Starting phenix.real_space_refine on Thu Sep 26 02:30:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/09_2024/6wth_21896.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/09_2024/6wth_21896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/09_2024/6wth_21896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/09_2024/6wth_21896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/09_2024/6wth_21896.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wth_21896/09_2024/6wth_21896.cif" } resolution = 3.06 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= 0.005 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 Na 1 4.78 5 C 7374 2.51 5 N 2015 2.21 5 O 2265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11740 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3093 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 19, 'TRANS': 361} Chain breaks: 2 Chain: "B" Number of atoms: 3316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3316 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 21, 'TRANS': 391} Chain breaks: 3 Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3135 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 370} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "F" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 365 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'TRANS': 72} Chain breaks: 3 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'UNK:plan-1': 73} Unresolved non-hydrogen planarities: 73 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' NA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.50, per 1000 atoms: 0.72 Number of scatterers: 11740 At special positions: 0 Unit cell: (101.26, 102.92, 162.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 Na 1 11.00 O 2265 8.00 N 2015 7.00 C 7374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 305 " distance=2.05 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 236 " distance=2.05 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 289 " distance=2.05 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 479 " distance=2.05 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 475 " distance=2.05 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 471 " distance=2.05 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 272 " distance=2.05 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 189 " distance=2.05 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 203 " distance=2.05 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 256 " distance=2.05 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 448 " distance=2.05 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 444 " distance=2.05 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 440 " distance=2.04 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 415 " distance=2.05 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 283 " distance=2.05 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 214 " distance=2.05 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 267 " distance=2.05 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 457 " distance=2.05 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 453 " distance=2.05 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 449 " distance=2.05 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 434 " distance=2.05 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 423 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 232 " " NAG A 702 " - " ASN A 397 " " NAG B 700 " - " ASN B 141 " " NAG B 705 " - " ASN B 449 " " NAG H 1 " - " ASN B 207 " " NAG I 1 " - " ASN B 260 " " NAG J 1 " - " ASN C 271 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.3 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 28.9% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 143 through 162 removed outlier: 3.536A pdb=" N GLU A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 412 through 430 Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 498 through 510 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.518A pdb=" N ILE B 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.508A pdb=" N ALA B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.869A pdb=" N TRP B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 228 removed outlier: 3.760A pdb=" N THR B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.225A pdb=" N GLU B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.598A pdb=" N ASP B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.550A pdb=" N PHE B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.611A pdb=" N ARG B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 481 Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 221 through 238 removed outlier: 3.677A pdb=" N ASN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.552A pdb=" N TYR C 317 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 Processing helix chain 