmp) cc_final: 0.3179 (mmm) REVERT: C 1119 THR cc_start: 0.9255 (p) cc_final: 0.8741 (p) REVERT: C 1123 ILE cc_start: 0.9587 (pt) cc_final: 0.9353 (pt) REVERT: C 1130 MET cc_start: 0.7654 (mmm) cc_final: 0.7287 (tpt) REVERT: C 1144 MET cc_start: 0.8415 (mmm) cc_final: 0.7743 (mmm) REVERT: C 1194 MET cc_start: 0.6710 (ppp) cc_final: 0.5753 (ppp) REVERT: C 1212 LYS cc_start: 0.9071 (mttt) cc_final: 0.8779 (mmtm) REVERT: C 1247 ASN cc_start: 0.8881 (m-40) cc_final: 0.8597 (m110) REVERT: C 1258 ILE cc_start: 0.9177 (mt) cc_final: 0.8908 (pt) REVERT: D 26 ASN cc_start: 0.9312 (t0) cc_final: 0.8715 (p0) REVERT: D 31 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9020 (tp) REVERT: D 85 PHE cc_start: 0.8973 (p90) cc_final: 0.8101 (p90) REVERT: D 136 LEU cc_start: 0.9339 (mt) cc_final: 0.9026 (mt) REVERT: D 142 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8649 (mt-10) REVERT: D 151 LEU cc_start: 0.9104 (mt) cc_final: 0.8860 (mt) REVERT: D 1000 MET cc_start: 0.9446 (mtt) cc_final: 0.9174 (mmm) REVERT: D 1083 MET cc_start: 0.8915 (mmp) cc_final: 0.8368 (tmm) REVERT: D 1111 GLU cc_start: 0.9373 (mp0) cc_final: 0.9023 (pm20) REVERT: D 1138 MET cc_start: 0.8828 (mtm) cc_final: 0.8598 (tmm) REVERT: D 1193 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.6976 (t) REVERT: D 1194 MET cc_start: 0.8730 (ptt) cc_final: 0.8114 (ptt) REVERT: D 1199 THR cc_start: 0.8838 (m) cc_final: 0.8392 (p) REVERT: D 1203 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.4202 (ptm) REVERT: D 1219 ILE cc_start: 0.8209 (mt) cc_final: 0.7862 (tt) REVERT: D 1254 SER cc_start: 0.8275 (t) cc_final: 0.7471 (p) REVERT: D 1255 LEU cc_start: 0.9512 (mt) cc_final: 0.9209 (mt) REVERT: D 1281 LYS cc_start: 0.9130 (ptmm) cc_final: 0.8824 (mmmt) REVERT: D 1296 LYS cc_start: 0.8614 (tmmt) cc_final: 0.8368 (tmmt) REVERT: E 623 HIS cc_start: 0.6271 (m170) cc_final: 0.6056 (m-70) REVERT: E 645 ASP cc_start: 0.8781 (m-30) cc_final: 0.8576 (m-30) outliers start: 54 outliers final: 26 residues processed: 301 average time/residue: 0.3521 time to fit residues: 164.9163 Evaluate side-chains 246 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1217 ILE Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1193 SER Chi-restraints excluded: chain D residue 1203 MET Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Chi-restraints excluded: chain E residue 688 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 chunk 195 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 166 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1284 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.108506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.079590 restraints weight = 86290.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082418 restraints weight = 45693.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083142 restraints weight = 25035.384| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22130 Z= 0.173 Angle : 0.662 13.198 29785 Z= 0.347 Chirality : 0.043 0.201 3259 Planarity : 0.004 0.054 3932 Dihedral : 5.908 105.276 2984 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.93 % Allowed : 12.84 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.21 (0.16), residues: 2662 helix: 1.64 (0.13), residues: 1341 sheet: 0.10 (0.27), residues: 378 loop : 0.00 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 655 HIS 0.006 0.001 HIS A 216 PHE 0.021 0.002 PHE A 520 TYR 0.028 0.002 TYR D1065 ARG 0.007 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.05660 ( 1260) hydrogen bonds : angle 4.98991 ( 3738) covalent geometry : bond 0.00357 (22130) covalent geometry : angle 0.66171 (29785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9144 (ppp) cc_final: 0.8839 (ppp) REVERT: A 61 ASP cc_start: 0.8740 (m-30) cc_final: 0.8381 (p0) REVERT: A 69 MET cc_start: 0.9430 (tpp) cc_final: 0.9060 (ttm) REVERT: A 116 ILE cc_start: 0.9466 (mt) cc_final: 0.9220 (mm) REVERT: A 125 HIS cc_start: 0.8834 (m90) cc_final: 0.8322 (m-70) REVERT: A 131 ASP cc_start: 0.9162 (m-30) cc_final: 0.8582 (t0) REVERT: A 177 MET cc_start: 0.8325 (tmm) cc_final: 0.7236 (tmm) REVERT: A 185 ILE cc_start: 0.9593 (tt) cc_final: 0.9329 (tp) REVERT: A 229 MET cc_start: 0.8967 (mmm) cc_final: 0.8429 (mmm) REVERT: A 230 LEU cc_start: 0.9201 (mm) cc_final: 0.8726 (mm) REVERT: A 316 PHE cc_start: 0.9142 (m-80) cc_final: 0.8474 (m-80) REVERT: A 334 MET cc_start: 0.9058 (mmm) cc_final: 0.8588 (mmm) REVERT: A 339 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8648 (tp30) REVERT: A 454 LEU cc_start: 0.9348 (mp) cc_final: 0.9130 (mm) REVERT: A 456 ILE cc_start: 0.8621 (pt) cc_final: 0.8373 (pt) REVERT: B 51 MET cc_start: 0.6821 (tmm) cc_final: 0.6602 (tmm) REVERT: B 73 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8287 (ttm) REVERT: B 80 CYS cc_start: 0.8130 (m) cc_final: 0.7675 (p) REVERT: B 83 MET cc_start: 0.8879 (mmp) cc_final: 0.8551 (mpp) REVERT: B 112 ILE cc_start: 0.9515 (mt) cc_final: 0.9290 (mm) REVERT: B 161 LYS cc_start: 0.9168 (mptt) cc_final: 0.8485 (mmtm) REVERT: B 217 TYR cc_start: 0.8168 (m-80) cc_final: 0.7813 (m-80) REVERT: B 340 MET cc_start: 0.8475 (mmm) cc_final: 0.8112 (mmm) REVERT: B 374 TYR cc_start: 0.8629 (p90) cc_final: 0.8243 (p90) REVERT: B 386 ASN cc_start: 0.9008 (t0) cc_final: 0.8053 (t0) REVERT: B 445 VAL cc_start: 0.9298 (m) cc_final: 0.8581 (m) REVERT: B 449 PHE cc_start: 0.7068 (m-10) cc_final: 0.6797 (m-80) REVERT: B 483 MET cc_start: 0.9101 (ppp) cc_final: 0.8813 (ppp) REVERT: C 10 LEU cc_start: 0.8791 (mt) cc_final: 0.8495 (mp) REVERT: C 82 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8394 (mmmt) REVERT: C 85 PHE cc_start: 0.9020 (p90) cc_final: 0.8370 (p90) REVERT: C 119 LEU cc_start: 0.9132 (mm) cc_final: 0.8669 (tt) REVERT: C 151 LEU cc_start: 0.9552 (mp) cc_final: 0.9350 (mp) REVERT: C 156 PHE cc_start: 0.8318 (m-10) cc_final: 0.8105 (m-10) REVERT: C 183 GLN cc_start: 0.9290 (mp10) cc_final: 0.8887 (pm20) REVERT: C 192 ILE cc_start: 0.9747 (mp) cc_final: 0.9256 (tp) REVERT: C 202 GLU cc_start: 0.8664 (tt0) cc_final: 0.8221 (tt0) REVERT: C 209 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8585 (ttp80) REVERT: C 1119 THR cc_start: 0.8968 (p) cc_final: 0.8759 (p) REVERT: C 1130 MET cc_start: 0.7637 (mmm) cc_final: 0.7159 (tpt) REVERT: C 1144 MET cc_start: 0.8366 (mmm) cc_final: 0.7954 (mmm) REVERT: C 1194 MET cc_start: 0.6616 (ppp) cc_final: 0.5752 (ppp) REVERT: C 1247 ASN cc_start: 0.8973 (m-40) cc_final: 0.8629 (m110) REVERT: C 1258 ILE cc_start: 0.9207 (mt) cc_final: 0.8920 (pt) REVERT: D 26 ASN cc_start: 0.9226 (t0) cc_final: 0.8660 (p0) REVERT: D 31 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8979 (tp) REVERT: D 85 PHE cc_start: 0.8913 (p90) cc_final: 0.8084 (p90) REVERT: D 136 LEU cc_start: 0.9346 (mt) cc_final: 0.9126 (mt) REVERT: D 142 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8637 (mt-10) REVERT: D 151 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8801 (mt) REVERT: D 190 GLU cc_start: 0.8741 (pp20) cc_final: 0.8474 (pp20) REVERT: D 1022 ARG cc_start: 0.9013 (tpt170) cc_final: 0.8693 (tpt-90) REVERT: D 1111 GLU cc_start: 0.9360 (mp0) cc_final: 0.9049 (pm20) REVERT: D 1123 ILE cc_start: 0.9468 (tp) cc_final: 0.9256 (pt) REVERT: D 1130 MET cc_start: 0.8633 (mmt) cc_final: 0.8052 (mmm) REVERT: D 1138 MET cc_start: 0.8678 (mtm) cc_final: 0.8443 (tmm) REVERT: D 1185 ARG cc_start: 0.8691 (tpm170) cc_final: 0.7968 (mmm160) REVERT: D 1194 MET cc_start: 0.8724 (ptt) cc_final: 0.8407 (ptt) REVERT: D 1199 THR cc_start: 0.8798 (m) cc_final: 0.8390 (p) REVERT: D 1219 ILE cc_start: 0.8275 (mt) cc_final: 0.7926 (tt) REVERT: D 1255 LEU cc_start: 0.9509 (mt) cc_final: 0.9230 (mt) REVERT: D 1281 LYS cc_start: 0.8891 (ptmm) cc_final: 0.8498 (mmmt) REVERT: E 616 TYR cc_start: 0.8235 (m-80) cc_final: 0.7921 (m-80) REVERT: E 669 GLU cc_start: 0.7765 (mt-10) cc_final: 0.6975 (mp0) outliers start: 46 outliers final: 27 residues processed: 272 average time/residue: 0.5362 time to fit residues: 226.9862 Evaluate side-chains 250 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1185 ARG Chi-restraints excluded: chain C residue 1217 ILE Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1117 GLU Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Chi-restraints excluded: chain E residue 688 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 193 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 234 optimal weight: 0.6980 chunk 194 optimal weight: 0.0570 chunk 129 optimal weight: 0.6980 chunk 241 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C1284 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.112382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083308 restraints weight = 88524.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085538 restraints weight = 52033.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087533 restraints weight = 29633.161| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22130 Z= 0.172 Angle : 0.646 10.548 29785 Z= 0.339 Chirality : 0.042 0.187 3259 Planarity : 0.004 0.055 3932 Dihedral : 5.826 105.722 2984 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.31 % Allowed : 13.64 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.30 (0.16), residues: 2662 helix: 1.75 (0.13), residues: 1339 sheet: 0.09 (0.27), residues: 376 loop : 0.02 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 239 HIS 0.007 0.001 HIS A 216 PHE 0.023 0.002 PHE B 469 TYR 0.021 0.002 TYR D 281 ARG 0.005 0.000 ARG B 513 Details of bonding type rmsd hydrogen bonds : bond 0.05331 ( 1260) hydrogen bonds : angle 4.88328 ( 3738) covalent geometry : bond 0.00354 (22130) covalent geometry : angle 0.64635 (29785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9195 (ppp) cc_final: 0.8811 (ppp) REVERT: A 61 ASP cc_start: 0.8812 (m-30) cc_final: 0.8263 (p0) REVERT: A 69 MET cc_start: 0.9421 (tpp) cc_final: 0.9062 (ttm) REVERT: A 116 ILE cc_start: 0.9449 (mt) cc_final: 0.9200 (mm) REVERT: A 125 HIS cc_start: 0.8788 (m90) cc_final: 0.8260 (m-70) REVERT: A 131 ASP cc_start: 0.9186 (m-30) cc_final: 0.8546 (t0) REVERT: A 177 MET cc_start: 0.8314 (tmm) cc_final: 0.7345 (tmm) REVERT: A 185 ILE cc_start: 0.9608 (tt) cc_final: 0.9329 (tp) REVERT: A 203 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7905 (p) REVERT: A 229 MET cc_start: 0.8979 (mmm) cc_final: 0.8570 (mmm) REVERT: A 230 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 316 PHE cc_start: 0.9153 (m-80) cc_final: 0.8472 (m-80) REVERT: A 334 MET cc_start: 0.9100 (mmm) cc_final: 0.8580 (mmm) REVERT: A 339 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8972 (tp30) REVERT: A 340 MET cc_start: 0.9108 (mtp) cc_final: 0.7783 (mtp) REVERT: A 347 MET cc_start: 0.8930 (mmm) cc_final: 0.8514 (mmm) REVERT: A 371 LYS cc_start: 0.9181 (tttp) cc_final: 0.8936 (tppt) REVERT: A 456 ILE cc_start: 0.8133 (pt) cc_final: 0.7777 (pt) REVERT: A 483 MET cc_start: 0.9500 (mpp) cc_final: 0.9258 (mpp) REVERT: A 491 ARG cc_start: 0.9116 (ppt170) cc_final: 0.8863 (ppt170) REVERT: A 505 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9017 (mp) REVERT: B 73 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8269 (ttm) REVERT: B 80 CYS cc_start: 0.8233 (m) cc_final: 0.7697 (p) REVERT: B 83 MET cc_start: 0.8878 (mmp) cc_final: 0.8549 (mpp) REVERT: B 112 ILE cc_start: 0.9518 (mt) cc_final: 0.9296 (mm) REVERT: B 161 LYS cc_start: 0.9225 (mptt) cc_final: 0.8740 (mmtm) REVERT: B 217 TYR cc_start: 0.8198 (m-80) cc_final: 0.7900 (m-80) REVERT: B 334 MET cc_start: 0.9005 (mmm) cc_final: 0.8771 (mmm) REVERT: B 340 MET cc_start: 0.8838 (mmm) cc_final: 0.8561 (mmm) REVERT: B 374 TYR cc_start: 0.8675 (p90) cc_final: 0.8232 (p90) REVERT: B 445 VAL cc_start: 0.9293 (m) cc_final: 0.8751 (m) REVERT: B 483 MET cc_start: 0.9110 (ppp) cc_final: 0.8876 (ppp) REVERT: C 10 LEU cc_start: 0.8820 (mt) cc_final: 0.8471 (mp) REVERT: C 48 LYS cc_start: 0.9622 (ttmm) cc_final: 0.8942 (tmmt) REVERT: C 85 PHE cc_start: 0.9091 (p90) cc_final: 0.8413 (p90) REVERT: C 119 LEU cc_start: 0.9109 (mm) cc_final: 0.8657 (tt) REVERT: C 151 LEU cc_start: 0.9428 (mp) cc_final: 0.9152 (mp) REVERT: C 156 PHE cc_start: 0.8315 (m-10) cc_final: 0.7907 (m-10) REVERT: C 183 GLN cc_start: 0.9281 (mp10) cc_final: 0.9044 (pm20) REVERT: C 190 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8739 (mm-30) REVERT: C 202 GLU cc_start: 0.8695 (tt0) cc_final: 0.8216 (tt0) REVERT: C 204 LYS cc_start: 0.9469 (pptt) cc_final: 0.8990 (tptt) REVERT: C 1119 THR cc_start: 0.8966 (p) cc_final: 0.8684 (p) REVERT: C 1130 MET cc_start: 0.7627 (mmm) cc_final: 0.7339 (tpt) REVERT: C 1138 MET cc_start: 0.9472 (ptp) cc_final: 0.9178 (ptp) REVERT: C 1144 MET cc_start: 0.8532 (mmm) cc_final: 0.8298 (mmm) REVERT: C 1194 MET cc_start: 0.6557 (ppp) cc_final: 0.6183 (ppp) REVERT: C 1247 ASN cc_start: 0.8943 (m-40) cc_final: 0.8566 (m-40) REVERT: C 1258 ILE cc_start: 0.9179 (mt) cc_final: 0.8870 (pt) REVERT: D 26 ASN cc_start: 0.9256 (t0) cc_final: 0.8684 (p0) REVERT: D 31 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8981 (tp) REVERT: D 85 PHE cc_start: 0.8904 (p90) cc_final: 0.8088 (p90) REVERT: D 136 LEU cc_start: 0.9394 (mt) cc_final: 0.9173 (mt) REVERT: D 142 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8613 (mt-10) REVERT: D 150 ILE cc_start: 0.8981 (mp) cc_final: 0.8742 (pt) REVERT: D 151 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8810 (mt) REVERT: D 166 MET cc_start: 0.8915 (mmm) cc_final: 0.8553 (mmm) REVERT: D 190 GLU cc_start: 0.8675 (pp20) cc_final: 0.8425 (pp20) REVERT: D 1022 ARG cc_start: 0.8966 (tpt170) cc_final: 0.8600 (tpt-90) REVERT: D 1111 GLU cc_start: 0.9357 (mp0) cc_final: 0.9072 (mp0) REVERT: D 1138 MET cc_start: 0.8694 (mtm) cc_final: 0.8460 (tmm) REVERT: D 1189 ASN cc_start: 0.8734 (t0) cc_final: 0.8028 (t0) REVERT: D 1193 SER cc_start: 0.7555 (OUTLIER) cc_final: 0.6647 (t) REVERT: D 1194 MET cc_start: 0.8747 (ptt) cc_final: 0.8261 (ptt) REVERT: D 1199 THR cc_start: 0.8851 (m) cc_final: 0.8445 (p) REVERT: D 1255 LEU cc_start: 0.9555 (mt) cc_final: 0.9253 (mt) REVERT: D 1281 LYS cc_start: 0.8875 (ptmm) cc_final: 0.8509 (mmmt) REVERT: E 616 TYR cc_start: 0.8585 (m-80) cc_final: 0.8310 (m-80) REVERT: E 623 HIS cc_start: 0.6580 (m-70) cc_final: 0.6099 (m-70) outliers start: 55 outliers final: 35 residues processed: 271 average time/residue: 0.3597 time to fit residues: 149.8759 Evaluate side-chains 255 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1097 GLU Chi-restraints excluded: chain C residue 1117 GLU Chi-restraints excluded: chain C residue 1185 ARG Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1274 THR Chi-restraints excluded: chain C residue 1303 SER Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1117 GLU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1193 SER Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Chi-restraints excluded: chain E residue 688 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 166 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 160 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1284 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.112118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.082948 restraints weight = 89363.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085205 restraints weight = 53352.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086515 restraints weight = 30340.637| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22130 Z= 0.211 Angle : 0.659 9.998 29785 Z= 0.348 Chirality : 0.043 0.238 3259 Planarity : 0.004 0.061 3932 Dihedral : 5.858 106.366 2984 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.85 % Allowed : 13.34 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.27 (0.16), residues: 2662 helix: 1.75 (0.13), residues: 1353 sheet: -0.02 (0.27), residues: 373 loop : -0.01 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 239 HIS 0.010 0.001 HIS A 216 PHE 0.022 0.002 PHE A 520 TYR 0.026 0.002 TYR C 35 ARG 0.009 0.000 ARG C 209 Details of bonding type rmsd hydrogen bonds : bond 0.05215 ( 1260) hydrogen bonds : angle 4.86664 ( 3738) covalent geometry : bond 0.00432 (22130) covalent geometry : angle 0.65859 (29785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 226 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9059 (ppp) cc_final: 0.8677 (ppp) REVERT: A 61 ASP cc_start: 0.8812 (m-30) cc_final: 0.8234 (p0) REVERT: A 83 MET cc_start: 0.8506 (pmm) cc_final: 0.8240 (tmm) REVERT: A 116 ILE cc_start: 0.9387 (mt) cc_final: 0.9108 (mm) REVERT: A 125 HIS cc_start: 0.8748 (m90) cc_final: 0.8432 (m-70) REVERT: A 177 MET cc_start: 0.8365 (tmm) cc_final: 0.7351 (tmm) REVERT: A 185 ILE cc_start: 0.9575 (tt) cc_final: 0.9353 (tp) REVERT: A 203 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7993 (p) REVERT: A 229 MET cc_start: 0.8964 (mmm) cc_final: 0.8537 (mmm) REVERT: A 230 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8823 (mm) REVERT: A 316 PHE cc_start: 0.9217 (m-80) cc_final: 0.8951 (m-10) REVERT: A 334 MET cc_start: 0.9171 (mmm) cc_final: 0.8602 (mmm) REVERT: A 340 MET cc_start: 0.9040 (mtp) cc_final: 0.7898 (mtp) REVERT: A 454 LEU cc_start: 0.9429 (mm) cc_final: 0.9198 (mp) REVERT: A 456 ILE cc_start: 0.8525 (pt) cc_final: 0.8177 (pt) REVERT: A 480 MET cc_start: 0.9303 (mpp) cc_final: 0.9091 (mtt) REVERT: A 505 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9051 (mt) REVERT: A 511 ASP cc_start: 0.9447 (t0) cc_final: 0.9077 (m-30) REVERT: B 73 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8243 (ttm) REVERT: B 83 MET cc_start: 0.8939 (mmp) cc_final: 0.8584 (mpp) REVERT: B 161 LYS cc_start: 0.9187 (mptt) cc_final: 0.8541 (mmtm) REVERT: B 217 TYR cc_start: 0.8252 (m-80) cc_final: 0.8022 (m-80) REVERT: B 346 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8100 (pp20) REVERT: B 374 TYR cc_start: 0.8688 (p90) cc_final: 0.8237 (p90) REVERT: C 10 LEU cc_start: 0.8844 (mt) cc_final: 0.8601 (mp) REVERT: C 48 LYS cc_start: 0.9624 (ttmm) cc_final: 0.8984 (tmmt) REVERT: C 80 GLN cc_start: 0.8678 (tt0) cc_final: 0.8462 (mp-120) REVERT: C 85 PHE cc_start: 0.9019 (p90) cc_final: 0.8358 (p90) REVERT: C 119 LEU cc_start: 0.9100 (mm) cc_final: 0.8674 (tt) REVERT: C 190 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8446 (mm-30) REVERT: C 192 ILE cc_start: 0.9825 (OUTLIER) cc_final: 0.9306 (tp) REVERT: C 195 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9198 (mm) REVERT: C 202 GLU cc_start: 0.8731 (tt0) cc_final: 0.8225 (tt0) REVERT: C 204 LYS cc_start: 0.9500 (pptt) cc_final: 0.9215 (tttt) REVERT: C 209 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8330 (mmp80) REVERT: C 1119 THR cc_start: 0.9005 (p) cc_final: 0.8693 (p) REVERT: C 1130 MET cc_start: 0.7856 (mmm) cc_final: 0.7460 (tpt) REVERT: C 1194 MET cc_start: 0.6641 (ppp) cc_final: 0.6296 (ppp) REVERT: C 1247 ASN cc_start: 0.8919 (m-40) cc_final: 0.8491 (m-40) REVERT: D 26 ASN cc_start: 0.9267 (t0) cc_final: 0.8732 (p0) REVERT: D 31 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9000 (tp) REVERT: D 85 PHE cc_start: 0.8939 (p90) cc_final: 0.8151 (p90) REVERT: D 136 LEU cc_start: 0.9451 (mt) cc_final: 0.9185 (mt) REVERT: D 142 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8651 (mt-10) REVERT: D 150 ILE cc_start: 0.9014 (mp) cc_final: 0.8755 (pt) REVERT: D 151 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8827 (mt) REVERT: D 163 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8757 (mp) REVERT: D 166 MET cc_start: 0.8924 (mmm) cc_final: 0.8578 (mmm) REVERT: D 190 GLU cc_start: 0.8658 (pp20) cc_final: 0.8408 (pp20) REVERT: D 348 GLU cc_start: 0.9812 (OUTLIER) cc_final: 0.9585 (pm20) REVERT: D 986 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8737 (mt) REVERT: D 1022 ARG cc_start: 0.8610 (tpt170) cc_final: 0.8253 (tpt-90) REVERT: D 1094 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8980 (tt) REVERT: D 1111 GLU cc_start: 0.9371 (mp0) cc_final: 0.9105 (mp0) REVERT: D 1123 ILE cc_start: 0.9499 (tp) cc_final: 0.9287 (pt) REVERT: D 1138 MET cc_start: 0.8687 (mtm) cc_final: 0.8483 (tmm) REVERT: D 1189 ASN cc_start: 0.8736 (t0) cc_final: 0.8063 (t0) REVERT: D 1194 MET cc_start: 0.8916 (ptt) cc_final: 0.8202 (ptt) REVERT: D 1199 THR cc_start: 0.8831 (m) cc_final: 0.8418 (p) REVERT: D 1219 ILE cc_start: 0.8454 (mt) cc_final: 0.8065 (tt) REVERT: D 1255 LEU cc_start: 0.9565 (mt) cc_final: 0.9276 (mt) REVERT: D 1281 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8819 (mmmt) REVERT: E 616 TYR cc_start: 0.8625 (m-80) cc_final: 0.8324 (m-80) REVERT: E 623 HIS cc_start: 0.6910 (m-70) cc_final: 0.6583 (m-70) REVERT: E 669 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7291 (mp0) outliers start: 68 outliers final: 37 residues processed: 280 average time/residue: 0.3733 time to fit residues: 162.7043 Evaluate side-chains 261 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1185 ARG Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1274 THR Chi-restraints excluded: chain C residue 1303 SER Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1094 LEU Chi-restraints excluded: chain D residue 1117 GLU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Chi-restraints excluded: chain E residue 688 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 141 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 173 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1284 GLN ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.112545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083229 restraints weight = 88851.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085363 restraints weight = 53668.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086881 restraints weight = 32053.140| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22130 Z= 0.199 Angle : 0.670 15.582 29785 Z= 0.353 Chirality : 0.043 0.390 3259 Planarity : 0.004 0.054 3932 Dihedral : 5.820 106.754 2983 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.73 % Allowed : 14.39 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.26 (0.16), residues: 2662 helix: 1.74 (0.13), residues: 1355 sheet: -0.01 (0.27), residues: 379 loop : -0.05 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 164 HIS 0.009 0.001 HIS A 216 PHE 0.021 0.002 PHE A 520 TYR 0.023 0.002 TYR D 281 ARG 0.005 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 1260) hydrogen bonds : angle 4.83792 ( 3738) covalent geometry : bond 0.00408 (22130) covalent geometry : angle 0.67046 (29785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9068 (ppp) cc_final: 0.8627 (ppp) REVERT: A 61 ASP cc_start: 0.8825 (m-30) cc_final: 0.8154 (p0) REVERT: A 83 MET cc_start: 0.8508 (pmm) cc_final: 0.8257 (tmm) REVERT: A 116 ILE cc_start: 0.9376 (mt) cc_final: 0.9092 (mm) REVERT: A 125 HIS cc_start: 0.8786 (m90) cc_final: 0.8445 (m-70) REVERT: A 177 MET cc_start: 0.8354 (tmm) cc_final: 0.7372 (tmm) REVERT: A 184 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7968 (tpt90) REVERT: A 185 ILE cc_start: 0.9550 (tt) cc_final: 0.9323 (tp) REVERT: A 203 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8037 (p) REVERT: A 229 MET cc_start: 0.9043 (mmm) cc_final: 0.8609 (mmm) REVERT: A 230 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8326 (mm) REVERT: A 316 PHE cc_start: 0.9251 (m-80) cc_final: 0.8990 (m-10) REVERT: A 334 MET cc_start: 0.8829 (mmm) cc_final: 0.8418 (mmm) REVERT: A 340 MET cc_start: 0.8969 (mtp) cc_final: 0.8311 (mtp) REVERT: A 347 MET cc_start: 0.8619 (mmm) cc_final: 0.8217 (mmm) REVERT: A 448 PHE cc_start: 0.8663 (m-80) cc_final: 0.8332 (m-80) REVERT: A 456 ILE cc_start: 0.8260 (pt) cc_final: 0.7901 (pt) REVERT: A 480 MET cc_start: 0.9282 (mpp) cc_final: 0.8960 (mtt) REVERT: A 511 ASP cc_start: 0.9452 (t0) cc_final: 0.9095 (m-30) REVERT: B 73 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8219 (ttm) REVERT: B 83 MET cc_start: 0.8939 (mmp) cc_final: 0.8551 (mpp) REVERT: B 161 LYS cc_start: 0.9195 (mptt) cc_final: 0.8759 (mmtm) REVERT: B 217 TYR cc_start: 0.8482 (m-80) cc_final: 0.8122 (m-80) REVERT: B 334 MET cc_start: 0.8976 (mmm) cc_final: 0.8696 (mmm) REVERT: B 374 TYR cc_start: 0.8635 (p90) cc_final: 0.8257 (p90) REVERT: B 483 MET cc_start: 0.9021 (ppp) cc_final: 0.8774 (ppp) REVERT: B 491 ARG cc_start: 0.9070 (tpm170) cc_final: 0.8655 (tpm170) REVERT: C 10 LEU cc_start: 0.8840 (mt) cc_final: 0.8468 (mp) REVERT: C 48 LYS cc_start: 0.9591 (ttmm) cc_final: 0.9060 (ttpt) REVERT: C 80 GLN cc_start: 0.8820 (tt0) cc_final: 0.8101 (mp10) REVERT: C 85 PHE cc_start: 0.9030 (p90) cc_final: 0.8385 (p90) REVERT: C 119 LEU cc_start: 0.9129 (mm) cc_final: 0.8694 (tt) REVERT: C 156 PHE cc_start: 0.8214 (m-10) cc_final: 0.7885 (m-10) REVERT: C 190 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8368 (mm-30) REVERT: C 192 ILE cc_start: 0.9716 (OUTLIER) cc_final: 0.8960 (tp) REVERT: C 202 GLU cc_start: 0.8705 (tt0) cc_final: 0.8193 (tt0) REVERT: C 204 LYS cc_start: 0.9503 (pptt) cc_final: 0.9214 (tttt) REVERT: C 1119 THR cc_start: 0.9015 (p) cc_final: 0.8674 (p) REVERT: C 1130 MET cc_start: 0.7881 (mmm) cc_final: 0.7467 (tpt) REVERT: C 1152 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8475 (tp) REVERT: C 1247 ASN cc_start: 0.8930 (m-40) cc_final: 0.8490 (m-40) REVERT: D 26 ASN cc_start: 0.9256 (t0) cc_final: 0.8745 (p0) REVERT: D 31 LEU cc_start: 0.9244 (mm) cc_final: 0.8957 (tp) REVERT: D 54 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8307 (tm-30) REVERT: D 83 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9283 (mm) REVERT: D 85 PHE cc_start: 0.8907 (p90) cc_final: 0.8101 (p90) REVERT: D 136 LEU cc_start: 0.9395 (mt) cc_final: 0.9082 (mt) REVERT: D 142 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8678 (mt-10) REVERT: D 150 ILE cc_start: 0.9068 (mp) cc_final: 0.8785 (pt) REVERT: D 151 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8815 (mt) REVERT: D 163 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 166 MET cc_start: 0.8738 (mmm) cc_final: 0.8403 (mmm) REVERT: D 188 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7898 (p) REVERT: D 190 GLU cc_start: 0.8642 (pp20) cc_final: 0.8386 (pp20) REVERT: D 986 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8723 (mt) REVERT: D 1079 ARG cc_start: 0.9193 (mmt180) cc_final: 0.8855 (mmt180) REVERT: D 1111 GLU cc_start: 0.9409 (mp0) cc_final: 0.9069 (mp0) REVERT: D 1189 ASN cc_start: 0.8744 (t0) cc_final: 0.8044 (t0) REVERT: D 1199 THR cc_start: 0.8807 (m) cc_final: 0.8448 (p) REVERT: D 1219 ILE cc_start: 0.8300 (mt) cc_final: 0.8096 (tt) REVERT: D 1255 LEU cc_start: 0.9548 (mt) cc_final: 0.9268 (mt) REVERT: E 623 HIS cc_start: 0.6965 (m-70) cc_final: 0.6638 (m-70) outliers start: 65 outliers final: 37 residues processed: 273 average time/residue: 0.3360 time to fit residues: 141.1247 Evaluate side-chains 254 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1185 ARG Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1274 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1193 SER Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Chi-restraints excluded: chain E residue 688 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 4 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 186 optimal weight: 0.7980 chunk 185 optimal weight: 0.3980 chunk 35 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 242 optimal weight: 0.5980 chunk 264 optimal weight: 0.0170 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN C 106 ASN C1269 GLN ** C1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.104628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.076152 restraints weight = 86634.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078373 restraints weight = 46148.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.079441 restraints weight = 26968.511| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22130 Z= 0.138 Angle : 0.687 15.282 29785 Z= 0.352 Chirality : 0.043 0.263 3259 Planarity : 0.004 0.055 3932 Dihedral : 5.694 106.370 2983 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.10 % Allowed : 15.15 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.33 (0.16), residues: 2662 helix: 1.76 (0.13), residues: 1358 sheet: 0.12 (0.27), residues: 380 loop : 0.00 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 164 HIS 0.009 0.001 HIS A 216 PHE 0.036 0.002 PHE A 520 TYR 0.023 0.002 TYR C 35 ARG 0.005 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 1260) hydrogen bonds : angle 4.68098 ( 3738) covalent geometry : bond 0.00278 (22130) covalent geometry : angle 0.68693 (29785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9111 (ppp) cc_final: 0.8581 (ppp) REVERT: A 61 ASP cc_start: 0.8948 (m-30) cc_final: 0.8212 (p0) REVERT: A 83 MET cc_start: 0.8517 (pmm) cc_final: 0.8260 (tmm) REVERT: A 116 ILE cc_start: 0.9268 (mt) cc_final: 0.9004 (pt) REVERT: A 125 HIS cc_start: 0.8849 (m90) cc_final: 0.8462 (m-70) REVERT: A 177 MET cc_start: 0.8283 (tmm) cc_final: 0.7318 (tmm) REVERT: A 185 ILE cc_start: 0.9530 (tt) cc_final: 0.9275 (tp) REVERT: A 203 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7748 (p) REVERT: A 229 MET cc_start: 0.9138 (mmm) cc_final: 0.8679 (mmm) REVERT: A 316 PHE cc_start: 0.9203 (m-80) cc_final: 0.8452 (m-80) REVERT: A 334 MET cc_start: 0.8809 (mmm) cc_final: 0.8427 (mmm) REVERT: A 340 MET cc_start: 0.8922 (mtp) cc_final: 0.7973 (mtp) REVERT: A 448 PHE cc_start: 0.8661 (m-80) cc_final: 0.8238 (m-80) REVERT: A 456 ILE cc_start: 0.8588 (pt) cc_final: 0.8268 (pt) REVERT: A 480 MET cc_start: 0.9279 (mpp) cc_final: 0.8925 (mtt) REVERT: A 483 MET cc_start: 0.9457 (mpp) cc_final: 0.9237 (pmm) REVERT: A 505 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9084 (mt) REVERT: A 511 ASP cc_start: 0.9441 (t0) cc_final: 0.9059 (m-30) REVERT: B 73 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8236 (ttm) REVERT: B 83 MET cc_start: 0.8838 (mmp) cc_final: 0.8565 (mpp) REVERT: B 161 LYS cc_start: 0.9174 (mptt) cc_final: 0.8680 (mmtm) REVERT: B 177 MET cc_start: 0.7637 (tmm) cc_final: 0.7131 (tmm) REVERT: B 197 TYR cc_start: 0.9031 (m-10) cc_final: 0.8592 (m-10) REVERT: B 217 TYR cc_start: 0.8324 (m-80) cc_final: 0.8106 (m-80) REVERT: B 229 MET cc_start: 0.8641 (mmm) cc_final: 0.7997 (ptp) REVERT: B 334 MET cc_start: 0.8990 (mmm) cc_final: 0.8690 (mmm) REVERT: B 347 MET cc_start: 0.8757 (ppp) cc_final: 0.8516 (ppp) REVERT: B 374 TYR cc_start: 0.8601 (p90) cc_final: 0.8246 (p90) REVERT: B 473 ASP cc_start: 0.9548 (t0) cc_final: 0.9111 (m-30) REVERT: B 483 MET cc_start: 0.8968 (ppp) cc_final: 0.8671 (ppp) REVERT: B 491 ARG cc_start: 0.9217 (tpm170) cc_final: 0.8877 (tpm170) REVERT: C 10 LEU cc_start: 0.8808 (mt) cc_final: 0.8423 (mp) REVERT: C 23 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8949 (mp) REVERT: C 48 LYS cc_start: 0.9424 (ttmm) cc_final: 0.8990 (ttpt) REVERT: C 80 GLN cc_start: 0.8761 (tt0) cc_final: 0.8402 (mp10) REVERT: C 85 PHE cc_start: 0.9162 (p90) cc_final: 0.8451 (p90) REVERT: C 119 LEU cc_start: 0.9135 (mm) cc_final: 0.8686 (tt) REVERT: C 156 PHE cc_start: 0.8151 (m-10) cc_final: 0.7799 (m-10) REVERT: C 190 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8238 (mm-30) REVERT: C 192 ILE cc_start: 0.9731 (OUTLIER) cc_final: 0.8954 (tp) REVERT: C 202 GLU cc_start: 0.8648 (tt0) cc_final: 0.8148 (tt0) REVERT: C 204 LYS cc_start: 0.9402 (pptt) cc_final: 0.9175 (tttt) REVERT: C 1119 THR cc_start: 0.8978 (p) cc_final: 0.8572 (p) REVERT: C 1130 MET cc_start: 0.7823 (mmm) cc_final: 0.7402 (tpt) REVERT: C 1152 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8412 (tp) REVERT: C 1165 ILE cc_start: 0.7538 (mt) cc_final: 0.7111 (mm) REVERT: C 1247 ASN cc_start: 0.8922 (m-40) cc_final: 0.8575 (m-40) REVERT: D 26 ASN cc_start: 0.9124 (t0) cc_final: 0.8674 (p0) REVERT: D 31 LEU cc_start: 0.9188 (mm) cc_final: 0.8937 (tp) REVERT: D 54 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8345 (tm-30) REVERT: D 85 PHE cc_start: 0.8858 (p90) cc_final: 0.8007 (p90) REVERT: D 136 LEU cc_start: 0.9450 (mt) cc_final: 0.9155 (mt) REVERT: D 142 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8599 (mt-10) REVERT: D 150 ILE cc_start: 0.9097 (mp) cc_final: 0.8870 (pt) REVERT: D 151 LEU cc_start: 0.9218 (mt) cc_final: 0.8783 (mt) REVERT: D 166 MET cc_start: 0.9070 (mmm) cc_final: 0.8756 (mmm) REVERT: D 188 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7737 (p) REVERT: D 190 GLU cc_start: 0.8583 (pp20) cc_final: 0.8300 (pp20) REVERT: D 986 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8718 (mt) REVERT: D 1111 GLU cc_start: 0.9359 (mp0) cc_final: 0.9085 (mp0) REVERT: D 1185 ARG