Starting phenix.real_space_refine on Wed Feb 21 23:48:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/02_2024/7zr1_14881_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/02_2024/7zr1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/02_2024/7zr1_14881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/02_2024/7zr1_14881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/02_2024/7zr1_14881_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/02_2024/7zr1_14881_updated.pdb" } 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 Residue "A TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C GLU 1117": "OE1" <-> "OE2" Residue "C GLU 1146": "OE1" <-> "OE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 11.40, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.14 Conformation dependent library (CDL) restraints added in 4.1 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... running ksdssp... Secondary structure from input PDB file: 75 helices and 16 sheets defined 52.1% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 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 66 through 80 removed outlier: 3.706A pdb=" N VAL A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 97 No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.835A pdb=" N LEU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 272 through 275 Processing helix chain 'A' and resid 327 through 351 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 387 through 394 removed outlier: 4.765A pdb=" N PHE A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 459 through 471 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 476 through 494 removed outlier: 3.501A pdb=" N GLY A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 506 through 520 removed outlier: 3.511A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.627A pdb=" N ARG A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.998A pdb=" N SER B 33 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TRP B 34 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG B 35 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.528A pdb=" N GLN B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 removed outlier: 3.538A pdb=" N VAL B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 137 through 143 removed outlier: 4.025A pdb=" N VAL B 142 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.603A pdb=" N ARG B 190 " --> pdb=" O HIS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 326 through 351 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 354 through 357 removed outlier: 3.875A pdb=" N ASP B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 357' Processing helix chain 'B' and resid 387 through 394 removed outlier: 4.399A pdb=" N PHE B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 450 removed outlier: 4.112A pdb=" N ALA B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 471 removed outlier: 3.655A pdb=" N VAL B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 495 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 526 through 531 removed outlier: 4.023A pdb=" N ARG B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 546 No H-bonds generated for 'chain 'B' and resid 543 through 546' Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 553 through 555 No H-bonds generated for 'chain 'B' and resid 553 through 555' Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 69 through 72 No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.859A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 169 through 179 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 182 through 292 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 300 through 376 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 388 through 412 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 972 removed outlier: 3.809A pdb=" N ILE C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 1050 removed outlier: 3.913A pdb=" N ALA C1019 " --> pdb=" O ASP C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1105 removed outlier: 3.795A pdb=" N GLU C1089 " --> pdb=" O SER C1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1159 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 1209 through 1227 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 1245 through 1265 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 1277 through 1286 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) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.771A pdb=" N ILE D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 133 through 144 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 148 through 153 Processing helix chain 'D' and resid 160 through 166 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 169 through 179 Processing helix chain 'D' and resid 182 through 206 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) Processing helix chain 'D' and resid 208 through 292 removed outlier: 3.765A pdb=" N ARG D 219 " --> pdb=" O ASN D 216 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 221 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS D 241 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 267 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 377 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 388 through 411 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 972 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 1050 removed outlier: 3.938A pdb=" N LYS D1021 " --> pdb=" O ASP D1018 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D1028 " --> pdb=" O ALA D1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1105 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) Processing helix chain 'D' and resid 1107 through 1158 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 1209 through 1227 Processing helix chain 'D' and resid 1245 through 1262 Processing helix chain 'D' and resid 1277 through 1285 removed outlier: 3.737A pdb=" N MET D1283 " --> pdb=" O PHE D1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 622 Processing helix chain 'E' and resid 642 through 648 Processing helix chain 'E' and resid 653 through 655 No H-bonds generated for 'chain 'E' and resid 653 through 655' Processing sheet with id= A, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.584A pdb=" N MET A 51 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 281 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 159 through 161 removed outlier: 7.071A pdb=" N ARG A 195 " --> pdb=" O VAL A 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 163 through 167 removed outlier: 5.997A pdb=" N PHE A 207 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR A 175 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 209 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET A 177 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR A 211 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 236 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LEU A 212 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 238 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N HIS A 258 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TRP A 239 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N MET A 260 " --> pdb=" O TRP A 239 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 303 through 309 removed outlier: 6.650A pdb=" N LEU A 367 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ARG A 306 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG A 369 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE A 308 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS A 371 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.656A pdb=" N MET B 51 " --> pdb=" O ARG B 11 " (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= F, first