Starting phenix.real_space_refine on Thu Jul 25 23:00:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/07_2024/7zr1_14881_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/07_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_14881/07_2024/7zr1_14881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/07_2024/7zr1_14881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/07_2024/7zr1_14881_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr1_14881/07_2024/7zr1_14881_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10626 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 6 5.49 5 Mg 2 5.21 5 S 93 5.16 5 C 13528 2.51 5 N 3941 2.21 5 O 4219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.82, per 1000 atoms: 0.54 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: 10.01 Conformation dependent library (CDL) restraints added in 3.9 seconds 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5126 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 17 sheets defined 56.6% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 31 through 48 removed outlier: 3.950A pdb=" N THR A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.706A pdb=" N VAL A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 98 removed outlier: 4.166A pdb=" N VAL A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.584A pdb=" N ASP A 127 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 removed outlier: 3.977A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.704A pdb=" N VAL A 276 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 352 removed outlier: 3.563A pdb=" N THR A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.691A pdb=" N VAL A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 496 removed outlier: 4.194A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 521 removed outlier: 3.511A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.627A pdb=" N ARG A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.672A pdb=" N ARG B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 removed outlier: 3.528A pdb=" N GLN B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.860A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.603A pdb=" N ARG B 190 " --> pdb=" O HIS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.838A pdb=" N ALA B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 276' Processing helix chain 'B' and resid 325 through 352 removed outlier: 4.099A pdb=" N THR B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.875A pdb=" N ASP B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 393 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 458 through 472 removed outlier: 3.655A pdb=" N VAL B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.873A pdb=" N PHE B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 507 through 521 Processing helix chain 'B' and resid 525 through 532 removed outlier: 3.639A pdb=" N GLN B 529 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 548 through 556 Proline residue: B 553 - end of helix Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.870A pdb=" N GLY C 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.966A pdb=" N VAL C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 Processing helix chain 'C' and resid 147 through 154 removed outlier: 4.170A pdb=" N LEU C 151 " --> pdb=" O PRO C 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.860A pdb=" N ARG C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 293 removed outlier: 4.453A pdb=" N TYR C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 377 removed outlier: 4.078A pdb=" N ASN C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 413 removed outlier: 3.597A pdb=" N ARG C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 973 removed outlier: 3.809A pdb=" N ILE C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 1051 removed outlier: 3.913A pdb=" N ALA C1019 " --> pdb=" O ASP C1015 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C1051 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1106 removed outlier: 4.011A pdb=" N ASP C1055 " --> pdb=" O ASN C1051 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C1089 " --> pdb=" O SER C1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1160 removed outlier: 3.815A pdb=" N LYS C1115 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C1116 " --> pdb=" O THR C1112 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C1131 " --> pdb=" O GLY C1127 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C1143 " --> pdb=" O GLN C1139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C1145 " --> pdb=" O HIS C1141 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C1154 " --> pdb=" O ARG C1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 1208 through 1228 removed outlier: 3.672A pdb=" N LYS C1212 " --> pdb=" O SER C1208 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C1225 " --> pdb=" O LEU C1221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C1227 " --> pdb=" O LEU C1223 " (cutoff:3.500A) Processing helix chain 'C' and resid 1244 through 1266 removed outlier: 3.920A pdb=" N ARG C1249 " --> pdb=" O SER C1245 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C1264 " --> pdb=" O LYS C1260 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN C1265 " --> pdb=" O ALA C1261 " (cutoff:3.500A) Processing helix chain 'C' and resid 1276 through 1287 removed outlier: 3.650A pdb=" N LEU C1280 " --> pdb=" O ASP C1276 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C1281 " --> pdb=" O GLU C1277 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR C1282 " --> pdb=" O GLU C1278 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET C1283 " --> pdb=" O PHE C1279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C1284 " --> pdb=" O LEU C1280 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C1286 " --> pdb=" O TYR C1282 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C1287 " --> pdb=" O MET C1283 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.771A pdb=" N ILE D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 removed outlier: 3.631A pdb=" N VAL D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.686A pdb=" N ASP D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 159 through 167 removed outlier: 3.698A pdb=" N LEU D 163 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 181 through 208 removed outlier: 4.208A pdb=" N TYR D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 293 removed outlier: 4.168A pdb=" N GLN D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 220 " --> pdb=" O ASN D 216 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 378 removed outlier: 4.417A pdb=" N GLU D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLN D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG D 371 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 412 removed outlier: 3.733A pdb=" N GLU D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 973 removed outlier: 3.741A pdb=" N ILE D 967 " --> pdb=" O ILE D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 1051 removed outlier: 3.726A pdb=" N LEU D 979 " --> pdb=" O GLY D 975 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG D1022 " --> pdb=" O ASP D1018 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN D1051 " --> pdb=" O LEU D1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1106 removed outlier: 4.205A pdb=" N ASP D1055 " --> pdb=" O ASN D1051 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D1092 " --> pdb=" O ASP D1088 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG D1093 " --> pdb=" O GLU D1089 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D1094 " --> pdb=" O GLU D1090 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D1100 " --> pdb=" O GLU D1096 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D1104 " --> pdb=" O LEU D1100 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS D1106 " --> pdb=" O LEU D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1106 through 1159 removed outlier: 4.265A pdb=" N LYS D1110 " --> pdb=" O LYS D1106 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D1111 " --> pdb=" O ALA D1107 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D1114 " --> pdb=" O LYS D1110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D1124 " --> pdb=" O LYS D1120 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D1125 " --> pdb=" O ALA D1121 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D1127 " --> pdb=" O ILE D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1208 through 1228 Processing