'C' and resid 390 through 407 Processing helix chain 'C' and resid 431 through 444 removed outlier: 3.531A pdb=" N TYR C 436 " --> pdb=" O MET C 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 removed outlier: 3.634A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Proline residue: C 482 - end of helix removed outlier: 3.634A pdb=" N GLN C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 121 removed outlier: 3.537A pdb=" N ASN A 121 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 533 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 534 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 523 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER A 329 " --> pdb=" O CYS A 282 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS A 282 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET A 331 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 121 removed outlier: 3.537A pdb=" N ASN A 121 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 533 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 534 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.107A pdb=" N LEU A 125 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 298 removed outlier: 4.615A pdb=" N ASN A 304 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 349 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.753A pdb=" N GLN A 189 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 226 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 79 through 86 removed outlier: 3.501A pdb=" N TYR B 504 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 500 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL B 348 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N PHE B 502 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N LYS B 350 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N TYR B 504 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 12.345A pdb=" N GLN B 352 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N THR B 506 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 254 through 255 removed outlier: 6.354A pdb=" N ILE B 298 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS B 249 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS B 296 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 500 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL B 348 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N PHE B 502 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N LYS B 350 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N TYR B 504 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 12.345A pdb=" N GLN B 352 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N THR B 506 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.963A pdb=" N MET B 90 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 266 removed outlier: 6.909A pdb=" N ASN B 271 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN B 99 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AB2, first strand: chain 'B' and resid 361 through 362 Processing sheet with id=AB3, first strand: chain 'C' and resid 81 through 89 removed outlier: 4.629A pdb=" N LEU C 359 " --> pdb=" O ASN C 512 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AB5, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.279A pdb=" N ASN C 282 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN C 101 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.279A pdb=" N ASN C 282 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN C 101 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.895A pdb=" N VAL C 201 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 257 through 259 removed outlier: 6.547A pdb=" N ILE C 309 " --> pdb=" O VAL C 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 49 removed outlier: 6.829A pdb=" N UNK D 36 " --> pdb=" O UNK D 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 17 through 23 Processing sheet with id=AC3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.712A pdb=" N UNK E 36 " --> pdb=" O UNK E 48 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N UNK E 50 " --> pdb=" O UNK E 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N UNK E 34 " --> pdb=" O UNK E 50 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N UNK E 111 " --> pdb=" O UNK E 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.601A pdb=" N UNK F 18 " --> pdb=" O UNK F 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 37 through 39 removed outlier: 3.584A pdb=" N UNK F 92 " --> pdb=" O UNK F 114 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N UNK F 112 " --> pdb=" O UNK F 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 49 through 51 Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 41 through 42 480 hydrogen bonds defined for protein. 