strand: chain 'B' and resid 159 through 161 removed outlier: 7.212A pdb=" N ARG B 195 " --> pdb=" O VAL B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.261A pdb=" N PHE B 207 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR B 175 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 209 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N MET B 177 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 211 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 236 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU B 212 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 238 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N HIS B 258 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N TRP B 239 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N MET B 260 " --> pdb=" O TRP B 239 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 303 through 309 removed outlier: 6.560A pdb=" N LEU B 367 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ARG B 306 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 369 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE B 308 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS B 371 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 372 " --> pdb=" O HIS B 406 " (cutoff:3.500A) Processing sheet with id= I, 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: 3.581A pdb=" N SER C 117 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER C 130 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C 120 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL C 128 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 1303 through 1308 removed outlier: 3.618A pdb=" N VAL C1306 " --> pdb=" O ARG C1294 " (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: 6.613A pdb=" N LEU C1270 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE C 32 " --> pdb=" O LEU C1270 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C1272 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLY C 34 " --> pdb=" O VAL C1272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C1273 " --> pdb=" O LEU C1236 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.562A pdb=" N LEU C 102 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id= L, 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= M, 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: 3.940A pdb=" N SER D 130 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 120 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL D 128 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN D 122 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG D 126 " --> pdb=" O ASN D 122 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 1303 through 1308 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) removed outlier: 6.781A pdb=" N LEU D1270 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE D 32 " --> pdb=" O LEU D1270 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D1272 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N GLY D 34 " --> pdb=" O VAL D1272 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 99 through 102 removed outlier: 3.972A pdb=" N THR D 110 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 1167 through 1170 1145 hydrogen bonds defined for protein. 2892 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: 7.96 Time building geometry restraints manager: 9.47 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: 97.56 - 104.93: 327 104.93 - 112.29: 10966 112.29 - 119.66: 8337 119.66 - 127.02: 9936 127.02 - 134.39: 219 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: 107 2.49 - 3.09: 17347 3.09 - 3.70: 34473 3.70 - 4.30: 49053 4.30 - 4.90: 76782 Nonbonded interactions: 177762 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 177757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 13.820 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 57.160 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.120 ------------------------------------------------------------------------------- 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 *********************** 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 fitting. rotamer outliers: 14 poor density : 365 time to evaluate : 2.334 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: 0.4230 time to fit residues: 232.3356 Evaluate side-chains 239 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 2.779 ------------------------------------------------------------------------------- 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: 3.9990 chunk 201 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN B 79 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 341 GLN C1051 ASN C1284 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 270 ASN E 623 HIS E 677 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 0.047 22130 Z= 0.352 Angle : 0.731 10.096 29785 Z= 0.394 Chirality : 0.045 0.214 3259 Planarity : 0.006 0.054 3932 Dihedral : 6.075 102.955 2987 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.93 % Allowed : 12.00 % Favored : 86.07 % 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: 0.63 (0.16), residues: 2662 helix: 1.01 (0.13), residues: 1331 sheet: -0.04 (0.26), residues: 379 loop : -0.06 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C1156 HIS 0.008 0.001 HIS A 216 PHE 0.023 0.002 PHE A 119 TYR 0.036 0.003 TYR D1065 ARG 0.006 0.001 ARG D 121 *********************** 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 301 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 255 time to evaluate : 2.931 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 23 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8287 (mt-10) REVERT: A 39 GLU cc_start: 0.9027 (tp30) cc_final: 0.8666 (tp30) REVERT: A 51 MET cc_start: 0.9215 (ppp) cc_final: 0.8864 (ppp) REVERT: A 61 ASP cc_start: 0.8806 (m-30) cc_final: 0.7921 (p0) REVERT: A 125 HIS cc_start: 0.9189 (m90) cc_final: 0.8573 (m-70) REVERT: A 131 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8591 (t0) REVERT: A 169 LYS cc_start: 0.8983 (tppt) cc_final: 0.8673 (tppt) REVERT: A 177 MET cc_start: 0.8147 (tmm) cc_final: 0.7004 (tmm) REVERT: A 185 ILE cc_start: 0.9585 (tt) cc_final: 0.9229 (tp) REVERT: A 189 PHE cc_start: 0.9159 (m-10) cc_final: 0.8831 (m-10) REVERT: A 229 MET cc_start: 0.8456 (mmm) cc_final: 0.8127 (mmm) REVERT: A 230 LEU cc_start: 0.9458 (mm) cc_final: 0.9157 (mm) REVERT: A 242 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7653 (mp0) REVERT: A 260 MET cc_start: 0.8280 (tmm) cc_final: 0.7914 (tmm) REVERT: A 316 PHE cc_start: 0.9300 (m-80) cc_final: 0.9068 (m-10) REVERT: A 334 MET cc_start: 0.8778 (mmm) cc_final: 0.8492 (mmm) REVERT: A 339 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8923 (tp30) REVERT: A 340 MET cc_start: 0.9048 (mtp) cc_final: 0.7667 (mtp) REVERT: A 347 MET cc_start: 0.8849 (mmm) cc_final: 0.8315 (mmm) REVERT: A 371 LYS cc_start: 0.9340 (tttp) cc_final: 0.8904 (tptt) REVERT: A 480 MET cc_start: 0.9324 (mpp) cc_final: 0.8930 (mpp) REVERT: B 51 MET cc_start: 0.6928 (tmm) cc_final: 0.6657 (tmm) REVERT: B 73 MET cc_start: 0.8803 (mtp) cc_final: 0.8015 (ttm) REVERT: B 80 CYS cc_start: 0.8131 (m) cc_final: 0.7675 (p) REVERT: B 83 MET cc_start: 0.8954 (mmp) cc_final: 0.8480 (mpp) REVERT: B 88 LEU cc_start: 0.9439 (mt) cc_final: 0.9236 (mt) REVERT: B 157 ASN cc_start: 0.8472 (t0) cc_final: 0.8013 (p0) REVERT: B 161 LYS cc_start: 0.9213 (mptt) cc_final: 0.8589 (mmtm) REVERT: B 217 TYR cc_start: 0.8478 (m-80) cc_final: 0.8097 (m-80) REVERT: B 442 ASP cc_start: 0.8137 (m-30) cc_final: 0.7849 (m-30) REVERT: B 445 VAL cc_start: 0.9122 (m) cc_final: 0.7934 (m) REVERT: C 3 LYS cc_start: 0.8895 (mttt) cc_final: 0.8641 (mmtt) REVERT: C 119 LEU cc_start: 