helix chain 'D' and resid 1244 through 1263 Processing helix chain 'D' and resid 1276 through 1286 removed outlier: 3.737A pdb=" N MET D1283 " --> pdb=" O PHE D1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 623 Processing helix chain 'E' and resid 641 through 649 Processing helix chain 'E' and resid 652 through 656 Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 148 removed outlier: 6.536A pdb=" N VAL A 118 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG A 11 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU A 53 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 13 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 281 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.560A pdb=" N MET A 177 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 208 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE A 238 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 210 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 237 " --> pdb=" O MET A 260 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 259 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP A 248 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 261 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.752A pdb=" N VAL A 160 " --> pdb=" O ARG A 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 309 removed outlier: 3.521A pdb=" N ARG A 369 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 306 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 371 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 308 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 373 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N HIS A 406 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A 370 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N TYR A 408 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 372 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.482A pdb=" N ARG A 533 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 148 removed outlier: 5.916A pdb=" N VAL B 118 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 52 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG B 11 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU B 53 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 13 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 281 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 293 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 90 removed outlier: 7.081A pdb=" N LYS B 171 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU B 209 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 173 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR B 211 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR B 175 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN B 208 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE B 238 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 210 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 237 " --> pdb=" O MET B 260 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN B 261 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP B 248 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'B' and resid 303 through 309 removed outlier: 3.542A pdb=" N ARG B 306 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS B 406 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 370 " --> pdb=" O HIS B 406 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR B 408 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 372 " --> pdb=" O TYR B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.736A pdb=" N LYS C 3 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER C 84 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 7 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS C 82 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE C 9 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN C 80 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 102 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.736A pdb=" N LYS C 3 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER C 84 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 7 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS C 82 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE C 9 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN C 80 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER C 92 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 121 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 117 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 118 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1233 through 1237 removed outlier: 6.361A pdb=" N ILE C1234 " --> pdb=" O ILE C1271 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ILE C1273 " --> pdb=" O ILE C1234 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU C1236 " --> pdb=" O ILE C1273 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N TYR C1293 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 31 " --> pdb=" O TYR C1293 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C1295 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C 33 " --> pdb=" O VAL C1295 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG C1297 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C1306 " --> pdb=" O ARG C1294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1167 through 1173 removed outlier: 3.536A pdb=" N ASN C1189 " --> pdb=" O ASP C1173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.815A pdb=" N SER D 84 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU D 7 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS D 82 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 9 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN D 80 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 110 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.815A pdb=" N SER D 84 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU D 7 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS D 82 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 9 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN D 80 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER D 92 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU D 118 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1235 through 1237 removed outlier: 8.509A pdb=" N TYR D1293 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU D 31 " --> pdb=" O TYR D1293 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL D1295 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL D 33 " --> pdb=" O VAL D1295 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ARG D1297 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1167 through 1170 1293 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 10.44 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: 106 2.49 - 3.09: 17144 3.09 - 3.70: 34574 3.70 - 4.30: 48755 4.30 - 4.90: 76723 Nonbonded interactions: 177302 Sorted by model distance: nonbonded pdb=" OD2 ASP B 17 " pdb="MN MN B 801 " model vdw 1.888 2.320 nonbonded pdb=" NE2 HIS A 213 " pdb="MN MN A 802 " model vdw 1.899 2.400 nonbonded pdb=" OD1 ASP A 17 " pdb="MN MN A 801 " model vdw 1.988 2.320 nonbonded pdb=" ND1 HIS A 241 " pdb="MN MN A 802 " model vdw 2.006 2.400 nonbonded pdb="MG MG C1401 " pdb=" O2G AGS C1402 " model vdw 2.007 2.170 ... (remaining 177297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 12.