1296 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: 4.19 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3911 1.34 - 1.46: 2375 1.46 - 1.58: 5566 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 11972 Sorted by residual: bond pdb=" C1 NAG B 700 " pdb=" O5 NAG B 700 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C3 NAG I 2 " pdb=" O3 NAG I 2 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B 705 " pdb=" O5 NAG B 705 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 11967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 15692 1.41 - 2.83: 542 2.83 - 4.24: 67 4.24 - 5.65: 6 5.65 - 7.06: 2 Bond angle restraints: 16309 Sorted by residual: angle pdb=" C UNK G 70 " pdb=" N UNK G 71 " pdb=" CA UNK G 71 " ideal model delta sigma weight residual 121.70 128.76 -7.06 1.80e+00 3.09e-01 1.54e+01 angle pdb=" N ILE B 108 " pdb=" CA ILE B 108 " pdb=" C ILE B 108 " ideal model delta sigma weight residual 113.20 109.49 3.71 9.60e-01 1.09e+00 1.49e+01 angle pdb=" C GLY A 520 " pdb=" N VAL A 521 " pdb=" CA VAL A 521 " ideal model delta sigma weight residual 120.49 123.67 -3.18 1.38e+00 5.25e-01 5.31e+00 angle pdb=" C GLU C 367 " pdb=" CA GLU C 367 " pdb=" CB GLU C 367 " ideal model delta sigma weight residual 113.57 110.32 3.25 1.57e+00 4.06e-01 4.28e+00 angle pdb=" C GLU C 374 " pdb=" N ASP C 375 " pdb=" CA ASP C 375 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.79e+00 ... (remaining 16304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.34: 6945 11.34 - 22.68: 286 22.68 - 34.02: 88 34.02 - 45.36: 23 45.36 - 56.70: 9 Dihedral angle restraints: 7351 sinusoidal: 2628 harmonic: 4723 Sorted by residual: dihedral pdb=" CA SER C 366 " pdb=" C SER C 366 " pdb=" N GLU C 367 " pdb=" CA GLU C 367 " ideal model delta harmonic sigma weight residual -180.00 -164.08 -15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" N ASN A 397 " pdb=" CA ASN A 397 " pdb=" CB ASN A 397 " pdb=" CG ASN A 397 " ideal model delta sinusoidal sigma weight residual -60.00 -116.70 56.70 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB CYS A 229 " pdb=" SG CYS A 229 " pdb=" SG CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sinusoidal sigma weight residual 93.00 117.12 -24.12 1 1.00e+01 1.00e-02 8.38e+00 ... (remaining 7348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 1883 0.226 - 0.453: 0 0.453 - 0.679: 0 0.679 - 0.905: 0 0.905 - 1.132: 1 Chirality restraints: 1884 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-02 2.50e+03 3.20e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.29e+01 ... (remaining 1881 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.035 2.00e-02 2.50e+03 2.85e-02 1.02e+01 pdb=" C7 NAG I 2 " -0.010 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.045 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 299 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 300 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 300 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 300 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 368 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.92e-01 pdb=" N PRO B 369 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 369 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 369 " 0.014 5.00e-02 4.00e+02 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1209 2.75 - 3.29: 10951 3.29 - 3.83: 18362 3.83 - 4.36: 21434 4.36 - 4.90: 38143 Nonbonded interactions: 90099 Sorted by model distance: nonbonded pdb=" OG SER A 295 " pdb=" OG1 THR A 307 " model vdw 2.217 3.040 nonbonded pdb=" O LEU C 365 " pdb=" OG SER C 370 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR C 385 " pdb=" OE1 GLN C 414 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP B 331 " pdb=" NH2 ARG B 388 " model vdw 2.274 3.120 nonbonded pdb=" O PHE A 254 " pdb=" ND2 ASN A 258 " model vdw 2.307 3.120 ... (remaining 90094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 16 through 122) selection = (chain 'F' and resid 11 through 116) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.020 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 : 0.002 0.044 11972 Z= 0.144 Angle : 0.562 7.064 16309 Z= 0.283 Chirality : 0.045 1.132 1884 Planarity : 0.002 0.029 2128 Dihedral : 7.452 56.696 4196 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.84 % Allowed : 2.80 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.20), residues: 1163 helix: -2.95 (0.19), residues: 292 sheet: -2.24 (0.25), residues: 307 loop : -1.87 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 462 HIS 0.002 0.000 HIS C 276 PHE 0.005 0.001 PHE A 297 TYR 0.008 0.001 TYR C 425 ARG 0.001 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: B 395 MET cc_start: 0.7966 (tpt) cc_final: 0.7256 (tpp) REVERT: C 231 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7522 (ttpp) outliers start: 9 outliers final: 4 residues processed: 191 average time/residue: 0.2636 time to fit residues: 69.0788 Evaluate side-chains 102 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 0.0370 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 336 GLN A 532 ASN B 403 