cc_start: 0.8579 (tpm170) cc_final: 0.7704 (mmm160) REVERT: D 1189 ASN cc_start: 0.8693 (t0) cc_final: 0.8000 (t0) REVERT: D 1199 THR cc_start: 0.8860 (m) cc_final: 0.8496 (p) REVERT: D 1255 LEU cc_start: 0.9546 (mt) cc_final: 0.9248 (mt) REVERT: E 623 HIS cc_start: 0.6909 (m-70) cc_final: 0.6668 (m-70) outliers start: 50 outliers final: 28 residues processed: 260 average time/residue: 0.3446 time to fit residues: 140.6420 Evaluate side-chains 245 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1117 GLU Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1303 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Chi-restraints excluded: chain E residue 688 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 198 optimal weight: 0.0870 chunk 98 optimal weight: 0.9990 chunk 177 optimal weight: 0.4980 chunk 174 optimal weight: 0.4980 chunk 208 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 245 optimal weight: 0.0770 chunk 185 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.104303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.074680 restraints weight = 88422.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077003 restraints weight = 50426.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.078151 restraints weight = 28762.143| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22130 Z= 0.151 Angle : 0.688 15.370 29785 Z= 0.352 Chirality : 0.043 0.234 3259 Planarity : 0.004 0.055 3932 Dihedral : 5.670 106.734 2983 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.85 % Allowed : 15.74 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.33 (0.16), residues: 2662 helix: 1.77 (0.13), residues: 1364 sheet: 0.15 (0.27), residues: 380 loop : -0.02 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 164 HIS 0.004 0.001 HIS D1113 PHE 0.032 0.002 PHE B 449 TYR 0.023 0.001 TYR D 281 ARG 0.005 0.000 ARG D1186 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 1260) hydrogen bonds : angle 4.67580 ( 3738) covalent geometry : bond 0.00309 (22130) covalent geometry : angle 0.68806 (29785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9069 (ppp) cc_final: 0.8550 (ppp) REVERT: A 61 ASP cc_start: 0.8960 (m-30) cc_final: 0.8201 (p0) REVERT: A 83 MET cc_start: 0.8500 (pmm) cc_final: 0.8275 (tmm) REVERT: A 116 ILE cc_start: 0.9335 (mt) cc_final: 0.9092 (pt) REVERT: A 125 HIS cc_start: 0.8836 (m90) cc_final: 0.8468 (m-70) REVERT: A 177 MET cc_start: 0.8311 (tmm) cc_final: 0.7294 (tmm) REVERT: A 185 ILE cc_start: 0.9536 (tt) cc_final: 0.9280 (tp) REVERT: A 203 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7573 (p) REVERT: A 229 MET cc_start: 0.9197 (mmm) cc_final: 0.8712 (mmm) REVERT: A 316 PHE cc_start: 0.9226 (m-80) cc_final: 0.8455 (m-80) REVERT: A 334 MET cc_start: 0.8802 (mmm) cc_final: 0.8422 (mmm) REVERT: A 340 MET cc_start: 0.8947 (mtp) cc_final: 0.8378 (mtp) REVERT: A 448 PHE cc_start: 0.8669 (m-80) cc_final: 0.8226 (m-80) REVERT: A 456 ILE cc_start: 0.8606 (pt) cc_final: 0.8305 (pt) REVERT: A 480 MET cc_start: 0.9270 (mpp) cc_final: 0.8924 (mtt) REVERT: A 483 MET cc_start: 0.9473 (mpp) cc_final: 0.9193 (pmm) REVERT: A 505 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9118 (mp) REVERT: A 511 ASP cc_start: 0.9507 (t0) cc_final: 0.9073 (m-30) REVERT: B 73 MET cc_start: 0.8709 (mtp) cc_final: 0.8215 (ttm) REVERT: B 83 MET cc_start: 0.8855 (mmp) cc_final: 0.8556 (mpp) REVERT: B 161 LYS cc_start: 0.9176 (mptt) cc_final: 0.8702 (mmtm) REVERT: B 177 MET cc_start: 0.7559 (tmm) cc_final: 0.7102 (tmm) REVERT: B 197 TYR cc_start: 0.9087 (m-10) cc_final: 0.8651 (m-10) REVERT: B 217 TYR cc_start: 0.8365 (m-80) cc_final: 0.8140 (m-80) REVERT: B 340 MET cc_start: 0.8418 (mmm) cc_final: 0.7966 (mmt) REVERT: B 347 MET cc_start: 0.8719 (ppp) cc_final: 0.8485 (ppp) REVERT: B 374 TYR cc_start: 0.8610 (p90) cc_final: 0.8351 (p90) REVERT: B 483 MET cc_start: 0.8917 (ppp) cc_final: 0.8592 (ppp) REVERT: B 491 ARG cc_start: 0.9226 (tpm170) cc_final: 0.8938 (tpm170) REVERT: C 10 LEU cc_start: 0.8761 (mt) cc_final: 0.8348 (mp) REVERT: C 48 LYS cc_start: 0.9448 (ttmm) cc_final: 0.9002 (ttpt) REVERT: C 80 GLN cc_start: 0.8687 (tt0) cc_final: 0.8422 (mp10) REVERT: C 85 PHE cc_start: 0.9169 (p90) cc_final: 0.8464 (p90) REVERT: C 119 LEU cc_start: 0.9157 (mm) cc_final: 0.8704 (tt) REVERT: C 156 PHE cc_start: 0.8181 (m-10) cc_final: 0.7860 (m-10) REVERT: C 190 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8257 (mm-30) REVERT: C 192 ILE cc_start: 0.9726 (OUTLIER) cc_final: 0.8950 (tp) REVERT: C 202 GLU cc_start: 0.8663 (tt0) cc_final: 0.8190 (tt0) REVERT: C 204 LYS cc_start: 0.9417 (pptt) cc_final: 0.9191 (tttt) REVERT: C 1117 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8690 (pm20) REVERT: C 1119 THR cc_start: 0.9001 (p) cc_final: 0.8568 (p) REVERT: C 1130 MET cc_start: 0.7833 (mmm) cc_final: 0.7420 (tpt) REVERT: C 1152 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8441 (tp) REVERT: C 1165 ILE cc_start: 0.7588 (mt) cc_final: 0.7203 (mm) REVERT: C 1194 MET cc_start: 0.4290 (ppp) cc_final: 0.3297 (ppp) REVERT: C 1247 ASN cc_start: 0.8946 (m-40) cc_final: 0.8598 (m-40) REVERT: D 26 ASN cc_start: 0.9113 (t0) cc_final: 0.8672 (p0) REVERT: D 31 LEU cc_start: 0.9196 (mm) cc_final: 0.8953 (tp) REVERT: D 54 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8403 (tm-30) REVERT: D 85 PHE cc_start: 0.8861 (p90) cc_final: 0.8081 (p90) REVERT: D 136 LEU cc_start: 0.9437 (mt) cc_final: 0.9184 (mt) REVERT: D 142 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8628 (mt-10) REVERT: D 150 ILE cc_start: 0.9060 (mp) cc_final: 0.8843 (pt) REVERT: D 151 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8876 (mt) REVERT: D 166 MET cc_start: 0.9009 (mmm) cc_final: 0.8714 (mmm) REVERT: D 188 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7746 (p) REVERT: D 190 GLU cc_start: 0.8618 (pp20) cc_final: 0.8332 (pp20) REVERT: D 986 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8738 (mt) REVERT: D 1079 ARG cc_start: 0.9498 (mmt180) cc_final: 0.8965 (tpp-160) REVERT: D 1111 GLU cc_start: 0.9370 (mp0) cc_final: 0.9099 (mp0) REVERT: D 1123 ILE cc_start: 0.9507 (tp) cc_final: 0.9299 (pt) REVERT: D 1189 ASN cc_start: 0.8720 (t0) cc_final: 0.8025 (t0) REVERT: D 1199 THR cc_start: 0.8881 (m) cc_final: 0.8527 (p) REVERT: D 1219 ILE cc_start: 0.7796 (tt) cc_final: 0.7501 (tp) REVERT: D 1255 LEU cc_start: 0.9545 (mt) cc_final: 0.9241 (mt) REVERT: E 616 TYR cc_start: 0.8229 (m-80) cc_final: 0.7756 (m-80) REVERT: E 623 HIS cc_start: 0.6874 (m-70) cc_final: 0.6620 (m-70) outliers start: 44 outliers final: 27 residues processed: 248 average time/residue: 0.3556 time to fit residues: 139.0208 Evaluate side-chains 251 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1117 GLU Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1303 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Chi-restraints excluded: chain E residue 688 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 255 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 259 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 120 optimal weight: 0.0770 chunk 215 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.102644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072506 restraints weight = 87477.