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 62.080 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.090 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: 0.030 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.630 ------------------------------------------------------------------------------- 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= 0.387 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 : 2.506 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: 0.4272 time to fit residues: 235.1233 Evaluate side-chains 239 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 249 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.3980 chunk 201 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 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 B 159 HIS ** 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 341 GLN C1051 ASN C1284 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 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: 0.7168 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22130 Z= 0.332 Angle : 0.722 10.277 29785 Z= 0.386 Chirality : 0.045 0.254 3259 Planarity : 0.005 0.053 3932 Dihedral : 6.074 103.218 2987 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.35 % Allowed : 11.12 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2662 helix: 1.48 (0.13), residues: 1339 sheet: -0.02 (0.27), residues: 379 loop : -0.08 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 164 HIS 0.009 0.001 HIS A 508 PHE 0.023 0.002 PHE A 119 TYR 0.033 0.002 TYR D1065 ARG 0.009 0.001 ARG E 687 *********************** 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 313 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 257 time to evaluate : 2.614 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: 0.8651 (mm-30) cc_final: 0.8293 (mt-10) REVERT: A 39 GLU cc_start: 0.9007 (tp30) cc_final: 0.8658 (tp30) REVERT: A 51 MET cc_start: 0.9155 (ppp) cc_final: 0.8907 (ppp) REVERT: A 61 ASP cc_start: 0.8802 (m-30) cc_final: 0.7920 (p0) REVERT: A 125 HIS cc_start: 0.9192 (m90) cc_final: 0.8585 (m-70) REVERT: A 131 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8580 (t0) REVERT: A 177 MET cc_start: 0.7833 (tmm) cc_final: 0.6994 (tmm) REVERT: A 185 ILE cc_start: 0.9612 (tt) cc_final: 0.9325 (tp) REVERT: A 189 PHE cc_start: 0.9158 (m-10) cc_final: 0.8834 (m-10) REVERT: A 229 MET cc_start: 0.8554 (mmm) cc_final: 0.8210 (mmm) REVERT: A 230 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8843 (mm) REVERT: A 260 MET cc_start: 0.8082 (tmm) cc_final: 0.7785 (tmm) REVERT: A 316 PHE cc_start: 0.9294 (m-80) cc_final: 0.9059 (m-10) REVERT: A 334 MET cc_start: 0.8778 (mmm) cc_final: 0.8484 (mmm) REVERT: A 339 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8916 (tp30) REVERT: A 340 MET cc_start: 0.9007 (mtp) cc_final: 0.7715 (mtp) REVERT: A 347 MET cc_start: 0.8934 (mmm) cc_final: 0.8419 (mmm) REVERT: A 371 LYS cc_start: 0.9274 (tttp) cc_final: 0.8814 (tptt) REVERT: A 456 ILE cc_start: 0.7301 (pt) cc_final: 0.7061 (pt) REVERT: A 480 MET cc_start: 0.9317 (mpp) cc_final: 0.8921 (mpp) REVERT: B 51 MET cc_start: 0.6753 (tmm) cc_final: 0.6515 (tmm) REVERT: B 73 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8028 (ttm) REVERT: B 80 CYS cc_start: 0.8143 (m) cc_final: 0.7641 (p) REVERT: B 83 MET cc_start: 0.8957 (mmp) cc_final: 0.8499 (mpp) REVERT: B 88 LEU cc_start: 0.9149 (mt) cc_final: 0.8929 (mt) REVERT: B 112 ILE cc_start: 0.9454 (mt) cc_final: 0.9253 (mm) REVERT: B 161 LYS cc_start: 0.9171 (mptt) cc_final: 0.8518 (mmtm) REVERT: B 217 TYR cc_start: 0.8461 (m-80) cc_final: 0.8079 (m-80) REVERT: B 374 TYR cc_start: 0.8723 (p90) cc_final: 0.8422 (p90) REVERT: B 442 ASP cc_start: 0.8003 (m-30) cc_final: 0.7706 (m-30) REVERT: B 445 VAL cc_start: 0.9123 (m) cc_final: 0.7934 (m) REVERT: B 473 ASP cc_start: 0.8936 (m-30) cc_final: 0.8702 (t0) REVERT: C 10 LEU cc_start: 0.8486 (mt) cc_final: 0.8276 (mt) REVERT: C 85 PHE cc_start: 0.8987 (p90) cc_final: 0.8398 (p90) REVERT: C 119 LEU cc_start: 0.9110 (mm) cc_final: 0.8666 (tt) REVERT: C 151 LEU cc_start: 0.9387 (mp) cc_final: 0.9058 (mp) REVERT: C 155 ILE cc_start: 0.9354 (mt) cc_final: 0.9001 (tt) REVERT: C 156 PHE cc_start: 0.8419 (m-10) cc_final: 0.8020 (m-10) REVERT: C 192 ILE cc_start: 0.9022 (mp) cc_final: 0.8636 (tp) REVERT: C 204 LYS cc_start: 0.8760 (pptt) cc_final: 0.8433 (pptt) REVERT: C 1081 MET cc_start: 0.3641 (mmp) cc_final: 0.2886 (mmm) REVERT: C 1119 THR cc_start: 0.8798 (p) cc_final: 0.8410 (p) REVERT: C 1144 MET cc_start: 0.8315 (mmm) cc_final: 0.7737 (mmm) REVERT: C 1194 MET cc_start: 0.6919 (ppp) cc_final: 0.5785 (ppp) REVERT: C 1212 LYS cc_start: 0.9246 (mttt) cc_final: 0.8906 (mmtm) REVERT: C 1247 ASN cc_start: 0.8809 (m-40) cc_final: 0.8466 (m-40) REVERT: C 1258 ILE cc_start: 0.9228 (mt) cc_final: 0.8947 (pt) REVERT: D 26 ASN cc_start: 0.9379 (t0) cc_final: 0.8656 (p0) REVERT: D 31 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9007 (tp) REVERT: D 83 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9349 (mm) REVERT: D 85 PHE cc_start: 0.9203 (p90) cc_final: 0.8263 (p90) REVERT: D 117 SER cc_start: 0.7441 (p) cc_final: 0.7209 (t) REVERT: D 136 LEU cc_start: 0.9447 (mt) cc_final: 0.9160 (mt) REVERT: D 142 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8434 (mp0) REVERT: D 1111 GLU cc_start: 0.8719 (mp0) cc_final: 0.8513 (pm20) REVERT: D 1144 MET cc_start: 0.8786 (mmp) cc_final: 0.8541 (mmm) REVERT: D 1145 MET cc_start: 0.8385 (mmp) cc_final: 0.8124 (mmp) REVERT: D 1194 MET cc_start: 0.8866 (ptt) cc_final: 0.8340 (ptt) REVERT: D 1199 THR cc_start: 0.8728 (m) cc_final: 0.8318 (p) REVERT: D 1201 MET cc_start: 0.9352 (ptm) cc_final: 0.9126 (ppp) REVERT: D 1203 MET cc_start: 0.4513 (OUTLIER) cc_final: 0.3073 (ptm) REVERT: D 1219 ILE cc_start: 0.8040 (mt) cc_final: 0.7831 (tt) REVERT: D 1254 SER cc_start: 0.8385 (t) cc_final: 0.7538 (p) REVERT: D 1255 LEU cc_start: 0.9542 (mt) cc_final: 0.9245 (mt) REVERT: D 1281 LYS cc_start: 0.8910 (ptmm) cc_final: 0.8536 (mmmt) REVERT: D 1296 LYS cc_start: 0.8365 (tmmt) cc_final: 0.8162 (tmmt) outliers start: 56 outliers final: 28 residues processed: 298 average time/residue: 0.3381 time to fit residues: 157.5854 Evaluate side-chains 259 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 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 31 LEU 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 241 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 215 optimal weight: 0.1980 chunk 239 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 194 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** C1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 ASN D1074 ASN ** E 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2706 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= 0.218 Angle : 0.640 13.290 29785 Z= 0.335 Chirality : 0.042 0.200 3259 Planarity : 0.004 0.064 3932 Dihedral : 5.790 102.806 2984 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.93 % Allowed : 13.64 % Favored : 84.43 % 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: 1.27 (0.16), residues: 2662 helix: 1.71 (0.13), residues: 1340 sheet: 0.11 (0.26), residues: 378 loop : 0.01 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 164 HIS 0.006 0.001 HIS C1113 PHE 0.022 0.002 PHE A 520 TYR 0.028 0.002 TYR D1065 ARG 0.005 0.000 ARG D 121 *********************** 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 280 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 2.531 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: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9193 (ppp) cc_final: 0.8671 (ppp) REVERT: A 61 ASP cc_start: 0.8771 (m-30) cc_final: 0.7906 (p0) REVERT: A 116 ILE cc_start: 0.9153 (mt) cc_final: 0.8936 (mm) REVERT: A 125 HIS cc_start: 0.9167 (m90) cc_final: 0.8382 (m170) REVERT: A 131 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8492 (t0) REVERT: A 177 MET cc_start: 0.8019 (tmm) cc_final: 0.6833 (tmm) REVERT: A 185 ILE cc_start: 0.9608 (tt) cc_final: 0.9317 (tp) REVERT: A 229 MET cc_start: 0.8697 (mmm) cc_final: 0.8177 (mmm) REVERT: A 230 LEU cc_start: 0.9221 (mm) cc_final: 0.8809 (mm) REVERT: A 316 PHE cc_start: 0.9291 (m-80) cc_final: 0.8589 (m-80) REVERT: A 334 MET cc_start: 0.8865 (mmm) cc_final: 0.8441 (mmm) REVERT: A 339 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8688 (tp30) REVERT: B 51 MET cc_start: 0.6824 (tmm) cc_final: 0.6573 (tmm) REVERT: B 73 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7942 (ttm) REVERT: B 80 CYS cc_start: 0.8081 (m) cc_final: 0.7541 (p) REVERT: B 83 MET cc_start: 0.8892 (mmp) cc_final: 0.8488 (mpp) REVERT: B 88 LEU cc_start: 0.9108 (mt) cc_final: 0.8883 (mt) REVERT: B 112 ILE cc_start: 0.9453 (mt) cc_final: 0.9249 (mm) REVERT: B 161 LYS cc_start: 0.9207 (mptt) cc_final: 0.8686 (mmtm) REVERT: B 217 TYR cc_start: 0.8335 (m-80) cc_final: 0.7973 (m-80) REVERT: B 340 MET cc_start: 0.8197 (mmm) cc_final: 0.7455 (mmm) REVERT: B 374 TYR cc_start: 0.8625 (p90) cc_final: 0.8221 (p90) REVERT: B 397 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9330 (mmtm) REVERT: B 442 ASP cc_start: 0.7899 (m-30) cc_final: 0.7651 (m-30) REVERT: B 445 VAL cc_start: 0.8801 (m) cc_final: 0.7457 (m) REVERT: B 473 ASP cc_start: 0.8889 (m-30) cc_final: 0.8499 (t0) REVERT: C 48 LYS cc_start: 0.9508 (ttmm) cc_final: 0.9007 (ttpt) REVERT: C 82 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8378 (mmmt) REVERT: C 85 PHE cc_start: 0.9070 (p90) cc_final: 0.8453 (p90) REVERT: C 95 VAL cc_start: 0.9517 (t) cc_final: 0.8885 (p) REVERT: C 119 LEU cc_start: 0.9090 (mm) cc_final: 0.8639 (tt) REVERT: C 155 ILE cc_start: 0.9311 (mt) cc_final: 0.8878 (tt) REVERT: C 156 PHE cc_start: 0.8317 (m-10) cc_final: 