0.9128 (mm) cc_final: 0.8571 (tt) REVERT: C 155 ILE cc_start: 0.9355 (mt) cc_final: 0.9018 (tt) REVERT: C 156 PHE cc_start: 0.8489 (m-10) cc_final: 0.8051 (m-10) REVERT: C 192 ILE cc_start: 0.9030 (mp) cc_final: 0.8642 (tp) REVERT: C 204 LYS cc_start: 0.8715 (pptt) cc_final: 0.8407 (pptt) REVERT: C 1081 MET cc_start: 0.3681 (mmp) cc_final: 0.2908 (mmm) REVERT: C 1119 THR cc_start: 0.8806 (p) cc_final: 0.8197 (p) REVERT: C 1144 MET cc_start: 0.8315 (mmm) cc_final: 0.7731 (mmm) REVERT: C 1194 MET cc_start: 0.6937 (ppp) cc_final: 0.5894 (ppp) REVERT: C 1212 LYS cc_start: 0.9212 (mttt) cc_final: 0.8993 (mmtm) REVERT: C 1247 ASN cc_start: 0.8853 (m-40) cc_final: 0.8517 (m-40) REVERT: D 26 ASN cc_start: 0.9358 (t0) cc_final: 0.8583 (p0) REVERT: D 83 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9375 (mm) REVERT: D 85 PHE cc_start: 0.9219 (p90) cc_final: 0.8095 (p90) REVERT: D 93 TYR cc_start: 0.9316 (m-80) cc_final: 0.8422 (m-80) REVERT: D 136 LEU cc_start: 0.9475 (mt) cc_final: 0.9234 (mt) REVERT: D 142 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8416 (mp0) REVERT: D 1083 MET cc_start: 0.8761 (mmp) cc_final: 0.8561 (ppp) REVERT: D 1111 GLU cc_start: 0.8729 (mp0) cc_final: 0.8510 (pm20) REVERT: D 1144 MET cc_start: 0.8808 (mmp) cc_final: 0.8583 (mmm) REVERT: D 1145 MET cc_start: 0.8515 (mmp) cc_final: 0.8295 (mmp) REVERT: D 1194 MET cc_start: 0.8897 (ptt) cc_final: 0.8373 (ptt) REVERT: D 1199 THR cc_start: 0.8731 (m) cc_final: 0.8327 (p) REVERT: D 1201 MET cc_start: 0.9346 (ptm) cc_final: 0.9139 (ppp) REVERT: D 1203 MET cc_start: 0.4564 (OUTLIER) cc_final: 0.3163 (ptm) REVERT: D 1219 ILE cc_start: 0.8060 (mt) cc_final: 0.7851 (tt) REVERT: D 1254 SER cc_start: 0.8416 (t) cc_final: 0.7565 (p) REVERT: D 1255 LEU cc_start: 0.9543 (mt) cc_final: 0.9242 (mt) REVERT: D 1281 LYS cc_start: 0.8940 (ptmm) cc_final: 0.8563 (mmmt) REVERT: D 1296 LYS cc_start: 0.8366 (tmmt) cc_final: 0.8163 (tmmt) outliers start: 46 outliers final: 25 residues processed: 291 average time/residue: 0.3484 time to fit residues: 158.2947 Evaluate side-chains 244 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP 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 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 C residue 1284 GLN Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE 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 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 201 optimal weight: 0.0970 chunk 164 optimal weight: 0.0870 chunk 66 optimal weight: 0.1980 chunk 241 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 239 optimal weight: 0.5980 chunk 82 optimal weight: 0.0000 chunk 194 optimal weight: 0.4980 overall best weight: 0.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN B 159 HIS ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** E 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22130 Z= 0.185 Angle : 0.631 14.073 29785 Z= 0.332 Chirality : 0.042 0.192 3259 Planarity : 0.005 0.068 3932 Dihedral : 5.697 102.130 2984 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.59 % Allowed : 13.72 % Favored : 84.68 % 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: 0.86 (0.16), residues: 2662 helix: 1.13 (0.14), residues: 1331 sheet: 0.26 (0.26), residues: 378 loop : 0.06 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 164 HIS 0.009 0.001 HIS A 216 PHE 0.019 0.002 PHE A 512 TYR 0.028 0.002 TYR D1065 ARG 0.008 0.000 ARG B 190 *********************** 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 273 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 2.397 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: 0.9172 (ppp) cc_final: 0.8847 (ppp) REVERT: A 61 ASP cc_start: 0.8758 (m-30) cc_final: 0.7910 (p0) REVERT: A 125 HIS cc_start: 0.9148 (m90) cc_final: 0.8496 (m-70) REVERT: A 131 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8458 (t0) REVERT: A 177 MET cc_start: 0.8354 (tmm) cc_final: 0.7008 (tmm) REVERT: A 185 ILE cc_start: 0.9576 (tt) cc_final: 0.9250 (tp) REVERT: A 217 TYR cc_start: 0.7669 (m-10) cc_final: 0.7337 (m-80) REVERT: A 229 MET cc_start: 0.8558 (mmm) cc_final: 0.8171 (mmm) REVERT: A 230 LEU cc_start: 0.9465 (mm) cc_final: 0.9143 (mm) REVERT: A 304 VAL cc_start: 0.9649 (OUTLIER) cc_final: 0.9180 (m) REVERT: A 316 PHE cc_start: 0.9253 (m-80) cc_final: 0.8547 (m-80) REVERT: A 334 MET cc_start: 0.8834 (mmm) cc_final: 0.8337 (mmm) REVERT: A 339 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8662 (tp30) REVERT: A 340 MET cc_start: 0.9014 (mtp) cc_final: 0.7255 (mtp) REVERT: A 371 LYS cc_start: 0.9198 (tttp) cc_final: 0.8818 (tptt) REVERT: A 374 TYR cc_start: 0.8530 (p90) cc_final: 0.8244 (p90) REVERT: A 480 MET cc_start: 0.9308 (mpp) cc_final: 0.8885 (mpp) REVERT: B 73 MET cc_start: 0.8757 (mtp) cc_final: 0.7902 (ttm) REVERT: B 80 CYS cc_start: 0.7991 (m) cc_final: 0.7589 (p) REVERT: B 83 MET cc_start: 0.8877 (mmp) cc_final: 0.8655 (mmp) REVERT: B 88 LEU cc_start: 0.9137 (mt) cc_final: 0.8917 (mt) REVERT: B 161 LYS cc_start: 0.9172 (mptt) cc_final: 0.8525 (mmtm) REVERT: B 217 TYR cc_start: 0.8308 (m-80) cc_final: 0.7922 (m-80) REVERT: B 340 MET cc_start: 0.8357 (mmm) cc_final: 0.8113 (mmm) REVERT: B 397 LYS cc_start: 0.9614 (mmmt) cc_final: 0.9332 (mmtm) REVERT: B 442 ASP cc_start: 0.7989 (m-30) cc_final: 0.7728 (m-30) REVERT: B 445 VAL cc_start: 0.8730 (m) cc_final: 0.7833 (m) REVERT: B 473 ASP cc_start: 0.8829 (m-30) cc_final: 0.8466 (t0) REVERT: C 3 LYS cc_start: 0.8881 (mttt) cc_final: 0.8631 (mmtt) REVERT: C 7 LEU cc_start: 0.8985 (tt) cc_final: 0.8091 (tp) REVERT: C 82 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8265 (mmmm) REVERT: C 85 PHE cc_start: 0.9019 (p90) cc_final: 0.8425 (p90) REVERT: C 119 LEU cc_start: 0.9111 (mm) cc_final: 0.8638 (tt) REVERT: C 155 ILE cc_start: 0.9283 (mt) cc_final: 0.8836 (tt) REVERT: C 156 PHE cc_start: 0.8296 (m-10) cc_final: 0.7819 (m-10) REVERT: C 192 ILE cc_start: 0.8950 (mp) cc_final: 0.8478 (tp) REVERT: C 202 GLU cc_start: 0.7330 (tt0) cc_final: 0.6821 (tt0) REVERT: C 204 LYS cc_start: 0.8778 (pptt) cc_final: 0.8260 (tptt) REVERT: C 248 MET cc_start: 0.6461 (mmp) cc_final: 0.6249 (mmp) REVERT: C 1119 THR cc_start: 0.8468 (p) cc_final: 0.8187 (p) REVERT: C 1144 MET cc_start: 0.8254 (mmm) cc_final: 0.7825 (mmm) REVERT: C 1194 MET cc_start: 0.6902 (ppp) cc_final: 0.5985 (ppp) REVERT: C 1247 ASN cc_start: 0.8868 (m-40) cc_final: 0.8361 (m110) REVERT: C 1284 GLN cc_start: 0.8224 (pp30) cc_final: 0.7949 (pp30) REVERT: D 26 ASN cc_start: 0.9303 (t0) cc_final: 0.8525 (p0) REVERT: D 85 PHE cc_start: 0.9113 (p90) cc_final: 0.8218 (p90) REVERT: D 136 LEU cc_start: 0.9479 (mt) cc_final: 0.9231 (mt) REVERT: D 142 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8399 (mp0) REVERT: D 1145 MET cc_start: 0.8315 (mmp) cc_final: 0.8108 (mmp) REVERT: D 1194 MET cc_start: 0.8989 (ptt) cc_final: 0.8379 (ptt) REVERT: D 1199 THR cc_start: 0.8693 (m) cc_final: 0.8293 (p) REVERT: D 1203 MET cc_start: 0.4287 (OUTLIER) cc_final: 0.2877 (ptm) REVERT: D 1227 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8406 (m-80) REVERT: D 1255 LEU cc_start: 0.9524 (mt) cc_final: 0.9215 (mt) REVERT: E 623 HIS cc_start: 0.6039 (m-70) cc_final: 0.5561 (m-70) outliers start: 38 outliers final: 19 residues processed: 262 average time/residue: 0.3522 time to fit residues: 140.5306 Evaluate side-chains 239 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 304 VAL 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 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 60 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1174 VAL Chi-restraints excluded: chain D residue 1203 MET Chi-restraints excluded: chain D residue 1227 PHE 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 239 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 