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074553 restraints weight = 52508.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.075869 restraints weight = 31914.212| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22130 Z= 0.190 Angle : 0.709 15.560 29785 Z= 0.364 Chirality : 0.044 0.515 3259 Planarity : 0.004 0.054 3932 Dihedral : 5.731 107.670 2983 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.01 % Allowed : 15.95 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.26 (0.16), residues: 2662 helix: 1.69 (0.13), residues: 1364 sheet: 0.16 (0.28), residues: 374 loop : -0.07 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 239 HIS 0.005 0.001 HIS B 216 PHE 0.044 0.002 PHE A 520 TYR 0.024 0.002 TYR D 281 ARG 0.006 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 1260) hydrogen bonds : angle 4.75897 ( 3738) covalent geometry : bond 0.00389 (22130) covalent geometry : angle 0.70908 (29785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8532 (mmm160) cc_final: 0.8031 (tpt90) REVERT: A 51 MET cc_start: 0.9044 (ppp) cc_final: 0.8561 (ppp) REVERT: A 61 ASP cc_start: 0.8972 (m-30) cc_final: 0.8011 (p0) REVERT: A 83 MET cc_start: 0.8467 (pmm) cc_final: 0.8143 (tmm) REVERT: A 131 ASP cc_start: 0.8472 (p0) cc_final: 0.8212 (p0) REVERT: A 177 MET cc_start: 0.8354 (tmm) cc_final: 0.7340 (tmm) REVERT: A 203 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7680 (p) REVERT: A 229 MET cc_start: 0.9149 (mmm) cc_final: 0.8603 (mmm) REVERT: A 316 PHE cc_start: 0.9287 (m-80) cc_final: 0.9017 (m-10) REVERT: A 334 MET cc_start: 0.8831 (mmm) cc_final: 0.8432 (mmm) REVERT: A 340 MET cc_start: 0.8979 (mtp) cc_final: 0.8424 (mtp) REVERT: A 448 PHE cc_start: 0.8673 (m-80) cc_final: 0.8246 (m-80) REVERT: A 456 ILE cc_start: 0.8652 (pt) cc_final: 0.8365 (pt) REVERT: A 480 MET cc_start: 0.9230 (mpp) cc_final: 0.8935 (mtt) REVERT: A 505 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9049 (mp) REVERT: A 511 ASP cc_start: 0.9521 (t0) cc_final: 0.9093 (m-30) REVERT: B 73 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8183 (ttm) REVERT: B 83 MET cc_start: 0.8941 (mmp) cc_final: 0.8562 (mpp) REVERT: B 161 LYS cc_start: 0.9202 (mptt) cc_final: 0.8782 (mmtm) REVERT: B 177 MET cc_start: 0.7573 (tmm) cc_final: 0.7091 (tmm) REVERT: B 340 MET cc_start: 0.8472 (mmm) cc_final: 0.8012 (mmt) REVERT: B 347 MET cc_start: 0.8662 (ppp) cc_final: 0.8293 (ppp) REVERT: B 374 TYR cc_start: 0.8758 (p90) cc_final: 0.8467 (p90) REVERT: B 386 ASN cc_start: 0.8751 (t0) cc_final: 0.8291 (t0) REVERT: B 483 MET cc_start: 0.8895 (ppp) cc_final: 0.8290 (ppp) REVERT: B 484 ASP cc_start: 0.9524 (t0) cc_final: 0.8877 (m-30) REVERT: B 491 ARG cc_start: 0.9196 (tpm170) cc_final: 0.8965 (tpm170) REVERT: C 10 LEU cc_start: 0.8791 (mt) cc_final: 0.8396 (mp) REVERT: C 80 GLN cc_start: 0.8667 (tt0) cc_final: 0.8355 (mp10) REVERT: C 85 PHE cc_start: 0.9179 (p90) cc_final: 0.8537 (p90) REVERT: C 107 ASN cc_start: 0.9120 (p0) cc_final: 0.8805 (p0) REVERT: C 119 LEU cc_start: 0.9185 (mm) cc_final: 0.8744 (tt) REVERT: C 190 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8322 (mm-30) REVERT: C 192 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.8952 (tp) REVERT: C 202 GLU cc_start: 0.8809 (tt0) cc_final: 0.8357 (tt0) REVERT: C 204 LYS cc_start: 0.9443 (pptt) cc_final: 0.9220 (tttt) REVERT: C 1119 THR cc_start: 0.9017 (p) cc_final: 0.8762 (p) REVERT: C 1130 MET cc_start: 0.7897 (mmm) cc_final: 0.7492 (tpt) REVERT: C 1152 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8492 (tp) REVERT: C 1165 ILE cc_start: 0.7644 (mt) cc_final: 0.7250 (mm) REVERT: C 1194 MET cc_start: 0.4563 (ppp) cc_final: 0.3520 (ppp) REVERT: C 1247 ASN cc_start: 0.8921 (m-40) cc_final: 0.8577 (m-40) REVERT: D 26 ASN cc_start: 0.9133 (t0) cc_final: 0.8699 (p0) REVERT: D 31 LEU cc_start: 0.9186 (mm) cc_final: 0.8948 (tp) REVERT: D 54 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8491 (tm-30) REVERT: D 85 PHE cc_start: 0.9023 (p90) cc_final: 0.8211 (p90) REVERT: D 136 LEU cc_start: 0.9364 (mt) cc_final: 0.9076 (mt) REVERT: D 150 ILE cc_start: 0.9108 (mp) cc_final: 0.8894 (pt) REVERT: D 151 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8858 (mt) REVERT: D 166 MET cc_start: 0.9031 (mmm) cc_final: 0.8750 (mmm) REVERT: D 167 SER cc_start: 0.9424 (m) cc_final: 0.8722 (p) REVERT: D 188 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7797 (p) REVERT: D 190 GLU cc_start: 0.8644 (pp20) cc_final: 0.8358 (pp20) REVERT: D 986 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8760 (mt) REVERT: D 1000 MET cc_start: 0.9254 (mmm) cc_final: 0.9000 (ptp) REVERT: D 1189 ASN cc_start: 0.8720 (t0) cc_final: 0.8042 (t0) REVERT: D 1199 THR cc_start: 0.8906 (m) cc_final: 0.8699 (t) REVERT: D 1219 ILE cc_start: 0.7844 (tt) cc_final: 0.7509 (tp) REVERT: D 1255 LEU cc_start: 0.9533 (mt) cc_final: 0.9220 (mt) outliers start: 48 outliers final: 31 residues processed: 253 average time/residue: 0.3371 time to fit residues: 134.7698 Evaluate side-chains 243 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1097 GLU Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1274 THR Chi-restraints excluded: chain C residue 1303 SER Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Chi-restraints excluded: chain E residue 688 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 118 optimal weight: 0.8980 chunk 119 optimal weight: 0.0980 chunk 75 optimal weight: 0.0050 chunk 148 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1074 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.103631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073852 restraints weight = 88575.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076704 restraints weight = 52104.