0.7654 (m-10) REVERT: C 192 ILE cc_start: 0.8974 (mp) cc_final: 0.8469 (tp) REVERT: C 202 GLU cc_start: 0.7199 (tt0) cc_final: 0.6763 (tt0) REVERT: C 1119 THR cc_start: 0.8631 (p) cc_final: 0.8162 (p) REVERT: C 1144 MET cc_start: 0.8366 (mmm) cc_final: 0.7980 (mmm) REVERT: C 1194 MET cc_start: 0.6746 (ppp) cc_final: 0.5816 (ppp) REVERT: C 1247 ASN cc_start: 0.9158 (m-40) cc_final: 0.8862 (m110) REVERT: C 1258 ILE cc_start: 0.9219 (mt) cc_final: 0.8931 (pt) REVERT: C 1284 GLN cc_start: 0.8337 (pp30) cc_final: 0.7897 (pp30) REVERT: D 26 ASN cc_start: 0.9348 (t0) cc_final: 0.8656 (p0) REVERT: D 85 PHE cc_start: 0.9056 (p90) cc_final: 0.8193 (p90) REVERT: D 142 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8441 (mp0) REVERT: D 177 ASP cc_start: 0.8178 (p0) cc_final: 0.7975 (p0) REVERT: D 1194 MET cc_start: 0.9030 (ptt) cc_final: 0.8439 (ptt) REVERT: D 1199 THR cc_start: 0.8717 (m) cc_final: 0.8327 (p) REVERT: D 1203 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.3040 (ptm) REVERT: D 1255 LEU cc_start: 0.9542 (mt) cc_final: 0.9270 (mt) REVERT: D 1281 LYS cc_start: 0.8912 (ptmm) cc_final: 0.8526 (mmmt) REVERT: E 623 HIS cc_start: 0.6130 (m-70) cc_final: 0.5610 (m-70) REVERT: E 643 GLU cc_start: 0.9536 (pp20) cc_final: 0.9276 (pm20) outliers start: 46 outliers final: 28 residues processed: 267 average time/residue: 0.3384 time to fit residues: 139.3184 Evaluate side-chains 251 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain C residue 46 CYS 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 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 1074 ASN Chi-restraints excluded: chain D residue 1078 GLU Chi-restraints excluded: chain D residue 1117 GLU Chi-restraints excluded: chain D residue 1123 ILE 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 D residue 1251 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 242 optimal weight: 0.5980 chunk 257 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1187 ASN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** 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: 0.7202 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22130 Z= 0.305 Angle : 0.654 9.798 29785 Z= 0.347 Chirality : 0.042 0.204 3259 Planarity : 0.004 0.057 3932 Dihedral : 5.708 102.902 2983 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.94 % Allowed : 14.86 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2662 helix: 1.72 (0.13), residues: 1348 sheet: -0.01 (0.26), residues: 376 loop : 0.01 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 239 HIS 0.008 0.001 HIS A 216 PHE 0.025 0.002 PHE B 449 TYR 0.023 0.002 TYR D 281 ARG 0.015 0.000 ARG D1204 *********************** 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 301 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 231 time to evaluate : 2.411 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 51 MET cc_start: 0.9190 (ppp) cc_final: 0.8688 (ppp) REVERT: A 61 ASP cc_start: 0.8836 (m-30) cc_final: 0.7868 (p0) REVERT: A 116 ILE cc_start: 0.8912 (mt) cc_final: 0.8687 (mm) REVERT: A 125 HIS cc_start: 0.9181 (m90) cc_final: 0.8508 (m-70) REVERT: A 131 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8411 (t0) REVERT: A 177 MET cc_start: 0.8296 (tmm) cc_final: 0.7062 (tmm) REVERT: A 185 ILE cc_start: 0.9633 (tt) cc_final: 0.9328 (tp) REVERT: A 203 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8127 (p) REVERT: A 229 MET cc_start: 0.8817 (mmm) cc_final: 0.8269 (mmm) REVERT: A 230 LEU cc_start: 0.9320 (mm) cc_final: 0.8842 (mm) REVERT: A 316 PHE cc_start: 0.9338 (m-80) cc_final: 0.8638 (m-80) REVERT: A 334 MET cc_start: 0.8931 (mmm) cc_final: 0.8468 (mmm) REVERT: A 340 MET cc_start: 0.9107 (mtp) cc_final: 0.8690 (mtp) REVERT: A 347 MET cc_start: 0.9013 (mmm) cc_final: 0.8543 (mmm) REVERT: A 371 LYS cc_start: 0.9299 (tttp) cc_final: 0.8910 (tppt) REVERT: A 491 ARG cc_start: 0.8892 (ppt170) cc_final: 0.8645 (ppt170) REVERT: A 505 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8853 (mp) REVERT: A 512 PHE cc_start: 0.9246 (m-10) cc_final: 0.8829 (m-80) REVERT: B 73 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8013 (ttm) REVERT: B 83 MET cc_start: 0.8931 (mmp) cc_final: 0.8492 (mpp) REVERT: B 88 LEU cc_start: 0.9098 (mt) cc_final: 0.8861 (mt) REVERT: B 112 ILE cc_start: 0.9438 (mt) cc_final: 0.9110 (mm) REVERT: B 161 LYS cc_start: 0.9179 (mptt) cc_final: 0.8503 (mmtm) REVERT: B 217 TYR cc_start: 0.8424 (m-80) cc_final: 0.8142 (m-80) REVERT: B 334 MET cc_start: 0.9090 (mmm) cc_final: 0.8827 (mmm) REVERT: B 340 MET cc_start: 0.8631 (mmm) cc_final: 0.8257 (mmm) REVERT: B 374 TYR cc_start: 0.8667 (p90) cc_final: 0.8235 (p90) REVERT: B 386 ASN cc_start: 0.8418 (t0) cc_final: 0.7819 (t0) REVERT: C 6 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8443 (tppt) REVERT: C 48 LYS cc_start: 0.9504 (ttmm) cc_final: 0.8900 (tmmt) REVERT: C 85 PHE cc_start: 0.9093 (p90) cc_final: 0.8523 (p90) REVERT: C 119 LEU cc_start: 0.9116 (mm) cc_final: 0.8678 (tt) REVERT: C 155 ILE cc_start: 0.9321 (mt) cc_final: 0.8900 (tt) REVERT: C 156 PHE cc_start: 0.8446 (m-10) cc_final: 0.7747 (m-10) REVERT: C 202 GLU cc_start: 0.7493 (tt0) cc_final: 0.7015 (tt0) REVERT: C 204 LYS cc_start: 0.9083 (pptt) cc_final: 0.8507 (tttt) REVERT: C 1119 THR cc_start: 0.8639 (p) cc_final: 0.8055 (p) REVERT: C 1194 MET cc_start: 0.6719 (ppp) cc_final: 0.6080 (ppp) REVERT: C 1247 ASN cc_start: 0.9154 (m-40) cc_final: 0.8806 (m110) REVERT: D 26 ASN cc_start: 0.9355 (t0) cc_final: 0.8639 (p0) REVERT: D 85 PHE cc_start: 0.9096 (p90) cc_final: 0.8303 (p90) REVERT: D 135 GLU cc_start: 0.9313 (tt0) cc_final: 0.8880 (mp0) REVERT: D 142 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8452 (mp0) REVERT: D 150 ILE cc_start: 0.9041 (mp) cc_final: 0.8804 (pt) REVERT: D 151 LEU cc_start: 0.9096 (mp) cc_final: 0.8842 (mp) REVERT: D 177 ASP cc_start: 0.8256 (p0) cc_final: 0.6534 (p0) REVERT: D 1145 MET cc_start: 0.8507 (mmp) cc_final: 0.8286 (mmp) REVERT: D 1194 MET cc_start: 0.9005 (ptt) cc_final: 0.8651 (ptt) REVERT: D 1199 THR cc_start: 0.8714 (m) cc_final: 0.8356 (p) REVERT: D 1219 ILE cc_start: 0.7672 (tt) cc_final: 0.7419 (tp) REVERT: D 1255 LEU cc_start: 0.9574 (mt) cc_final: 0.9304 (mt) REVERT: D 1281 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8525 (mmmt) REVERT: E 616 TYR cc_start: 0.8187 (m-80) cc_final: 0.7872 (m-80) REVERT: E 623 HIS cc_start: 0.6490 (m-70) cc_final: 0.5690 (m-70) REVERT: E 643 GLU cc_start: 0.9544 (pp20) cc_final: 0.9276 (pm20) outliers start: 70 outliers final: 43 residues processed: 285 average time/residue: 0.3219 time to fit residues: 142.3247 Evaluate side-chains 260 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 2.329 ------------------------------------------------------------------------------- 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 131 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 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 41 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 51 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 1002 GLU Chi-restraints excluded: chain C residue 1055 ASP Chi-restraints excluded: chain C residue 1231 CYS Chi-restraints excluded: chain C residue 1248 ILE Chi-restraints excluded: chain C residue 1274 THR Chi-restraints excluded: chain C residue 1303 SER Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1055 ASP 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 1170 ILE Chi-restraints excluded: chain D residue 1201 MET Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1240 THR Chi-restraints excluded: chain E residue 636 HIS Chi-restraints excluded: chain E residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 191 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 230 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1284 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22130 Z= 0.272 Angle : 0.652 10.471 29785 Z= 0.342 Chirality : 0.042 0.309 3259 Planarity : 0.004 0.054 3932 Dihedral : 5.629 102.241 2983 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.32 % Allowed : 15.23 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2662 helix: 1.74 (0.13), residues: 1350 sheet: -0.00 (0.26), residues: 376 loop : 0.05 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 164 HIS 0.008 0.001 HIS A 216 PHE 0.025 0.002 PHE A 520 TYR 0.023 0.002 TYR D 281 ARG 0.010 0.000 ARG D1204 *********************** 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 301 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 222 time to evaluate : 2.536 