242 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 202 GLN ** 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** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN ** C1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1187 ASN C1284 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 22130 Z= 0.511 Angle : 0.810 12.187 29785 Z= 0.431 Chirality : 0.045 0.194 3259 Planarity : 0.006 0.052 3932 Dihedral : 5.999 103.031 2983 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.73 % Allowed : 15.19 % Favored : 81.07 % 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: 0.33 (0.16), residues: 2662 helix: 0.69 (0.14), residues: 1336 sheet: -0.22 (0.26), residues: 376 loop : -0.04 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 34 HIS 0.011 0.002 HIS B 216 PHE 0.025 0.003 PHE A 520 TYR 0.023 0.003 TYR D 281 ARG 0.011 0.001 ARG A 409 *********************** 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 314 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 225 time to evaluate : 2.639 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 23 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8277 (mt-10) REVERT: A 51 MET cc_start: 0.9149 (ppp) cc_final: 0.8900 (ppp) REVERT: A 61 ASP cc_start: 0.8876 (m-30) cc_final: 0.7840 (p0) REVERT: A 177 MET cc_start: 0.8674 (tmm) cc_final: 0.7458 (tmm) REVERT: A 185 ILE cc_start: 0.9660 (tt) cc_final: 0.9356 (tp) REVERT: A 229 MET cc_start: 0.8771 (mmm) cc_final: 0.8359 (mmm) REVERT: A 230 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9233 (mm) REVERT: A 316 PHE cc_start: 0.9379 (m-80) cc_final: 0.9156 (m-10) REVERT: A 334 MET cc_start: 0.8775 (mmm) cc_final: 0.8435 (mmm) REVERT: A 340 MET cc_start: 0.9158 (mtp) cc_final: 0.7622 (mtp) REVERT: A 347 MET cc_start: 0.9071 (mmm) cc_final: 0.8616 (mmm) REVERT: B 51 MET cc_start: 0.7323 (tmm) cc_final: 0.6583 (tmm) REVERT: B 61 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.7575 (p0) REVERT: B 73 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8081 (ttm) REVERT: B 88 LEU cc_start: 0.9082 (mt) cc_final: 0.8584 (tp) REVERT: B 161 LYS cc_start: 0.9306 (mptt) cc_final: 0.8755 (mmtm) REVERT: B 217 TYR cc_start: 0.8739 (m-80) cc_final: 0.8438 (m-80) REVERT: B 239 TRP cc_start: 0.8407 (OUTLIER) cc_final: 0.8021 (m-10) REVERT: B 442 ASP cc_start: 0.8096 (m-30) cc_final: 0.7872 (m-30) REVERT: C 6 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8092 (tppt) REVERT: C 136 LEU cc_start: 0.9201 (mt) cc_final: 0.8974 (mp) REVERT: C 155 ILE cc_start: 0.9307 (mt) cc_final: 0.8958 (tt) REVERT: C 156 PHE cc_start: 0.8626 (m-10) cc_final: 0.8228 (m-10) REVERT: C 192 ILE cc_start: 0.8849 (mp) cc_final: 0.7972 (mp) REVERT: C 202 GLU cc_start: 0.7461 (tt0) cc_final: 0.7032 (tt0) REVERT: C 1119 THR cc_start: 0.8604 (p) cc_final: 0.8234 (p) REVERT: C 1152 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8171 (pt) REVERT: C 1194 MET cc_start: 0.6527 (ppp) cc_final: 0.6080 (ppp) REVERT: C 1247 ASN cc_start: 0.8840 (m-40) cc_final: 0.8297 (m110) REVERT: D 26 ASN cc_start: 0.9371 (t0) cc_final: 0.9148 (t0) REVERT: D 85 PHE cc_start: 0.9208 (p90) cc_final: 0.8454 (p90) REVERT: D 142 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8611 (mt-10) REVERT: D 1079 ARG cc_start: 0.9031 (mmt180) cc_final: 0.8508 (tpp-160) REVERT: D 1194 MET cc_start: 0.8609 (ptt) cc_final: 0.8388 (ptt) REVERT: D 1199 THR cc_start: 0.8789 (m) cc_final: 0.8415 (p) REVERT: D 1203 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.4664 (ptm) REVERT: D 1219 ILE cc_start: 0.7870 (tt) cc_final: 0.7618 (tp) REVERT: D 1255 LEU cc_start: 0.9579 (mt) cc_final: 0.9320 (mt) REVERT: E 623 HIS cc_start: 0.6500 (m-70) cc_final: 0.5975 (m-70) outliers start: 89 outliers final: 56 residues processed: 291 average time/residue: 0.3464 time to fit residues: 155.1435 Evaluate side-chains 264 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 201 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLU 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 61 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 TRP 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 B residue 548 HIS Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 95 VAL 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 1055 ASP 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 1251 LEU Chi-restraints excluded: chain C residue 1274 THR Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1303 SER Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 35 TYR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 1055 ASP Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1201 MET Chi-restraints excluded: chain D residue 1203 MET 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 D residue 1258 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 641 THR Chi-restraints excluded: chain E residue 645 ASP Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 ASP 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 214 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 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 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN C 341 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22130 Z= 0.268 Angle : 0.665 10.627 29785 Z= 0.349 Chirality : 0.042 0.324 3259 Planarity : 0.005 0.053 3932 Dihedral : 5.726 102.168 2983 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.81 % Allowed : 17.37 % Favored : 79.82 % 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: 0.55 (0.16), residues: 2662 helix: 0.85 (0.14), residues: 1340 sheet: -0.09 (0.26), residues: 372 loop : 0.07 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1156 HIS 0.012 0.001 HIS A 216 PHE 0.032 0.002 PHE B 449 TYR 0.021 0.002 TYR A 107 ARG 0.008 0.000 ARG A 184 *********************** 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 287 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 220 time to evaluate : 2.569 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: symmetry clash REVERT: A 51 MET cc_start: 0.9135 (ppp) cc_final: 0.8915 (ppp) REVERT: A 61 ASP cc_start: 0.8884 (m-30) cc_final: 0.7795 (p0) REVERT: A 174 LEU cc_start: 0.9235 (tp) cc_final: 0.8977 (tp) REVERT: A 177 MET cc_start: 0.8539 (tmm) cc_final: 0.7000 (tmm) REVERT: A 185 ILE cc_start: 0.9585 (tt) cc_final: 0.9264 (tp) REVERT: A 203 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8208 (p) REVERT: A 229 MET cc_start: 0.8733 (mmm) cc_final: 0.8167 (mmm) REVERT: A 316 PHE cc_start: 0.9334 (m-80) cc_final: 0.9090 (m-10) REVERT: A 334 MET cc_start: 0.8951 (mmm) cc_final: 0.8614 (mmm) REVERT: A 340 MET cc_start: 0.8985 (mtp) cc_final: 0.7524 (mtp) REVERT: A 343 GLU cc_start: 0.8921 (pp20) cc_final: 0.8548 (pp20) REVERT: A 371 LYS cc_start: 0.9132 (tttp) cc_final: 0.8843 (tptt) REVERT: A 374 TYR cc_start: 0.8958 (p90) cc_final: 0.8210 (p90) REVERT: A 456 ILE cc_start: 0.8066 (pt) cc_final: 0.7850 (pt) REVERT: B 31 ASP cc_start: 0.9110 (p0) cc_final: 0.8875 (p0) REVERT: B 41 MET cc_start: 0.8772 (mpp) cc_final: 0.8143 (mpp) REVERT: B 51 MET cc_start: 0.6985 (tmm) cc_final: 0.6612 (tmm) REVERT: B 52 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.7941 (t) REVERT: B 73 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7986 (ttm) REVERT: B 80 CYS cc_start: 0.8310 (p) cc_final: 0.7741 (p) REVERT: B 88 LEU cc_start: 0.9116 (mt) cc_final: 0.8610 (tp) REVERT: B 161 LYS cc_start: 0.9235 (mptt) cc_final: 0.8707 (mmtm) REVERT: B 217 TYR cc_start: 0.8630 (m-80) cc_final: 0.8332 (m-80) REVERT: B 334 MET cc_start: 0.9050 (mmp) cc_final: 0.8685 (mmp) REVERT: C 6 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7928 (tppt) REVERT: C 85 PHE cc_start: 0.8938 (p90) cc_final: 0.8387 (p90) REVERT: C 155 ILE cc_start: 0.9267 (mt) cc_final: 