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077409 restraints weight = 30126.378| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22130 Z= 0.183 Angle : 0.722 15.549 29785 Z= 0.370 Chirality : 0.044 0.394 3259 Planarity : 0.004 0.053 3932 Dihedral : 5.742 107.855 2983 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.76 % Allowed : 16.32 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.28 (0.16), residues: 2662 helix: 1.72 (0.13), residues: 1359 sheet: 0.13 (0.28), residues: 377 loop : -0.04 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 239 HIS 0.006 0.001 HIS E 623 PHE 0.021 0.002 PHE D 25 TYR 0.027 0.002 TYR C 35 ARG 0.007 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 1260) hydrogen bonds : angle 4.77602 ( 3738) covalent geometry : bond 0.00377 (22130) covalent geometry : angle 0.72171 (29785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8042 (tpt90) REVERT: A 51 MET cc_start: 0.9037 (ppp) cc_final: 0.8555 (ppp) REVERT: A 61 ASP cc_start: 0.8986 (m-30) cc_final: 0.8070 (p0) REVERT: A 125 HIS cc_start: 0.8588 (m170) cc_final: 0.8325 (m-70) REVERT: A 131 ASP cc_start: 0.8359 (p0) cc_final: 0.8124 (p0) REVERT: A 177 MET cc_start: 0.8425 (tmm) cc_final: 0.7324 (tmm) REVERT: A 203 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7584 (p) REVERT: A 229 MET cc_start: 0.9127 (mmm) cc_final: 0.8601 (mmm) REVERT: A 316 PHE cc_start: 0.9235 (m-80) cc_final: 0.8953 (m-10) REVERT: A 334 MET cc_start: 0.8826 (mmm) cc_final: 0.8430 (mmm) REVERT: A 340 MET cc_start: 0.8969 (mtp) cc_final: 0.8428 (mtp) REVERT: A 448 PHE cc_start: 0.8673 (m-80) cc_final: 0.8209 (m-80) REVERT: A 456 ILE cc_start: 0.8673 (pt) cc_final: 0.8398 (pt) REVERT: A 480 MET cc_start: 0.9232 (mpp) cc_final: 0.8942 (mtt) REVERT: A 505 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9030 (mp) REVERT: B 73 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8226 (ttm) REVERT: B 83 MET cc_start: 0.8950 (mmp) cc_final: 0.8598 (mpp) REVERT: B 161 LYS cc_start: 0.9183 (mptt) cc_final: 0.8762 (mmtm) REVERT: B 197 TYR cc_start: 0.9095 (m-10) cc_final: 0.8724 (m-10) REVERT: B 217 TYR cc_start: 0.8682 (m-80) cc_final: 0.8371 (m-80) REVERT: B 340 MET cc_start: 0.8414 (mmm) cc_final: 0.8138 (mmt) REVERT: B 347 MET cc_start: 0.8643 (ppp) cc_final: 0.8293 (ppp) REVERT: B 374 TYR cc_start: 0.8750 (p90) cc_final: 0.8448 (p90) REVERT: B 386 ASN cc_start: 0.8766 (t0) cc_final: 0.8314 (t0) REVERT: B 483 MET cc_start: 0.8906 (ppp) cc_final: 0.8289 (ppp) REVERT: B 484 ASP cc_start: 0.9525 (t0) cc_final: 0.8849 (m-30) REVERT: C 10 LEU cc_start: 0.8772 (mt) cc_final: 0.8407 (mp) REVERT: C 48 LYS cc_start: 0.9440 (ttmm) cc_final: 0.8896 (tmmt) REVERT: C 80 GLN cc_start: 0.8712 (tt0) cc_final: 0.8344 (mp10) REVERT: C 85 PHE cc_start: 0.9173 (p90) cc_final: 0.8525 (p90) REVERT: C 107 ASN cc_start: 0.9095 (p0) cc_final: 0.8785 (p0) REVERT: C 119 LEU cc_start: 0.9170 (mm) cc_final: 0.8738 (tt) REVERT: C 156 PHE cc_start: 0.8185 (m-10) cc_final: 0.7948 (m-10) REVERT: C 190 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8371 (mm-30) REVERT: C 192 ILE cc_start: 0.9722 (OUTLIER) cc_final: 0.8938 (tp) REVERT: C 202 GLU cc_start: 0.8775 (tt0) cc_final: 0.8383 (tt0) REVERT: C 1117 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8799 (pm20) REVERT: C 1119 THR cc_start: 0.9028 (p) cc_final: 0.8757 (p) REVERT: C 1130 MET cc_start: 0.7888 (mmm) cc_final: 0.7507 (tpt) REVERT: C 1152 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8541 (tp) REVERT: C 1165 ILE cc_start: 0.7663 (mt) cc_final: 0.7274 (mm) REVERT: C 1194 MET cc_start: 0.4709 (ppp) cc_final: 0.3639 (ppp) REVERT: C 1247 ASN cc_start: 0.8891 (m-40) cc_final: 0.8544 (m-40) REVERT: D 26 ASN cc_start: 0.9130 (t0) cc_final: 0.8697 (p0) REVERT: D 31 LEU cc_start: 0.9197 (mm) cc_final: 0.8969 (tp) REVERT: D 85 PHE cc_start: 0.8950 (p90) cc_final: 0.8177 (p90) REVERT: D 136 LEU cc_start: 0.9395 (mt) cc_final: 0.9118 (mt) REVERT: D 150 ILE cc_start: 0.9075 (mp) cc_final: 0.8865 (pt) REVERT: D 151 LEU cc_start: 0.9284 (mt) cc_final: 0.8869 (mt) REVERT: D 166 MET cc_start: 0.9021 (mmm) cc_final: 0.8736 (mmm) REVERT: D 167 SER cc_start: 0.9328 (m) cc_final: 0.8657 (p) REVERT: D 986 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8753 (mt) REVERT: D 1189 ASN cc_start: 0.9029 (t0) cc_final: 0.8759 (t0) REVERT: D 1199 THR cc_start: 0.8999 (m) cc_final: 0.8798 (t) REVERT: D 1219 ILE cc_start: 0.7894 (tt) cc_final: 0.7558 (tp) REVERT: D 1255 LEU cc_start: 0.9539 (mt) cc_final: 0.9227 (mt) outliers start: 42 outliers final: 31 residues processed: 241 average time/residue: 0.3307 time to fit residues: 125.2709 Evaluate side-chains 239 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1097 GLU Chi-restraints excluded: chain C residue 1117 GLU Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1274 THR Chi-restraints excluded: chain C residue 1303 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1048 GLU Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 676 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 205 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 6 optimal weight: 0.2980 chunk 219 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 262 optimal weight: 0.5980 chunk 257 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 ASN D1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.103522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.073733 restraints weight = 88458.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076763 restraints weight = 51755.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077562 restraints weight = 29844.204| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22130 Z= 0.178 Angle : 0.733 16.798 29785 Z= 0.378 Chirality : 0.044 0.364 3259 Planarity : 0.004 0.053 3932 Dihedral : 5.738 107.855 2983 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.68 % Allowed : 16.74 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.30 (0.16), residues: 2662 helix: 1.75 (0.13), residues: 1353 sheet: 0.14 (0.28), residues: 377 loop : -0.04 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 164 HIS 0.007 0.001 HIS A 216 PHE 0.021 0.002 PHE D 25 TYR 0.023 0.002 TYR D 281 ARG 0.007 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 1260) hydrogen bonds : angle 4.78774 ( 3738) covalent geometry : bond 0.00368 (22130) covalent geometry : angle 0.73281 (29785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7846.78 seconds wall clock time: 141 minutes 27.99 seconds (8487.99 seconds total)