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: 0.8392 (mm-30) cc_final: 0.7932 (mt-10) REVERT: A 51 MET cc_start: 0.9191 (ppp) cc_final: 0.8669 (ppp) REVERT: A 61 ASP cc_start: 0.8858 (m-30) cc_final: 0.7845 (p0) REVERT: A 66 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7701 (mtt180) REVERT: A 83 MET cc_start: 0.8606 (pmm) cc_final: 0.8188 (tmm) REVERT: A 116 ILE cc_start: 0.8887 (mt) cc_final: 0.8651 (mm) REVERT: A 125 HIS cc_start: 0.9145 (m90) cc_final: 0.8572 (m-70) REVERT: A 131 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8273 (t70) REVERT: A 177 MET cc_start: 0.8254 (tmm) cc_final: 0.7092 (tmm) REVERT: A 185 ILE cc_start: 0.9594 (tt) cc_final: 0.9349 (tp) REVERT: A 203 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8111 (p) REVERT: A 217 TYR cc_start: 0.7547 (m-80) cc_final: 0.7321 (m-80) REVERT: A 229 MET cc_start: 0.8887 (mmm) cc_final: 0.8241 (mmm) REVERT: A 230 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8665 (mm) REVERT: A 316 PHE cc_start: 0.9334 (m-80) cc_final: 0.8614 (m-80) REVERT: A 334 MET cc_start: 0.8932 (mmm) cc_final: 0.8607 (mmm) REVERT: A 340 MET cc_start: 0.8881 (mtp) cc_final: 0.7531 (mtp) REVERT: A 343 GLU cc_start: 0.8753 (pp20) cc_final: 0.8450 (pp20) REVERT: A 374 TYR cc_start: 0.8930 (p90) cc_final: 0.8126 (p90) REVERT: A 480 MET cc_start: 0.9307 (mpp) cc_final: 0.8873 (mtt) REVERT: A 505 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8842 (mp) REVERT: A 512 PHE cc_start: 0.9233 (m-10) cc_final: 0.8817 (m-80) REVERT: B 61 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.7407 (p0) REVERT: B 73 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8021 (ttm) REVERT: B 80 CYS cc_start: 0.8510 (p) cc_final: 0.7835 (p) REVERT: B 83 MET cc_start: 0.8961 (mmp) cc_final: 0.8489 (mpp) REVERT: B 88 LEU cc_start: 0.9115 (mt) cc_final: 0.8823 (mt) REVERT: B 112 ILE cc_start: 0.9433 (mt) cc_final: 0.9108 (mm) REVERT: B 161 LYS cc_start: 0.9239 (mptt) cc_final: 0.8742 (mmtm) REVERT: B 217 TYR cc_start: 0.8642 (m-80) cc_final: 0.8312 (m-80) REVERT: B 334 MET cc_start: 0.9069 (mmm) cc_final: 0.8795 (mmm) REVERT: B 346 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8067 (pp20) REVERT: B 374 TYR cc_start: 0.8610 (p90) cc_final: 0.8326 (p90) REVERT: C 48 LYS cc_start: 0.9463 (ttmm) cc_final: 0.8887 (tmmt) REVERT: C 52 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8605 (p) REVERT: C 85 PHE cc_start: 0.9059 (p90) cc_final: 0.8417 (p90) REVERT: C 119 LEU cc_start: 0.9124 (mm) cc_final: 0.8687 (tt) REVERT: C 155 ILE cc_start: 0.9238 (mt) cc_final: 0.8957 (tt) REVERT: C 156 PHE cc_start: 0.8439 (m-10) cc_final: 0.7888 (m-10) REVERT: C 192 ILE cc_start: 0.8646 (mp) cc_final: 0.7654 (tp) REVERT: C 202 GLU cc_start: 0.7473 (tt0) cc_final: 0.6994 (tt0) REVERT: C 204 LYS cc_start: 0.9062 (pptt) cc_final: 0.8542 (tttt) REVERT: C 248 MET cc_start: 0.6111 (mmp) cc_final: 0.5306 (mmp) REVERT: C 1119 THR cc_start: 0.8635 (p) cc_final: 0.8272 (p) REVERT: C 1194 MET cc_start: 0.6748 (ppp) cc_final: 0.6282 (ppp) REVERT: C 1247 ASN cc_start: 0.9140 (m-40) cc_final: 0.8672 (m-40) REVERT: D 26 ASN cc_start: 0.9352 (t0) cc_final: 0.8648 (p0) REVERT: D 54 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8044 (tm-30) REVERT: D 85 PHE cc_start: 0.9101 (p90) cc_final: 0.8281 (p90) REVERT: D 135 GLU cc_start: 0.9301 (tt0) cc_final: 0.8938 (mp0) REVERT: D 142 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8440 (mp0) REVERT: D 151 LEU cc_start: 0.9115 (mp) cc_final: 0.8839 (mp) REVERT: D 1194 MET cc_start: 0.8972 (ptt) cc_final: 0.8514 (ptt) REVERT: D 1199 THR cc_start: 0.8802 (m) cc_final: 0.8435 (p) REVERT: D 1202 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8649 (t0) REVERT: D 1219 ILE cc_start: 0.7635 (tt) cc_final: 0.7394 (tp) REVERT: D 1255 LEU cc_start: 0.9582 (mt) cc_final: 0.9316 (mt) REVERT: E 623 HIS cc_start: 0.6879 (m-70) cc_final: 0.6128 (m-70) REVERT: E 643 GLU cc_start: 0.9567 (pp20) cc_final: 0.9236 (pm20) outliers start: 79 outliers final: 50 residues processed: 284 average time/residue: 0.3309 time to fit residues: 145.3267 Evaluate side-chains 265 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 205 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 66 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 61 ASP 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 346 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 484 ASP 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 1002 GLU Chi-restraints excluded: chain C residue 1055 ASP Chi-restraints excluded: chain C residue 1097 GLU 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 1284 GLN 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 95 VAL Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1055 ASP 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 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 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 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: 1.9990 chunk 231 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 257 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 119 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** D1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 22130 Z= 0.335 Angle : 0.689 15.602 29785 Z= 0.363 Chirality : 0.043 0.215 3259 Planarity : 0.004 0.053 3932 Dihedral : 5.673 102.157 2983 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.48 % Allowed : 15.95 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 2662 helix: 1.68 (0.13), residues: 1352 sheet: -0.14 (0.26), residues: 383 loop : -0.01 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C1156 HIS 0.010 0.001 HIS A 216 PHE 0.023 0.002 PHE B 448 TYR 0.024 0.002 TYR D 281 ARG 0.009 0.000 ARG A 184 *********************** 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 299 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 216 time to evaluate : 2.589 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 39 GLU cc_start: 0.8983 (tp30) cc_final: 0.8432 (tm-30) REVERT: A 51 MET cc_start: 0.9180 (ppp) cc_final: 0.8678 (ppp) REVERT: A 61 ASP cc_start: 0.8893 (m-30) cc_final: 0.7825 (p0) REVERT: A 66 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7685 (mtt180) REVERT: A 83 MET cc_start: 0.8635 (pmm) cc_final: 0.8224 (tmm) REVERT: A 116 ILE cc_start: 0.8821 (mt) cc_final: 0.8595 (mm) REVERT: A 131 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8296 (t70) REVERT: A 177 MET cc_start: 0.8312 (tmm) cc_final: 0.6891 (tmm) REVERT: A 185 ILE cc_start: 0.9605 (tt) cc_final: 0.9323 (tp) REVERT: A 203 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8204 (p) REVERT: A 229 MET cc_start: 0.8997 (mmm) cc_final: 0.8550 (mmm) REVERT: A 230 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8731 (mm) REVERT: A 316 PHE cc_start: 0.9357 (m-80) cc_final: 0.9103 (m-10) REVERT: A 334 MET cc_start: 0.8962 (mmm) cc_final: 0.8616 (mmm) REVERT: A 340 MET cc_start: 0.8913 (mtp) cc_final: 0.7841 (mtp) REVERT: A 343 GLU cc_start: 0.8772 (pp20) cc_final: 0.8399 (pp20) REVERT: A 371 LYS cc_start: 0.9387 (tttp) cc_final: 0.9182 (tptp) REVERT: A 480 MET cc_start: 0.9186 (mpp) cc_final: 0.8817 (mpp) REVERT: A 483 MET cc_start: 0.8654 (pmm) cc_final: 0.8360 (pmm) REVERT: A 512 PHE cc_start: 0.9232 (m-10) cc_final: 0.8790 (m-80) REVERT: B 52 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8549 (t) REVERT: B 61 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.7552 (p0) REVERT: B 73 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8052 (ttm) REVERT: B 83 MET cc_start: 0.9020 (mmp) cc_final: 0.8535 (mpp) REVERT: B 88 LEU cc_start: 0.9074 (mt) cc_final: 0.8782 (mt) REVERT: B 112 ILE cc_start: 0.9427 (mt) cc_final: 0.9128 (mm) REVERT: B 161 LYS cc_start: 0.9257 (mptt) cc_final: 0.8799 (mmtm) REVERT: B 217 TYR cc_start: 0.8676 (m-80) cc_final: 0.8393 (m-80) REVERT: B 334 MET cc_start: 0.9086 (mmm) cc_final: 0.8805 (mmm) REVERT: B 346 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8025 (pp20) REVERT: B 374 TYR cc_start: 0.8607 (p90) cc_final: 0.8334 (p90) REVERT: C 48 LYS cc_start: 0.9457 (ttmm) cc_final: 0.8867 (tmmt) REVERT: C 52 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8579 (p) REVERT: C 85 PHE cc_start: 0.8974 (p90) cc_final: 0.8213 (p90) REVERT: C 119 LEU cc_start: 0.9145 (mm) cc_final: 0.8714 (tt) REVERT: C 155 ILE cc_start: 0.9278 (mt) cc_final: 0.8993 (tt) REVERT: C 156 PHE cc_start: 0.8477 (m-10) cc_final: 0.7974 (m-10) REVERT: C 192 ILE cc_start: 0.8635 (mp) cc_final: 0.7810 (tp) REVERT: C 202 GLU cc_start: 0.7537 (tt0) cc_final: 0.7086 (tt0) REVERT: C 204 LYS cc_start: 0.9078 (pptt) cc_final: 0.8568 (tttt) REVERT: C 248 MET cc_start: 0.6568 (mmp) cc_final: 0.6253 (mmp) REVERT: C 1119 THR cc_start: 0.8616 (p) cc_final: 0.8244 (p) REVERT: C 1165 ILE cc_start: 0.7675 (mt) cc_final: 0.7141 (mm) REVERT: C 1194 MET cc_start: 0.6379 (ppp) cc_final: 0.5995 (ppp) REVERT: C 1247 ASN cc_start: 0.8950 (m-40) cc_final: 0.8675 (m-40) REVERT: D 26 ASN cc_start: 0.9372 (t0) cc_final: 0.8671 (p0) REVERT: D 54 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 85 PHE cc_start: 0.9132 (p90) cc_final: 0.8524 (p90) REVERT: D 135 GLU cc_start: 0.9314 (tt0) cc_final: 0.8925 (mp0) REVERT: D 142 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8455 (mp0) REVERT: D 151 LEU cc_start: 0.9088 (mp) cc_final: 0.8876 (mp) REVERT: D 1194 MET cc_start: 0.8992 (ptt) cc_final: 0.8505 (ptt) REVERT: D 1199 THR cc_start: 0.8765 (m) cc_final: 0.8354 (p) REVERT: D 1202 ASP cc_start: 0.9400 (OUTLIER) cc_final: 0.8813 (t0) REVERT: D 1219 ILE cc_start: 0.7700 (tt) cc_final: 0.7460 (tp) REVERT: D 1255 LEU cc_start: 0.9588 (mt) cc_final: 0.9317 (mt) REVERT: D 1281 LYS cc_start: 0.9098 (ptmm) cc_final: 0.8768 (mmmt) REVERT: E 623 HIS cc_start: 0.6830 (m-70) cc_final: 0.6471 (m-70) outliers start: 83 outliers final: 57 residues processed: 280 average time/residue: 0.3240 time to fit residues: 143.7521 Evaluate side-chains 270 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 203 time to evaluate : 2.531 ------------------------------------------------------------------------------- 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 66 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 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 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 372 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 473 ASP 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 51 THR 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 1002 GLU Chi-restraints excluded: chain C residue 1018 ASP Chi-restraints excluded: chain C residue 1055 ASP Chi-restraints excluded: chain C residue 1192 VAL 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 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 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 1055 ASP 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 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 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 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: 0.0980 chunk 29 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 187 optimal weight: 0.0970 chunk 145 optimal weight: 0.6980 chunk 216 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 256 optimal weight: 0.7980 chunk 160 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS D1157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22130 Z= 0.186 Angle : 0.638 14.634 29785 Z= 0.330 Chirality : 0.043 0.514 3259 Planarity : 0.004 0.056 3932 Dihedral : 5.490 101.939 2983 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.56 % Allowed : 16.91 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.16), residues: 2662 helix: 1.81 (0.14), residues: 1352 sheet: 0.17 (0.27), residues: 372 loop : 0.03 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 164 HIS 0.009 0.001 HIS C1113 PHE 0.023 0.001 PHE A 520 TYR 0.023 0.001 TYR A 107 ARG 0.007 0.000 ARG D1204 *********************** 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 286 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 225 time to evaluate : 2.628 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: A 23 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7950 (mt-10) REVERT: A 51 MET cc_start: 0.8975 (ppp) cc_final: 0.8514 (ppp) REVERT: A 61 ASP cc_start: 0.8905 (m-30) cc_final: 0.7820 (p0) REVERT: A 83 MET cc_start: 0.8598 (pmm) cc_final: 0.8185 (tmm) REVERT: A 131 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8135 (t0) REVERT: A 177 MET cc_start: 0.8174 (tmm) cc_final: 0.7006 (tmm) REVERT: A 185 ILE cc_start: 0.9542 (tt) cc_final: 0.9241 (tp) REVERT: A 203 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8094 (p) REVERT: A 229 MET cc_start: 0.8984 (mmm) cc_final: 0.8543 (mmm) REVERT: A 230 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8674 (mm) REVERT: A 316 PHE cc_start: 0.9311 (m-80) cc_final: 0.8541 (m-80) REVERT: A 334 MET cc_start: 0.9005 (mmm) cc_final: 0.8536 (mmm) REVERT: A 340 MET cc_start: 0.8861 (mtp) cc_final: 0.7888 (mtp) REVERT: A 343 GLU cc_start: 0.8751 (pp20) cc_final: 0.8290 (pp20) REVERT: A 371 LYS cc_start: 0.9335 (tttp) cc_final: 0.9018 (tptt) REVERT: A 480 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8782 (mtt) REVERT: B 73 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7956 (ttm) REVERT: B 83 MET cc_start: 0.8995 (mmp) cc_final: 0.8484 (mpp) REVERT: B 88 LEU cc_start: 0.9037 (mt) cc_final: 0.8753 (mt) REVERT: B 112 ILE cc_start: 0.9406 (mt) cc_final: 0.9096 (mm) REVERT: B 161 LYS cc_start: 0.9204 (mptt) cc_final: 0.8710 (mmtm) REVERT: B 217 TYR cc_start: 0.8648 (m-80) cc_final: 0.8375 (m-80) REVERT: B 334 MET cc_start: 0.9028 (mmm) cc_final: 0.8668 (mmm) REVERT: B 346 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7992 (pp20) REVERT: B 374 TYR cc_start: 0.8807 (p90) cc_final: 0.8580 (p90) REVERT: C 48 LYS cc_start: 0.9291 (ttmm) cc_final: 0.8837 (tmmt) REVERT: C 52 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 85 PHE cc_start: 0.9202 (p90) cc_final: 0.8503 (p90) REVERT: C 119 LEU cc_start: 0.9129 (mm) cc_final: 0.8695 (tt) REVERT: C 155 ILE cc_start: 0.9221 (mt) cc_final: 0.8814 (tt) REVERT: C 156 PHE cc_start: 0.8386 (m-10) cc_final: 0.7847 (m-10) REVERT: C 192 ILE cc_start: 0.8569 (mp) cc_final: 0.7837 (tp) REVERT: C 202 GLU cc_start: 0.7494 (tt0) cc_final: 0.7018 (tt0) REVERT: C 204 LYS cc_start: 0.9022 (pptt) cc_final: 0.8551 (tttt) REVERT: C 248 MET cc_start: 0.6435 (mmp) cc_final: 0.6157 (mmp) REVERT: C 1119 THR cc_start: 0.8581 (p) cc_final: 0.8127 (p) REVERT: C 1165 ILE cc_start: 0.7650 (mt) cc_final: 0.7120 (mm) REVERT: C 1194 MET cc_start: 0.6233 (ppp) cc_final: 0.5869 (ppp) REVERT: C 1247 ASN cc_start: 0.8939 (m-40) cc_final: 0.8655 (m-40) REVERT: D 26 ASN cc_start: 0.9358 (t0) cc_final: 0.8651 (p0) REVERT: D 54 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8156 (tm-30) REVERT: D 85 PHE cc_start: 0.9176 (p90) cc_final: 0.8307 (p90) REVERT: D 93 TYR cc_start: 0.9120 (m-80) cc_final: 0.8416 (m-80) REVERT: D 135 GLU cc_start: 0.9287 (tt0) cc_final: 0.8889 (mp0) REVERT: D 142 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8472 (mp0) REVERT: D 151 LEU cc_start: 0.9146 (mp) cc_final: 0.8926 (mp) REVERT: D 1081 MET cc_start: 0.6468 (mmm) cc_final: 0.6212 (mmm) REVERT: D 1194 MET cc_start: 0.8949 (ptt) cc_final: 0.8506 (ptt) REVERT: D 1199 THR cc_start: 0.8785 (m) cc_final: 0.8376 (p) REVERT: D 1202 ASP cc_start: 0.9375 (OUTLIER) cc_final: 0.8804 (t0) REVERT: D 1219 ILE cc_start: 0.7862 (tt) cc_final: 0.7657 (tp) REVERT: D 1255 LEU cc_start: 0.9586 (mt) cc_final: 0.9299 (mt) REVERT: E 623 HIS cc_start: 0.6883 (m-70) cc_final: 0.6502 (m-70) REVERT: E 643 GLU cc_start: 0.9537 (pp20) cc_final: 0.9211 (pm20) outliers start: 61 outliers final: 41 residues processed: 270 average time/residue: 0.3208 time to fit residues: 139.3214 Evaluate side-chains 253 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 203 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 480 MET 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 346 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE 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 51 THR 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 146 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1055 ASP 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 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 95 VAL 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 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 619 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: 6.9990 chunk 102 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1284 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** D1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 22130 Z= 0.361 Angle : 0.722 14.520 29785 Z= 0.378 Chirality : 0.044 0.421 3259 Planarity : 0.004 0.052 3932 Dihedral : 5.666 102.645 2983 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.06 % Allowed : 17.33 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2662 helix: 1.62 (0.13), residues: 1355 sheet: -0.01 (0.27), residues: 376 loop : -0.05 