0.8973 (tt) REVERT: C 156 PHE cc_start: 0.8272 (m-10) cc_final: 0.7731 (m-10) REVERT: C 202 GLU cc_start: 0.7305 (tt0) cc_final: 0.6759 (tt0) REVERT: C 248 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.6030 (mmp) REVERT: C 1119 THR cc_start: 0.8573 (p) cc_final: 0.8092 (p) REVERT: C 1138 MET cc_start: 0.5396 (ptp) cc_final: 0.5187 (ptp) REVERT: C 1152 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8244 (pt) REVERT: C 1194 MET cc_start: 0.6456 (ppp) cc_final: 0.6019 (ppp) REVERT: C 1247 ASN cc_start: 0.8991 (m-40) cc_final: 0.8743 (m110) REVERT: D 26 ASN cc_start: 0.9370 (t0) cc_final: 0.9138 (t0) REVERT: D 85 PHE cc_start: 0.9179 (p90) cc_final: 0.8351 (p90) REVERT: D 142 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8455 (mp0) REVERT: D 1079 ARG cc_start: 0.9002 (mmt180) cc_final: 0.8452 (tpp-160) REVERT: D 1194 MET cc_start: 0.8998 (ptt) cc_final: 0.8641 (ptt) REVERT: D 1199 THR cc_start: 0.8835 (m) cc_final: 0.8478 (p) REVERT: D 1219 ILE cc_start: 0.7756 (tt) cc_final: 0.7497 (tp) REVERT: D 1255 LEU cc_start: 0.9591 (mt) cc_final: 0.9317 (mt) REVERT: E 623 HIS cc_start: 0.6498 (m-70) cc_final: 0.5779 (m-70) outliers start: 67 outliers final: 45 residues processed: 268 average time/residue: 0.3468 time to fit residues: 144.9552 Evaluate side-chains 254 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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 242 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 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 B residue 484 ASP Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 52 THR 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 248 MET Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1018 ASP Chi-restraints excluded: chain C residue 1055 ASP Chi-restraints excluded: chain C residue 1117 GLU Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1246 ASP 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 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 1081 MET Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1201 MET 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 625 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 641 THR Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 ASP 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 86 optimal weight: 0.8980 chunk 231 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS B 124 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3935 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= 0.295 Angle : 0.675 15.519 29785 Z= 0.354 Chirality : 0.042 0.223 3259 Planarity : 0.005 0.052 3932 Dihedral : 5.681 104.220 2983 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.44 % Allowed : 17.29 % Favored : 79.27 % 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: 0.58 (0.16), residues: 2662 helix: 0.91 (0.14), residues: 1334 sheet: -0.12 (0.27), residues: 378 loop : 0.06 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1156 HIS 0.009 0.001 HIS B 122 PHE 0.030 0.002 PHE A 520 TYR 0.023 0.002 TYR C 35 ARG 0.006 0.000 ARG A 409 *********************** 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 303 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 221 time to evaluate : 2.593 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.8963 (tp30) cc_final: 0.8454 (tm-30) REVERT: A 51 MET cc_start: 0.9138 (ppp) cc_final: 0.8907 (ppp) REVERT: A 61 ASP cc_start: 0.8925 (m-30) cc_final: 0.7807 (p0) REVERT: A 131 ASP cc_start: 0.8754 (p0) cc_final: 0.8539 (p0) REVERT: A 174 LEU cc_start: 0.9266 (tp) cc_final: 0.8993 (tp) REVERT: A 177 MET cc_start: 0.8643 (tmm) cc_final: 0.7263 (tmm) REVERT: A 185 ILE cc_start: 0.9558 (tt) cc_final: 0.9192 (tp) REVERT: A 203 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 229 MET cc_start: 0.8629 (mmm) cc_final: 0.8047 (mmm) REVERT: A 230 LEU cc_start: 0.9515 (tp) cc_final: 0.8964 (tp) REVERT: A 304 VAL cc_start: 0.9664 (OUTLIER) cc_final: 0.9295 (t) REVERT: A 316 PHE cc_start: 0.9348 (m-80) cc_final: 0.9093 (m-10) REVERT: A 334 MET cc_start: 0.8962 (mmm) cc_final: 0.8606 (mmm) REVERT: A 340 MET cc_start: 0.8985 (mtp) cc_final: 0.7300 (mtp) REVERT: A 343 GLU cc_start: 0.8885 (pp20) cc_final: 0.8440 (pp20) REVERT: B 31 ASP cc_start: 0.9179 (p0) cc_final: 0.8886 (p0) REVERT: B 41 MET cc_start: 0.8806 (mpp) cc_final: 0.8158 (mpp) REVERT: B 51 MET cc_start: 0.7056 (tmm) cc_final: 0.6715 (tmm) REVERT: B 52 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8017 (t) REVERT: B 73 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.7981 (ttm) REVERT: B 88 LEU cc_start: 0.9094 (mt) cc_final: 0.8577 (tp) REVERT: B 139 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8922 (tp) REVERT: B 161 LYS cc_start: 0.9236 (mptt) cc_final: 0.8723 (mmtm) REVERT: B 217 TYR cc_start: 0.8679 (m-80) cc_final: 0.8421 (m-80) REVERT: B 334 MET cc_start: 0.9072 (mmp) cc_final: 0.8660 (mmm) REVERT: B 340 MET cc_start: 0.8929 (mmm) cc_final: 0.8686 (mmt) REVERT: B 386 ASN cc_start: 0.8299 (t0) cc_final: 0.7933 (t0) REVERT: C 6 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8167 (tppt) REVERT: C 48 LYS cc_start: 0.9527 (ttmm) cc_final: 0.8813 (tmmt) REVERT: C 85 PHE cc_start: 0.8820 (p90) cc_final: 0.8235 (p90) REVERT: C 155 ILE cc_start: 0.9273 (mt) cc_final: 0.8963 (tt) REVERT: C 156 PHE cc_start: 0.8389 (m-10) cc_final: 0.7716 (m-10) REVERT: C 202 GLU cc_start: 0.7340 (tt0) cc_final: 0.6836 (tt0) REVERT: C 248 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6284 (mmp) REVERT: C 1119 THR cc_start: 0.8573 (p) cc_final: 0.8058 (p) REVERT: C 1152 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8250 (tp) REVERT: C 1194 MET cc_start: 0.6381 (ppp) cc_final: 0.5982 (ppp) REVERT: C 1247 ASN cc_start: 0.8980 (m-40) cc_final: 0.8773 (m-40) REVERT: D 26 ASN cc_start: 0.9377 (t0) cc_final: 0.9149 (t0) REVERT: D 83 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9320 (mm) REVERT: D 85 PHE cc_start: 0.9194 (p90) cc_final: 0.8286 (p90) REVERT: D 93 TYR cc_start: 0.9154 (m-80) cc_final: 0.8752 (m-80) REVERT: D 142 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8616 (mt-10) REVERT: D 1194 MET cc_start: 0.9126 (ptt) cc_final: 0.8863 (ptt) REVERT: D 1199 THR cc_start: 0.8783 (m) cc_final: 0.8373 (p) REVERT: D 1203 MET cc_start: 0.4282 (ptm) cc_final: 0.3909 (ptm) REVERT: D 1219 ILE cc_start: 0.7789 (tt) cc_final: 0.7544 (tp) REVERT: D 1255 LEU cc_start: 0.9598 (mt) cc_final: 0.9320 (mt) REVERT: E 623 HIS cc_start: 0.6430 (m-70) cc_final: 0.5540 (m-70) outliers start: 82 outliers final: 57 residues processed: 280 average time/residue: 0.3399 time to fit residues: 148.5014 Evaluate side-chains 279 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 213 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP 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 242 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 139 LEU 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 442 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1018 ASP Chi-restraints excluded: chain C residue 1055 ASP Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1192 VAL Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1251 LEU 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 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1055 ASP Chi-restraints excluded: chain D residue 1081 MET Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1201 MET Chi-restraints excluded: chain D residue 1202 ASP 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 625 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 641 THR Chi-restraints excluded: chain E residue 645 ASP Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 ASP 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 248 optimal weight: 0.4980 chunk 29 optimal weight: 0.0970 chunk 