HIS ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 358 HIS C 426 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 11972 Z= 0.466 Angle : 0.691 8.561 16309 Z= 0.344 Chirality : 0.045 0.180 1884 Planarity : 0.004 0.043 2128 Dihedral : 5.780 57.648 1907 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.77 % Allowed : 7.92 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.22), residues: 1163 helix: -0.89 (0.27), residues: 282 sheet: -1.78 (0.25), residues: 303 loop : -1.32 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 462 HIS 0.007 0.002 HIS B 473 PHE 0.018 0.002 PHE B 208 TYR 0.018 0.002 TYR C 508 ARG 0.006 0.001 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.8019 (tt0) cc_final: 0.7678 (tm-30) REVERT: B 510 SER cc_start: 0.8838 (m) cc_final: 0.8342 (p) REVERT: C 231 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7458 (ttpp) REVERT: C 304 TYR cc_start: 0.8839 (m-80) cc_final: 0.8609 (m-80) outliers start: 19 outliers final: 13 residues processed: 117 average time/residue: 0.2404 time to fit residues: 42.0382 Evaluate side-chains 98 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 113 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11972 Z= 0.171 Angle : 0.489 9.683 16309 Z= 0.246 Chirality : 0.038 0.138 1884 Planarity : 0.003 0.040 2128 Dihedral : 5.019 52.606 1907 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.14 % Allowed : 8.11 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1163 helix: 0.11 (0.30), residues: 287 sheet: -1.41 (0.25), residues: 316 loop : -1.10 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.004 0.001 HIS C 276 PHE 0.012 0.001 PHE C 219 TYR 0.018 0.001 TYR C 389 ARG 0.005 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.7885 (tt0) cc_final: 0.7589 (tm-30) REVERT: B 510 SER cc_start: 0.8821 (m) cc_final: 0.8311 (p) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 0.2121 time to fit residues: 36.6250 Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11972 Z= 0.297 Angle : 0.550 6.880 16309 Z= 0.274 Chirality : 0.040 0.148 1884 Planarity : 0.003 0.041 2128 Dihedral : 4.924 50.798 1907 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.52 % Allowed : 8.29 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.24), residues: 1163 helix: 0.27 (0.30), residues: 306 sheet: -1.23 (0.25), residues: 323 loop : -0.96 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.004 0.001 HIS A 255 PHE 0.011 0.001 PHE C 219 TYR 0.013 0.001 TYR C 508 ARG 0.003 0.001 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.5973 (mpp) REVERT: B 323 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: B 341 GLU cc_start: 0.7950 (tt0) cc_final: 0.7646 (tm-30) REVERT: B 510 SER cc_start: 0.8774 (m) cc_final: 0.8289 (p) outliers start: 27 outliers final: 19 residues processed: 111 average time/residue: 0.2099 time to fit residues: 35.7240 Evaluate side-chains 102 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11972 Z= 0.384 Angle : 0.605 6.784 16309 Z= 0.301 Chirality : 0.042 0.145 1884 Planarity : 0.003 0.042 2128 Dihedral : 5.101 53.811 1907 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.70 % Allowed : 8.48 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1163 helix: 0.61 (0.30), residues: 294 sheet: -1.06 (0.25), residues: 325 loop : -0.87 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 462 HIS 0.005 0.001 HIS A 255 PHE 0.011 0.001 PHE C 219 TYR 0.022 0.002 TYR C 389 ARG 0.007 0.001 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 82 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6030 (mpp) REVERT: B 323 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: B 341 GLU cc_start: 0.8009 (tt0) cc_final: 0.7724 (tm-30) REVERT: B 510 SER cc_start: 0.8784 (m) cc_final: 0.8334 (p) outliers start: 29 outliers final: 19 residues processed: 105 average time/residue: 0.2300 time to fit residues: 36.4118 Evaluate side-chains 99 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 532 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11972 Z= 0.172 Angle : 0.487 6.027 16309 Z= 0.245 Chirality : 0.038 0.185 1884 Planarity : 0.003 0.039 2128 Dihedral : 4.588 52.594 1907 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.89 % Allowed : 9.23 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1163 helix: 0.86 (0.31), residues: 303 sheet: -0.86 (0.26), residues: 325 loop : -0.66 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 470 HIS 0.004 0.001 HIS C 276 PHE 0.010 0.001 PHE C 219 TYR 0.015 0.001 TYR C 389 ARG 0.010 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.5989 (mpp) REVERT: B 323 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: B 341 GLU cc_start: 0.7939 (tt0) cc_final: 0.7715 (tm-30) REVERT: B 510 SER cc_start: 0.8786 (m) cc_final: 0.8340 (p) outliers start: 31 outliers final: 22 residues processed: 112 average time/residue: 0.2094 time to fit residues: 36.4394 Evaluate side-chains 104 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11972 