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 239 HIS 0.008 0.001 HIS B 216 PHE 0.025 0.002 PHE D 15 TYR 0.049 0.002 TYR E 616 ARG 0.008 0.001 ARG A 409 *********************** 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 291 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 218 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8985 (ppp) cc_final: 0.8595 (ppp) REVERT: A 61 ASP cc_start: 0.8949 (m-30) cc_final: 0.7796 (p0) REVERT: A 66 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7650 (mtt180) REVERT: A 83 MET cc_start: 0.8536 (pmm) cc_final: 0.8080 (tmm) REVERT: A 131 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8291 (t70) REVERT: A 177 MET cc_start: 0.8347 (tmm) cc_final: 0.6942 (tmm) REVERT: A 185 ILE cc_start: 0.9589 (tt) cc_final: 0.9347 (tp) REVERT: A 203 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 227 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8059 (mm-30) REVERT: A 229 MET cc_start: 0.8852 (mmm) cc_final: 0.8482 (mmm) REVERT: A 230 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 316 PHE cc_start: 0.9366 (m-80) cc_final: 0.9101 (m-10) REVERT: A 334 MET cc_start: 0.9000 (mmm) cc_final: 0.8624 (mmm) REVERT: A 340 MET cc_start: 0.8955 (mtp) cc_final: 0.7694 (mtp) REVERT: A 343 GLU cc_start: 0.8950 (pp20) cc_final: 0.8344 (pp20) REVERT: B 73 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8116 (ttm) REVERT: B 83 MET cc_start: 0.9050 (mmp) cc_final: 0.8578 (mpp) REVERT: B 88 LEU cc_start: 0.9080 (mt) cc_final: 0.8756 (mt) REVERT: B 112 ILE cc_start: 0.9401 (mt) cc_final: 0.9112 (mm) REVERT: B 161 LYS cc_start: 0.9327 (mptt) cc_final: 0.8943 (mmtm) REVERT: B 217 TYR cc_start: 0.8710 (m-80) cc_final: 0.8472 (m-80) REVERT: B 299 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8714 (p) REVERT: B 334 MET cc_start: 0.9092 (mmm) cc_final: 0.8774 (mmm) REVERT: B 346 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8085 (pp20) REVERT: B 374 TYR cc_start: 0.8743 (p90) cc_final: 0.8478 (p90) REVERT: B 454 LEU cc_start: 0.8654 (mt) cc_final: 0.8367 (mt) REVERT: C 48 LYS cc_start: 0.9305 (ttmm) cc_final: 0.8893 (tmmt) REVERT: C 52 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 85 PHE cc_start: 0.9009 (p90) cc_final: 0.8258 (p90) REVERT: C 119 LEU cc_start: 0.9135 (mm) cc_final: 0.8710 (tt) REVERT: C 155 ILE cc_start: 0.9267 (mt) cc_final: 0.8849 (tt) REVERT: C 192 ILE cc_start: 0.8653 (mp) cc_final: 0.7575 (tt) REVERT: C 202 GLU cc_start: 0.7456 (tt0) cc_final: 0.6966 (tt0) REVERT: C 204 LYS cc_start: 0.9009 (pptt) cc_final: 0.8653 (tttt) REVERT: C 1119 THR cc_start: 0.8615 (p) cc_final: 0.8154 (p) REVERT: C 1130 MET cc_start: 0.6627 (tpt) cc_final: 0.6123 (tpp) REVERT: C 1165 ILE cc_start: 0.7724 (mt) cc_final: 0.7198 (mm) REVERT: C 1194 MET cc_start: 0.6226 (ppp) cc_final: 0.5839 (ppp) REVERT: C 1221 LEU cc_start: 0.8851 (tp) cc_final: 0.8591 (tp) REVERT: C 1247 ASN cc_start: 0.8963 (m-40) cc_final: 0.8670 (m-40) REVERT: D 26 ASN cc_start: 0.9382 (t0) cc_final: 0.8704 (p0) REVERT: D 54 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 85 PHE cc_start: 0.9233 (p90) cc_final: 0.8446 (p90) REVERT: D 93 TYR cc_start: 0.9120 (m-80) cc_final: 0.8429 (m-80) REVERT: D 135 GLU cc_start: 0.9252 (tt0) cc_final: 0.8903 (mp0) REVERT: D 151 LEU cc_start: 0.9131 (mp) cc_final: 0.8916 (mp) REVERT: D 1194 MET cc_start: 0.9088 (ptt) cc_final: 0.8724 (ptt) REVERT: D 1199 THR cc_start: 0.8854 (m) cc_final: 0.8460 (p) REVERT: D 1202 ASP cc_start: 0.9404 (OUTLIER) cc_final: 0.8769 (t0) REVERT: D 1219 ILE cc_start: 0.7762 (tt) cc_final: 0.7515 (tp) REVERT: D 1255 LEU cc_start: 0.9589 (mt) cc_final: 0.9306 (mt) REVERT: E 623 HIS cc_start: 0.7099 (m-70) cc_final: 0.6887 (m-70) REVERT: E 643 GLU cc_start: 0.9554 (pp20) cc_final: 0.9179 (pm20) outliers start: 73 outliers final: 54 residues processed: 272 average time/residue: 0.3145 time to fit residues: 134.1910 Evaluate side-chains 273 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 473 ASP 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 120 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 195 LEU 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 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 70 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 95 VAL 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 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 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: 0.9990 chunk 224 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 0.0670 chunk 187 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 225 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1284 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** D1023 ASN D1157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4348 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= 0.257 Angle : 0.689 15.462 29785 Z= 0.360 Chirality : 0.043 0.330 3259 Planarity : 0.004 0.057 3932 Dihedral : 5.572 101.277 2983 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.60 % Allowed : 18.09 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.16), residues: 2662 helix: 1.70 (0.14), residues: 1340 sheet: 0.03 (0.27), residues: 381 loop : -0.08 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 239 HIS 0.008 0.001 HIS A 216 PHE 0.021 0.002 PHE D 25 TYR 0.044 0.002 TYR E 616 ARG 0.007 0.000 ARG C1092 *********************** 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 275 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 213 time to evaluate : 2.583 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: A 23 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7943 (mt-10) REVERT: A 39 GLU cc_start: 0.8935 (tp30) cc_final: 0.8677 (tm-30) REVERT: A 51 MET cc_start: 0.8977 (ppp) cc_final: 0.8530 (ppp) REVERT: A 61 ASP cc_start: 0.8949 (m-30) cc_final: 0.7798 (p0) REVERT: A 83 MET cc_start: 0.8536 (pmm) cc_final: 0.8079 (tmm) REVERT: A 131 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8252 (t70) REVERT: A 177 MET cc_start: 0.8272 (tmm) cc_final: 0.7141 (tmm) REVERT: A 185 ILE cc_start: 0.9578 (tt) cc_final: 0.9355 (tp) REVERT: A 203 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 229 MET cc_start: 0.8858 (mmm) cc_final: 0.8470 (mmm) REVERT: A 316 PHE cc_start: 0.9341 (m-80) cc_final: 0.8566 (m-80) REVERT: A 334 MET cc_start: 0.8813 (mmm) cc_final: 0.8542 (mmm) REVERT: A 340 MET cc_start: 0.8910 (mtp) cc_final: 0.7608 (mtp) REVERT: A 343 GLU cc_start: 0.8947 (pp20) cc_final: 0.8387 (pp20) REVERT: A 480 MET cc_start: 0.9034 (mtt) cc_final: 0.8537 (mpp) REVERT: A 483 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8276 (pmm) REVERT: A 514 LYS cc_start: 0.9610 (mmtt) cc_final: 0.9392 (mmtt) REVERT: B 73 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8009 (ttm) REVERT: B 83 MET cc_start: 0.9027 (mmp) cc_final: 0.8534 (mpp) REVERT: B 88 LEU cc_start: 0.9022 (mt) cc_final: 0.8760 (mt) REVERT: B 112 ILE cc_start: 0.9386 (mt) cc_final: 0.9097 (mm) REVERT: B 161 LYS cc_start: 0.9303 (mptt) cc_final: 0.8915 (mmtm) REVERT: B 217 TYR cc_start: 0.8697 (m-80) cc_final: 0.8463 (m-80) REVERT: B 299 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 334 MET cc_start: 0.9027 (mmm) cc_final: 0.8604 (mmm) REVERT: B 346 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8118 (pp20) REVERT: B 374 TYR cc_start: 0.8723 (p90) cc_final: 0.8451 (p90) REVERT: B 491 ARG cc_start: 0.8846 (tpm170) cc_final: 0.8562 (tpm170) REVERT: C 48 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8839 (tmmt) REVERT: C 52 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8441 (p) REVERT: C 85 PHE cc_start: 0.9045 (p90) cc_final: 0.8234 (p90) REVERT: C 119 LEU cc_start: 0.9173 (mm) cc_final: 0.8728 (tt) REVERT: C 155 ILE cc_start: 0.9290 (mt) cc_final: 0.9021 (tt) REVERT: C 156 PHE cc_start: 0.8370 (m-10) cc_final: 0.7826 (m-10) REVERT: C 192 ILE cc_start: 0.8613 (mp) cc_final: 0.7510 (tt) REVERT: C 202 GLU cc_start: 0.7381 (tt0) cc_final: 0.6842 (tt0) REVERT: C 204 LYS cc_start: 0.8988 (pptt) cc_final: 0.8657 (tttt) REVERT: C 248 MET cc_start: 0.6153 (mmp) cc_final: 0.5793 (mmp) REVERT: C 1119 THR cc_start: 0.8588 (p) cc_final: 0.8075 (p) REVERT: C 1130 MET cc_start: 0.6583 (tpt) cc_final: 0.6096 (tpp) REVERT: C 1165 ILE cc_start: 0.7920 (mt) cc_final: 0.7435 (mm) REVERT: C 1194 MET cc_start: 0.6133 (ppp) cc_final: 0.5742 (ppp) REVERT: C 1247 ASN cc_start: 0.8949 (m-40) cc_final: 0.8650 (m-40) REVERT: D 26 ASN cc_start: 0.9381 (t0) cc_final: 0.8702 (p0) REVERT: D 54 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8326 (tm-30) REVERT: D 85 PHE cc_start: 