146 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 160 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 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 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 HIS ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 GLN D 995 ASN ** D1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22130 Z= 0.221 Angle : 0.649 15.557 29785 Z= 0.339 Chirality : 0.042 0.195 3259 Planarity : 0.004 0.054 3932 Dihedral : 5.557 104.203 2983 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.90 % Allowed : 18.34 % Favored : 78.77 % 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: 0.65 (0.16), residues: 2662 helix: 0.94 (0.14), residues: 1336 sheet: -0.02 (0.27), residues: 378 loop : 0.08 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 164 HIS 0.007 0.001 HIS B 122 PHE 0.019 0.002 PHE C1091 TYR 0.020 0.002 TYR D 281 ARG 0.005 0.000 ARG A 184 *********************** 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 289 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 220 time to evaluate : 2.529 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 23 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7940 (mt-10) REVERT: A 51 MET cc_start: 0.9110 (ppp) cc_final: 0.8761 (ppp) REVERT: A 61 ASP cc_start: 0.8940 (m-30) cc_final: 0.7785 (p0) REVERT: A 131 ASP cc_start: 0.8643 (p0) cc_final: 0.8395 (p0) REVERT: A 174 LEU cc_start: 0.9307 (tp) cc_final: 0.9018 (tp) REVERT: A 177 MET cc_start: 0.8588 (tmm) cc_final: 0.7256 (tmm) REVERT: A 185 ILE cc_start: 0.9547 (tt) cc_final: 0.9180 (tp) REVERT: A 203 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8166 (p) REVERT: A 229 MET cc_start: 0.8509 (mmm) cc_final: 0.8126 (mmm) REVERT: A 316 PHE cc_start: 0.9329 (m-80) cc_final: 0.8563 (m-80) REVERT: A 334 MET cc_start: 0.8920 (mmm) cc_final: 0.8586 (mmm) REVERT: A 340 MET cc_start: 0.8999 (mtp) cc_final: 0.7572 (mtp) REVERT: A 343 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8419 (pp20) REVERT: A 371 LYS cc_start: 0.9174 (tttp) cc_final: 0.8914 (tptt) REVERT: A 483 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8305 (pmm) REVERT: A 491 ARG cc_start: 0.8780 (ppt170) cc_final: 0.8550 (ppt170) REVERT: B 31 ASP cc_start: 0.9102 (p0) cc_final: 0.8768 (p0) REVERT: B 41 MET cc_start: 0.8854 (mpp) cc_final: 0.8189 (mpp) REVERT: B 51 MET cc_start: 0.6878 (tmm) cc_final: 0.6602 (tmm) REVERT: B 52 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8028 (t) REVERT: B 73 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7931 (ttm) REVERT: B 83 MET cc_start: 0.8898 (mmm) cc_final: 0.8429 (mpp) REVERT: B 88 LEU cc_start: 0.9096 (mt) cc_final: 0.8875 (mt) REVERT: B 139 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8893 (tp) REVERT: B 161 LYS cc_start: 0.9198 (mptt) cc_final: 0.8685 (mmtm) REVERT: B 177 MET cc_start: 0.7432 (tmm) cc_final: 0.7227 (tmm) REVERT: B 217 TYR cc_start: 0.8683 (m-80) cc_final: 0.8445 (m-80) REVERT: B 334 MET cc_start: 0.9052 (mmp) cc_final: 0.8660 (mmm) REVERT: B 340 MET cc_start: 0.8935 (mmm) cc_final: 0.8305 (mmt) REVERT: B 386 ASN cc_start: 0.8287 (t0) cc_final: 0.7905 (t0) REVERT: C 6 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8192 (tppt) REVERT: C 48 LYS cc_start: 0.9530 (ttmm) cc_final: 0.8789 (tmmt) REVERT: C 82 LYS cc_start: 0.8782 (mmtp) cc_final: 0.8443 (mmmt) REVERT: C 85 PHE cc_start: 0.8884 (p90) cc_final: 0.8226 (p90) REVERT: C 155 ILE cc_start: 0.9239 (mt) cc_final: 0.8932 (tt) REVERT: C 156 PHE cc_start: 0.8318 (m-10) cc_final: 0.7678 (m-10) REVERT: C 202 GLU cc_start: 0.7381 (tt0) cc_final: 0.6914 (tt0) REVERT: C 204 LYS cc_start: 0.9003 (pptt) cc_final: 0.8493 (tttt) REVERT: C 248 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5806 (mmp) REVERT: C 1119 THR cc_start: 0.8553 (p) cc_final: 0.7977 (p) REVERT: C 1152 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8246 (tp) REVERT: C 1194 MET cc_start: 0.6269 (ppp) cc_final: 0.5986 (ppp) REVERT: C 1247 ASN cc_start: 0.8970 (m-40) cc_final: 0.8742 (m-40) REVERT: D 26 ASN cc_start: 0.9375 (t0) cc_final: 0.9140 (t0) REVERT: D 85 PHE cc_start: 0.9178 (p90) cc_final: 0.8278 (p90) REVERT: D 93 TYR cc_start: 0.9126 (m-80) cc_final: 0.8731 (m-80) REVERT: D 142 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8455 (mp0) REVERT: D 1079 ARG cc_start: 0.9129 (mmt180) cc_final: 0.8785 (mmt-90) REVERT: D 1194 MET cc_start: 0.9115 (ptt) cc_final: 0.8355 (ptt) REVERT: D 1199 THR cc_start: 0.8812 (m) cc_final: 0.8385 (p) REVERT: D 1202 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.8595 (t0) REVERT: D 1219 ILE cc_start: 0.7745 (tt) cc_final: 0.7458 (tp) REVERT: D 1255 LEU cc_start: 0.9599 (mt) cc_final: 0.9306 (mt) REVERT: D 1281 LYS cc_start: 0.8973 (ptmm) cc_final: 0.8575 (mmmt) REVERT: E 623 HIS cc_start: 0.6347 (m-70) cc_final: 0.5900 (m-70) outliers start: 69 outliers final: 45 residues processed: 268 average time/residue: 0.3274 time to fit residues: 137.3997 Evaluate side-chains 267 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 212 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 139 LEU 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 322 LYS Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 52 THR 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 195 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1055 ASP Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1192 VAL 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 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1055 ASP Chi-restraints excluded: chain D residue 1081 MET Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1202 ASP 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 625 ILE Chi-restraints excluded: chain E residue 641 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 158 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.0870 chunk 162 optimal weight: 0.5980 chunk 174 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22130 Z= 0.209 Angle : 0.659 15.674 29785 Z= 0.344 Chirality : 0.043 0.425 3259 Planarity : 0.004 0.055 3932 Dihedral : 5.490 104.933 2982 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.43 % Allowed : 18.93 % Favored : 78.64 % 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: 0.69 (0.16), residues: 2662 helix: 0.96 (0.14), residues: 1331 sheet: 0.13 (0.27), residues: 375 loop : 0.09 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 164 HIS 0.008 0.001 HIS C1113 PHE 0.021 0.002 PHE A 512 TYR 0.027 0.002 TYR C 35 ARG 0.004 0.000 ARG A 184 *********************** 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 275 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 217 time to evaluate : 2.891 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 23 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7926 (mt-10) REVERT: A 51 MET cc_start: 0.9134 (ppp) cc_final: 0.8700 (ppp) REVERT: A 61 ASP cc_start: 0.8957 (m-30) cc_final: 0.7783 (p0) REVERT: A 131 ASP cc_start: 0.8556 (p0) cc_final: 0.8310 (p0) REVERT: A 174 LEU cc_start: 0.9387 (tp) cc_final: 0.9091 (tp) REVERT: A 177 MET cc_start: 0.8620 (tmm) cc_final: 0.7379 (tmm) REVERT: A 185 ILE cc_start: 0.9552 (tt) cc_final: 0.9208 (tp) REVERT: A 203 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8069 (p) REVERT: A 229 MET cc_start: 0.8632 (mmm) cc_final: 0.8268 (mmm) REVERT: A 316 PHE cc_start: 0.9323 (m-80) cc_final: 0.8545 (m-80) REVERT: A 334 MET cc_start: 0.8914 (mmm) cc_final: 0.8571 (mmm) REVERT: A 340 MET cc_start: 0.8989 (mtp) cc_final: 0.7551 (mtp) REVERT: A 343 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8399 (pp20) REVERT: A 347 MET cc_start: 0.8854 (tmm) cc_final: 0.8460 (tmm) REVERT: A 483 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8212 (pmm) REVERT: B 31 ASP cc_start: 0.9046 (p0) cc_final: 