Z= 0.260 Angle : 0.538 8.904 16309 Z= 0.269 Chirality : 0.039 0.168 1884 Planarity : 0.003 0.042 2128 Dihedral : 4.611 52.503 1907 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.61 % Allowed : 9.69 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1163 helix: 0.78 (0.30), residues: 308 sheet: -0.82 (0.26), residues: 325 loop : -0.68 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 229 HIS 0.003 0.001 HIS C 276 PHE 0.010 0.001 PHE C 219 TYR 0.018 0.001 TYR C 389 ARG 0.009 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 83 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6026 (mpp) REVERT: B 193 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8655 (ttm) REVERT: B 323 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: B 341 GLU cc_start: 0.7952 (tt0) cc_final: 0.7746 (tm-30) REVERT: B 510 SER cc_start: 0.8778 (m) cc_final: 0.8320 (p) outliers start: 28 outliers final: 22 residues processed: 102 average time/residue: 0.2000 time to fit residues: 31.9687 Evaluate side-chains 103 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11972 Z= 0.312 Angle : 0.566 8.446 16309 Z= 0.282 Chirality : 0.041 0.160 1884 Planarity : 0.003 0.039 2128 Dihedral : 4.738 53.869 1907 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.61 % Allowed : 10.16 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1163 helix: 0.86 (0.31), residues: 302 sheet: -0.78 (0.26), residues: 325 loop : -0.70 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 470 HIS 0.004 0.001 HIS B 110 PHE 0.010 0.001 PHE C 219 TYR 0.016 0.001 TYR C 389 ARG 0.009 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.5978 (mpp) REVERT: B 323 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: B 341 GLU cc_start: 0.7965 (tt0) cc_final: 0.7744 (tm-30) REVERT: B 510 SER cc_start: 0.8792 (m) cc_final: 0.8322 (p) outliers start: 28 outliers final: 24 residues processed: 101 average time/residue: 0.2108 time to fit residues: 33.3580 Evaluate side-chains 104 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN B 160 HIS ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 11972 Z= 0.503 Angle : 0.692 9.800 16309 Z= 0.342 Chirality : 0.045 0.181 1884 Planarity : 0.004 0.041 2128 Dihedral : 5.228 49.026 1907 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.80 % Allowed : 10.53 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1163 helix: 0.74 (0.30), residues: 295 sheet: -0.91 (0.26), residues: 325 loop : -0.90 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 462 HIS 0.006 0.001 HIS B 110 PHE 0.012 0.002 PHE C 154 TYR 0.015 0.002 TYR C 389 ARG 0.007 0.001 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6065 (mpp) REVERT: B 193 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8764 (ttm) REVERT: B 323 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7923 (mp10) REVERT: B 341 GLU cc_start: 0.8021 (tt0) cc_final: 0.7761 (tm-30) REVERT: B 510 SER cc_start: 0.8809 (m) cc_final: 0.8341 (p) outliers start: 30 outliers final: 19 residues processed: 101 average time/residue: 0.2058 time to fit residues: 32.4589 Evaluate side-chains 100 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11972 Z= 0.296 Angle : 0.570 9.542 16309 Z= 0.283 Chirality : 0.040 0.186 1884 Planarity : 0.003 0.039 2128 Dihedral : 4.737 43.468 1904 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.14 % Allowed : 11.00 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1163 helix: 0.80 (0.31), residues: 302 sheet: -0.82 (0.26), residues: 325 loop : -0.78 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 470 HIS 0.004 0.001 HIS C 276 PHE 0.009 0.001 PHE C 219 TYR 0.015 0.001 TYR C 389 ARG 0.009 0.000 ARG B 410 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6043 (mpp) REVERT: B 323 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: B 341 GLU cc_start: 0.7942 (tt0) cc_final: 0.7725 (tm-30) REVERT: B 510 SER cc_start: 0.8794 (m) cc_final: 0.8339 (p) outliers start: 23 outliers final: 18 residues processed: 95 average time/residue: 0.2049 time to fit residues: 30.5978 Evaluate side-chains 97 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094925 restraints weight = 19691.584| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.56 r_work: 0.3186 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11972 Z= 0.221 Angle : 0.522 8.974 16309 Z= 0.261 Chirality : 0.039 0.183 1884 Planarity : 0.003 0.038 2128 Dihedral : 4.286 31.189 1902 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.96 % Allowed : 11.28 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1163 helix: 1.02 (0.31), residues: 302 sheet: -0.67 (0.27), residues: 325 loop : -0.63 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 470 HIS 0.004 0.001 HIS C 276 PHE 0.008 0.001 PHE C 219 TYR 0.014 0.001 TYR C 389 ARG 0.009 0.000 ARG B 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.97 seconds wall clock time: 44 minutes 13.79 seconds (2653.79 seconds total)