0.9200 (p90) cc_final: 0.8356 (p90) REVERT: D 93 TYR cc_start: 0.9106 (m-80) cc_final: 0.8417 (m-80) REVERT: D 135 GLU cc_start: 0.9251 (tt0) cc_final: 0.8885 (mp0) REVERT: D 151 LEU cc_start: 0.9119 (mp) cc_final: 0.8810 (mt) REVERT: D 1194 MET cc_start: 0.9076 (ptt) cc_final: 0.8712 (ptt) REVERT: D 1199 THR cc_start: 0.8888 (m) cc_final: 0.8496 (p) REVERT: D 1202 ASP cc_start: 0.9445 (OUTLIER) cc_final: 0.8774 (t0) REVERT: D 1219 ILE cc_start: 0.7990 (tt) cc_final: 0.7779 (tp) REVERT: D 1255 LEU cc_start: 0.9590 (mt) cc_final: 0.9295 (mt) REVERT: E 623 HIS cc_start: 0.7154 (m-70) cc_final: 0.6945 (m-70) outliers start: 62 outliers final: 45 residues processed: 259 average time/residue: 0.3252 time to fit residues: 131.9641 Evaluate side-chains 258 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 205 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 113 ASN 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 224 TYR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 33 VAL 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 146 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1055 ASP Chi-restraints excluded: chain C residue 1097 GLU 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 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 95 VAL 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 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 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 252 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 0.0770 chunk 175 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 243 optimal weight: 0.2980 chunk 211 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 167 optimal weight: 0.3980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 186 HIS A 214 GLN A 392 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1269 GLN ** C1284 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** D1157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22130 Z= 0.218 Angle : 0.694 16.269 29785 Z= 0.359 Chirality : 0.044 0.306 3259 Planarity : 0.004 0.059 3932 Dihedral : 5.538 101.534 2983 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.06 % Allowed : 18.97 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2662 helix: 1.70 (0.14), residues: 1348 sheet: 0.11 (0.27), residues: 370 loop : -0.04 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 239 HIS 0.007 0.001 HIS A 216 PHE 0.021 0.002 PHE D 25 TYR 0.042 0.002 TYR E 616 ARG 0.007 0.000 ARG C1092 ********************** 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 261 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 212 time to evaluate : 2.322 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: 0.8438 (mm-30) cc_final: 0.7927 (mt-10) REVERT: A 51 MET cc_start: 0.8963 (ppp) cc_final: 0.8503 (ppp) REVERT: A 61 ASP cc_start: 0.8960 (m-30) cc_final: 0.7798 (p0) REVERT: A 80 CYS cc_start: 0.8811 (m) cc_final: 0.7949 (p) REVERT: A 83 MET cc_start: 0.8535 (pmm) cc_final: 0.8307 (tmm) REVERT: A 131 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8216 (t70) REVERT: A 177 MET cc_start: 0.8187 (tmm) cc_final: 0.6948 (tmm) REVERT: A 185 ILE cc_start: 0.9595 (tt) cc_final: 0.9303 (tp) REVERT: A 203 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8034 (p) REVERT: A 229 MET cc_start: 0.8868 (mmm) cc_final: 0.8468 (mmm) REVERT: A 316 PHE cc_start: 0.9320 (m-80) cc_final: 0.8528 (m-80) REVERT: A 334 MET cc_start: 0.8836 (mmm) cc_final: 0.8441 (mmm) REVERT: A 340 MET cc_start: 0.8916 (mtp) cc_final: 0.7609 (mtp) REVERT: A 343 GLU cc_start: 0.8963 (pp20) cc_final: 0.8377 (pp20) REVERT: A 347 MET cc_start: 0.8744 (tmm) cc_final: 0.8320 (tmm) REVERT: A 480 MET cc_start: 0.9057 (mtt) cc_final: 0.8763 (ptp) REVERT: A 514 LYS cc_start: 0.9611 (mmtt) cc_final: 0.9383 (mmtt) REVERT: B 73 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7982 (ttm) REVERT: B 83 MET cc_start: 0.9034 (mmp) cc_final: 0.8528 (mpp) REVERT: B 88 LEU cc_start: 0.9030 (mt) cc_final: 0.8735 (mt) REVERT: B 112 ILE cc_start: 0.9372 (mt) cc_final: 0.9083 (mm) REVERT: B 161 LYS cc_start: 0.9258 (mptt) cc_final: 0.8848 (mmtm) REVERT: B 217 TYR cc_start: 0.8703 (m-80) cc_final: 0.8478 (m-80) REVERT: B 299 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 334 MET cc_start: 0.8904 (mmm) cc_final: 0.8584 (mmm) REVERT: B 346 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8345 (pp20) REVERT: B 347 MET cc_start: 0.8794 (ppp) cc_final: 0.8489 (ppp) REVERT: B 374 TYR cc_start: 0.8707 (p90) cc_final: 0.8447 (p90) REVERT: B 386 ASN cc_start: 0.8153 (t0) cc_final: 0.7772 (t0) REVERT: B 491 ARG cc_start: 0.8824 (tpm170) cc_final: 0.8466 (tpm170) REVERT: C 48 LYS cc_start: 0.9278 (ttmm) cc_final: 0.8830 (tmmt) REVERT: C 52 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8404 (p) REVERT: C 85 PHE cc_start: 0.9092 (p90) cc_final: 0.8245 (p90) REVERT: C 119 LEU cc_start: 0.9167 (mm) cc_final: 0.8721 (tt) REVERT: C 155 ILE cc_start: 0.9273 (mt) cc_final: 0.9009 (tt) REVERT: C 156 PHE cc_start: 0.8321 (m-10) cc_final: 0.7806 (m-10) REVERT: C 192 ILE cc_start: 0.8571 (mp) cc_final: 0.7459 (tt) REVERT: C 202 GLU cc_start: 0.7351 (tt0) cc_final: 0.6821 (tt0) REVERT: C 204 LYS cc_start: 0.9005 (pptt) cc_final: 0.8767 (tttt) REVERT: C 248 MET cc_start: 0.6171 (mmp) cc_final: 0.5926 (mmp) REVERT: C 1119 THR cc_start: 0.8581 (p) cc_final: 0.8047 (p) REVERT: C 1130 MET cc_start: 0.6535 (tpt) cc_final: 0.6066 (tpp) REVERT: C 1165 ILE cc_start: 0.7905 (mt) cc_final: 0.7408 (mm) REVERT: C 1194 MET cc_start: 0.6070 (ppp) cc_final: 0.5673 (ppp) REVERT: C 1247 ASN cc_start: 0.8938 (m-40) cc_final: 0.8645 (m-40) REVERT: D 26 ASN cc_start: 0.9385 (t0) cc_final: 0.8686 (p0) REVERT: D 54 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8452 (tm-30) REVERT: D 85 PHE cc_start: 0.9184 (p90) cc_final: 0.8312 (p90) REVERT: D 93 TYR cc_start: 0.9098 (m-80) cc_final: 0.8378 (m-80) REVERT: D 135 GLU cc_start: 0.9206 (tt0) cc_final: 0.8825 (mp0) REVERT: D 151 LEU cc_start: 0.9098 (mp) cc_final: 0.8754 (mt) REVERT: D 1081 MET cc_start: 0.4265 (mmm) cc_final: 0.3836 (mmm) REVERT: D 1194 MET cc_start: 0.9079 (ptt) cc_final: 0.8750 (ptt) REVERT: D 1199 THR cc_start: 0.8894 (m) cc_final: 0.8502 (p) REVERT: D 1255 LEU cc_start: 0.9585 (mt) cc_final: 0.9290 (mt) outliers start: 49 outliers final: 39 residues processed: 245 average time/residue: 0.3254 time to fit residues: 125.9939 Evaluate side-chains 251 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 206 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 113 ASN 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 224 TYR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 1002 GLU Chi-restraints excluded: chain C residue 1055 ASP 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 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 95 VAL 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 1201 MET Chi-restraints excluded: chain D residue 1227 PHE Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain E residue 619 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: 0.8980 chunk 64 optimal weight: 0.8980 chunk 194 optimal weight: 0.0040 chunk 31 optimal weight: 0.0670 chunk 58 optimal weight: 0.0980 chunk 211 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 217 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 185 optimal weight: 0.0470 overall best weight: 0.0828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 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** D1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.107019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.077719 restraints weight = 87906.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080720 restraints weight = 51283.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081693 restraints weight = 28574.354| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4487 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= 0.177 Angle : 0.708 18.746 29785 Z= 0.360 Chirality : 0.044 0.266 3259 Planarity : 0.004 0.060 3932 Dihedral : 5.407 100.385 2983 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.80 % Allowed : 19.39 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2662 helix: 1.74 (0.14), residues: 1354 sheet: 0.40 (0.28), residues: 366 loop : -0.15 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 164 HIS 0.007 0.001 HIS C1113 PHE 0.020 0.001 PHE B 449 TYR 0.033 0.001 TYR E 616 ARG 0.006 0.000 ARG C1092 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4146.53 seconds wall clock time: 76 minutes 42.88 seconds (4602.88 seconds total)