0.8695 (p0) REVERT: B 41 MET cc_start: 0.8907 (mpp) cc_final: 0.8190 (mpp) REVERT: B 52 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8525 (t) REVERT: B 73 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7930 (ttm) REVERT: B 83 MET cc_start: 0.8863 (mmm) cc_final: 0.8394 (mpp) REVERT: B 88 LEU cc_start: 0.9085 (mt) cc_final: 0.8856 (mt) REVERT: B 139 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8920 (tp) REVERT: B 161 LYS cc_start: 0.9183 (mptt) cc_final: 0.8667 (mmtm) REVERT: B 217 TYR cc_start: 0.8698 (m-80) cc_final: 0.8477 (m-80) REVERT: B 334 MET cc_start: 0.9071 (mmp) cc_final: 0.8679 (mmp) REVERT: B 340 MET cc_start: 0.8875 (mmm) cc_final: 0.8520 (mmt) REVERT: B 346 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8082 (pp20) REVERT: B 386 ASN cc_start: 0.8477 (t0) cc_final: 0.8113 (t0) REVERT: B 491 ARG cc_start: 0.8843 (tpm170) cc_final: 0.8337 (tpm170) REVERT: C 48 LYS cc_start: 0.9497 (ttmm) cc_final: 0.8777 (tmmt) REVERT: C 82 LYS cc_start: 0.8778 (mmtp) cc_final: 0.8417 (mmmt) REVERT: C 85 PHE cc_start: 0.8937 (p90) cc_final: 0.8246 (p90) REVERT: C 156 PHE cc_start: 0.8352 (m-10) cc_final: 0.7731 (m-10) REVERT: C 204 LYS cc_start: 0.8932 (pptt) cc_final: 0.8617 (tttt) REVERT: C 248 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5774 (mmp) REVERT: C 1119 THR cc_start: 0.8564 (p) cc_final: 0.7919 (p) REVERT: C 1152 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8139 (tp) REVERT: C 1165 ILE cc_start: 0.7693 (mt) cc_final: 0.7174 (mm) REVERT: C 1194 MET cc_start: 0.6177 (ppp) cc_final: 0.5861 (ppp) REVERT: C 1247 ASN cc_start: 0.8967 (m-40) cc_final: 0.8736 (m-40) REVERT: D 26 ASN cc_start: 0.9379 (t0) cc_final: 0.9143 (t0) REVERT: D 54 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8198 (tm-30) REVERT: D 85 PHE cc_start: 0.9185 (p90) cc_final: 0.8289 (p90) REVERT: D 93 TYR cc_start: 0.9106 (m-80) cc_final: 0.8681 (m-80) REVERT: D 142 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8471 (mp0) REVERT: D 1111 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8569 (pm20) REVERT: D 1199 THR cc_start: 0.8783 (m) cc_final: 0.8397 (p) REVERT: D 1202 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8730 (t0) REVERT: D 1219 ILE cc_start: 0.7722 (tt) cc_final: 0.7480 (tp) REVERT: D 1255 LEU cc_start: 0.9596 (mt) cc_final: 0.9301 (mt) REVERT: D 1281 LYS cc_start: 0.8974 (ptmm) cc_final: 0.8577 (mmmt) REVERT: E 623 HIS cc_start: 0.6543 (m-70) cc_final: 0.6112 (m-70) outliers start: 58 outliers final: 43 residues processed: 257 average time/residue: 0.3417 time to fit residues: 138.0710 Evaluate side-chains 266 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 212 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 139 LEU 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 322 LYS Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1018 ASP Chi-restraints excluded: chain C residue 1055 ASP 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 D residue 60 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 1081 MET Chi-restraints excluded: chain D residue 1111 GLU Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1202 ASP Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 641 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 233 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 187 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 225 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 186 HIS ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22130 Z= 0.281 Angle : 0.687 15.313 29785 Z= 0.359 Chirality : 0.043 0.378 3259 Planarity : 0.004 0.054 3932 Dihedral : 5.574 105.417 2982 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.02 % Allowed : 18.55 % Favored : 78.43 % 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: 0.63 (0.16), residues: 2662 helix: 0.89 (0.14), residues: 1326 sheet: -0.01 (0.27), residues: 373 loop : 0.14 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1156 HIS 0.007 0.001 HIS B 122 PHE 0.020 0.002 PHE D 25 TYR 0.023 0.002 TYR D 281 ARG 0.006 0.000 ARG A 409 *********************** 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 286 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 214 time to evaluate : 2.811 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: 0.8401 (mm-30) cc_final: 0.8035 (mp0) REVERT: A 39 GLU cc_start: 0.8938 (tp30) cc_final: 0.8430 (tm-30) REVERT: A 51 MET cc_start: 0.9137 (ppp) cc_final: 0.8706 (ppp) REVERT: A 61 ASP cc_start: 0.8975 (m-30) cc_final: 0.7781 (p0) REVERT: A 131 ASP cc_start: 0.8599 (p0) cc_final: 0.8343 (p0) REVERT: A 174 LEU cc_start: 0.9286 (tp) cc_final: 0.9013 (tp) REVERT: A 177 MET cc_start: 0.8677 (tmm) cc_final: 0.7226 (tmm) REVERT: A 185 ILE cc_start: 0.9582 (tt) cc_final: 0.9225 (tp) REVERT: A 203 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8125 (p) REVERT: A 229 MET cc_start: 0.8749 (mmm) cc_final: 0.8532 (mmm) REVERT: A 316 PHE cc_start: 0.9350 (m-80) cc_final: 0.9077 (m-10) REVERT: A 334 MET cc_start: 0.8950 (mmm) cc_final: 0.8593 (mmm) REVERT: A 340 MET cc_start: 0.8996 (mtp) cc_final: 0.7566 (mtp) REVERT: A 343 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8431 (pp20) REVERT: A 347 MET cc_start: 0.8922 (tmm) cc_final: 0.8648 (tmm) REVERT: B 31 ASP cc_start: 0.8984 (p0) cc_final: 0.8731 (p0) REVERT: B 41 MET cc_start: 0.8904 (mpp) cc_final: 0.8187 (mpp) REVERT: B 73 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.7993 (ttm) REVERT: B 83 MET cc_start: 0.8866 (mmm) cc_final: 0.8391 (mpp) REVERT: B 88 LEU cc_start: 0.9101 (mt) cc_final: 0.8859 (mt) REVERT: B 139 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9126 (tp) REVERT: B 161 LYS cc_start: 0.9216 (mptt) cc_final: 0.8724 (mmtm) REVERT: B 217 TYR cc_start: 0.8732 (m-80) cc_final: 0.8527 (m-80) REVERT: B 346 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8106 (pp20) REVERT: B 347 MET cc_start: 0.8806 (ppp) cc_final: 0.8437 (ppp) REVERT: C 85 PHE cc_start: 0.8937 (p90) cc_final: 0.8278 (p90) REVERT: C 202 GLU cc_start: 0.7539 (tt0) cc_final: 0.7117 (tt0) REVERT: C 248 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5872 (mmp) REVERT: C 1119 THR cc_start: 0.8490 (p) cc_final: 0.7885 (p) REVERT: C 1152 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8304 (tp) REVERT: C 1165 ILE cc_start: 0.7898 (mt) cc_final: 0.7417 (mm) REVERT: C 1194 MET cc_start: 0.6169 (ppp) cc_final: 0.5737 (ppp) REVERT: C 1247 ASN cc_start: 0.8973 (m-40) cc_final: 0.8744 (m-40) REVERT: D 26 ASN cc_start: 0.9400 (t0) cc_final: 0.9179 (t0) REVERT: D 54 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8269 (tm-30) REVERT: D 83 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9325 (mm) REVERT: D 85 PHE cc_start: 0.9220 (p90) cc_final: 0.8307 (p90) REVERT: D 93 TYR cc_start: 0.9096 (m-80) cc_final: 0.8659 (m-80) REVERT: D 142 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8623 (mt-10) REVERT: D 1079 ARG cc_start: 0.9057 (mmt-90) cc_final: 0.8835 (tpp-160) REVERT: D 1111 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8636 (pm20) REVERT: D 1199 THR cc_start: 0.8861 (m) cc_final: 0.8455 (p) REVERT: D 1202 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8289 (t0) REVERT: D 1219 ILE cc_start: 0.7799 (tt) cc_final: 0.7548 (tp) REVERT: D 1255 LEU cc_start: 0.9590 (mt) cc_final: 0.9293 (mt) REVERT: D 1281 LYS cc_start: 0.8987 (ptmm) cc_final: 0.8590 (mmmt) REVERT: E 623 HIS cc_start: 0.6664 (m-70) cc_final: 0.6217 (m-70) outliers start: 72 outliers final: 51 residues processed: 264 average time/residue: 0.3325 time to fit residues: 137.9116 Evaluate side-chains 270 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 209 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 139 LEU 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 346 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 1018 ASP Chi-restraints excluded: chain C residue 1055 ASP 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 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 1055 ASP Chi-restraints excluded: chain D residue 1081 MET Chi-restraints excluded: chain D residue 1111 GLU Chi-restraints excluded: chain D residue 1117 GLU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1163 THR Chi-restraints excluded: chain D residue 1164 ASP Chi-restraints excluded: chain D residue 1170 ILE Chi-restraints excluded: chain D residue 1202 ASP Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 641 THR Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 648 ASP 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 252 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 0.0770 chunk 175 optimal weight: 0.4980 chunk 265 optimal weight: 0.9990 chunk 243 optimal weight: 0.0970 chunk 211 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 186 HIS ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22130 Z= 0.215 Angle : 0.697 16.635 29785 Z= 0.362 Chirality : 0.043 0.358 3259 Planarity : 0.004 0.056 3932 Dihedral : 5.522 104.309 2982 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.18 % Allowed : 19.60 % Favored : 78.22 % 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: 0.62 (0.16), residues: 2662 helix: 0.83 (0.14), residues: 1327 sheet: 0.07 (0.28), residues: 372 loop : 0.18 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 164 HIS 0.010 0.001 HIS A 216 PHE 0.023 0.002 PHE A 520 TYR 0.028 0.002 TYR C 35 ARG 0.004 0.000 ARG D1206 ********************** 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 265 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 213 time to evaluate : 2.675 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 23 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7877 (mt-10) REVERT: A 51 MET cc_start: 0.9131 (ppp) cc_final: 0.8701 (ppp) REVERT: A 61 ASP cc_start: 0.8978 (m-30) cc_final: 0.7784 (p0) REVERT: A 131 ASP cc_start: 0.8508 (p0) cc_final: 0.8269 (p0) REVERT: A 174 LEU cc_start: 0.9440 (tp) cc_final: 0.9153 (tp) REVERT: A 177 MET cc_start: 0.8654 (tmm) cc_final: 0.7305 (tmm) REVERT: A 185 ILE cc_start: 0.9573 (tt) cc_final: 0.9212 (tp) REVERT: A 203 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8028 (p) REVERT: A 229 MET cc_start: 0.8739 (mmm) cc_final: 0.8517 (mmm) REVERT: A 316 PHE cc_start: 0.9323 (m-80) cc_final: 0.8536 (m-80) REVERT: A 334 MET cc_start: 0.8803 (mmm) cc_final: 0.8511 (mmm) REVERT: A 340 MET cc_start: 0.8993 (mtp) cc_final: 0.7547 (mtp) REVERT: A 343 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8406 (pp20) REVERT: A 347 MET cc_start: 0.8929 (tmm) cc_final: 0.8652 (tmm) REVERT: B 31 ASP cc_start: 0.8863 (p0) cc_final: 0.8574 (p0) REVERT: B 41 MET cc_start: 0.8919 (mpp) cc_final: 0.8169 (mpp) REVERT: B 73 MET cc_start: 0.8882 (mtp) cc_final: 0.7943 (ttm) REVERT: B 83 MET cc_start: 0.8830 (mmm) cc_final: 0.8342 (mpp) REVERT: B 88 LEU cc_start: 0.9095 (mt) cc_final: 0.8843 (mt) REVERT: B 139 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 161 LYS cc_start: 0.9179 (mptt) cc_final: 0.8679 (mmtm) REVERT: B 217 TYR cc_start: 0.8729 (m-80) cc_final: 0.8525 (m-80) REVERT: B 340 MET cc_start: 0.8578 (mmm) cc_final: 0.8362 (mmt) REVERT: B 346 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8123 (pp20) REVERT: B 347 MET cc_start: 0.8767 (ppp) cc_final: 0.8457 (ppp) REVERT: C 48 LYS cc_start: 0.9471 (ttmm) cc_final: 0.8822 (tmmt) REVERT: C 82 LYS cc_start: 0.8936 (mmtp) cc_final: 0.8418 (mmmt) REVERT: C 85 PHE cc_start: 0.8974 (p90) cc_final: 0.8272 (p90) REVERT: C 156 PHE cc_start: 0.8204 (m-10) cc_final: 0.7856 (m-10) REVERT: C 202 GLU cc_start: 0.7473 (tt0) cc_final: 0.7067 (tt0) REVERT: C 248 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5794 (mmp) REVERT: C 1119 THR cc_start: 0.8524 (p) cc_final: 0.7822 (p) REVERT: C 1152 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8298 (tp) REVERT: C 1165 ILE cc_start: 0.7893 (mt) cc_final: 0.7404 (mm) REVERT: C 1194 MET cc_start: 0.5966 (ppp) cc_final: 0.5743 (ppp) REVERT: C 1221 LEU cc_start: 0.8691 (mm) cc_final: 0.8477 (tp) REVERT: C 1247 ASN cc_start: 0.8968 (m-40) cc_final: 0.8733 (m-40) REVERT: C 1283 MET cc_start: 0.8769 (mpp) cc_final: 0.8502 (mpp) REVERT: D 26 ASN cc_start: 0.9403 (t0) cc_final: 0.9177 (t0) REVERT: D 54 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8396 (tm-30) REVERT: D 83 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9323 (mm) REVERT: D 85 PHE cc_start: 0.9204 (p90) cc_final: 0.8269 (p90) REVERT: D 93 TYR cc_start: 0.8826 (m-80) cc_final: 0.8477 (m-80) REVERT: D 142 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8486 (mp0) REVERT: D 177 ASP cc_start: 0.8179 (p0) cc_final: 0.7936 (p0) REVERT: D 1111 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: D 1199 THR cc_start: 0.8670 (m) cc_final: 0.8188 (p) REVERT: D 1201 MET cc_start: 0.8653 (ppp) cc_final: 0.8286 (ppp) REVERT: D 1202 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8091 (t0) REVERT: D 1219 ILE cc_start: 0.7756 (tt) cc_final: 0.7515 (tp) REVERT: D 1255 LEU cc_start: 0.9588 (mt) cc_final: 0.9289 (mt) REVERT: D 1281 LYS cc_start: 0.8980 (ptmm) cc_final: 0.8587 (mmmt) REVERT: E 623 HIS cc_start: 0.6691 (m-70) cc_final: 0.6425 (m-70) outliers start: 52 outliers final: 42 residues processed: 250 average time/residue: 0.3332 time to fit residues: 131.4941 Evaluate side-chains 258 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 207 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 139 LEU 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 346 GLU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 1055 ASP 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 60 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 1111 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 1202 ASP Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain E residue 619 ILE Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 641 THR Chi-restraints excluded: chain E residue 646 ILE 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 224 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 194 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 211 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 217 optimal weight: 10.0000 chunk 26 optimal weight: 0.0020 chunk 38 optimal weight: 0.2980 chunk 185 optimal weight: 4.9990 overall best weight: 0.2386 ------------------------------------------------------------------------------- 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 186 HIS ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN ** C1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.106984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.077772 restraints weight = 89492.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079880 restraints weight = 52142.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080976 restraints weight = 30575.984| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22130 Z= 0.183 Angle : 0.692 17.196 29785 Z= 0.357 Chirality : 0.043 0.305 3259 Planarity : 0.004 0.057 3932 Dihedral : 5.451 103.933 2982 Min Nonbonded Distance : 1.434 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.18 % Allowed : 19.89 % Favored : 77.93 % 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: 0.67 (0.16), residues: 2662 helix: 0.85 (0.14), residues: 1326 sheet: 0.19 (0.28), residues: 371 loop : 0.18 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 164 HIS 0.009 0.001 HIS A 216 PHE 0.017 0.001 PHE D 25 TYR 0.020 0.001 TYR D 281 ARG 0.004 0.000 ARG A 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4147.10 seconds wall clock time: 77 minutes 49.03 seconds (4669.03 seconds total)