Starting phenix.real_space_refine on Wed Jul 30 01:00:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wth_21896/07_2025/6wth_21896.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wth_21896/07_2025/6wth_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/cci-nas-00/data/ceres_data/6wth_21896/07_2025/6wth_21896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wth_21896/07_2025/6wth_21896.map" model { file = "/net/cci-nas-00/data/ceres_data/6wth_21896/07_2025/6wth_21896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wth_21896/07_2025/6wth_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-5711/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: 8.00, per 1000 atoms: 0.68 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: 3.23 Conformation dependent library (CDL) restraints added in 1.5 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: 1.61 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: 3.88 Time building geometry restraints manager: 3.55 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.820 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- 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 : 0.003 0.065 12007 Z= 0.139 Angle : 0.605 18.580 16389 Z= 0.293 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 7) link_NAG-ASN : angle 1.05777 ( 21) link_BETA1-4 : bond 0.05311 ( 3) link_BETA1-4 : angle 9.55475 ( 9) hydrogen bonds : bond 0.23561 ( 457) hydrogen bonds : angle 8.90039 ( 1296) SS BOND : bond 0.01870 ( 25) SS BOND : angle 0.58241 ( 50) covalent geometry : bond 0.00244 (11972) covalent geometry : angle 0.56155 (16309) *********************** 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 to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 1.143 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: 0.2767 time to fit residues: 72.4855 Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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: 0.9980 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 HIS C 103 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS C 426 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092389 restraints weight = 19731.238| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.54 r_work: 0.3134 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.099 12007 Z= 0.445 Angle : 0.844 9.546 16389 Z= 0.417 Chirality : 0.050 0.203 1884 Planarity : 0.005 0.053 2128 Dihedral : 6.277 57.603 1907 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.05 % Allowed : 8.48 % Favored : 89.47 % 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: -2.21 (0.22), residues: 1163 helix: -0.93 (0.28), residues: 275 sheet: -1.84 (0.25), residues: 298 loop : -1.43 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 462 HIS 0.009 0.002 HIS B 473 PHE 0.019 0.003 PHE B 208 TYR 0.022 0.003 TYR B 269 ARG 0.007 0.001 ARG B 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 7) link_NAG-ASN : angle 2.45703 ( 21) link_BETA1-4 : bond 0.00684 ( 3) link_BETA1-4 : angle 1.99271 ( 9) hydrogen bonds : bond 0.04991 ( 457) hydrogen bonds : angle 5.65365 ( 1296) SS BOND : bond 0.00580 ( 25) SS BOND : angle 1.96350 ( 50) covalent geometry : bond 0.01055 (11972) covalent geometry : angle 0.83318 (16309) *********************** 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 115 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7780 (tppt) REVERT: B 341 GLU cc_start: 0.8620 (tt0) cc_final: 0.8236 (tm-30) REVERT: B 510 SER cc_start: 0.9134 (m) cc_final: 0.8714 (p) REVERT: C 231 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8274 (ttpp) outliers start: 22 outliers final: 15 residues processed: 113 average time/residue: 0.2167 time to fit residues: 36.9061 Evaluate side-chains 92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU 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 81 VAL 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 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.114815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095746 restraints weight = 19694.839| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.56 r_work: 0.3201 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12007 Z= 0.145 Angle : 0.530 8.333 16389 Z= 0.264 Chirality : 0.039 0.157 1884 Planarity : 0.003 0.043 2128 Dihedral : 5.297 52.511 1907 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.42 % Allowed : 8.20 % Favored : 89.38 % 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: -1.54 (0.23), residues: 1163 helix: -0.11 (0.30), residues: 294 sheet: -1.47 (0.25), residues: 315 loop : -1.13 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.005 0.001 HIS C 276 PHE 0.012 0.001 PHE C 219 TYR 0.018 0.001 TYR C 389 ARG 0.008 0.000 ARG B 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 7) link_NAG-ASN : angle 1.53150 ( 21) link_BETA1-4 : bond 0.00533 ( 3) link_BETA1-4 : angle 1.24974 ( 9) hydrogen bonds : bond 0.03670 ( 457) hydrogen bonds : angle 5.11791 ( 1296) SS BOND : bond 0.00275 ( 25) SS BOND : angle 1.43866 ( 50) covalent geometry : bond 0.00332 (11972) covalent geometry : angle 0.52138 (16309) *********************** 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 114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7700 (tppt) REVERT: B 323 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8358 (mp10) REVERT: B 341 GLU cc_start: 0.8461 (tt0) cc_final: 0.8137 (tm-30) REVERT: B 510 SER cc_start: 0.9130 (m) cc_final: 0.8718 (p) REVERT: C 231 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8254 (ttpp) outliers start: 26 outliers final: 17 residues processed: 109 average time/residue: 0.1980 time to fit residues: 33.0970 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 162 MET 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 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 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 93 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.096206 restraints weight = 19525.640| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.52 r_work: 0.3211 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12007 Z= 0.136 Angle : 0.506 6.694 16389 Z= 0.252 Chirality : 0.039 0.139 1884 Planarity : 0.003 0.040 2128 Dihedral : 4.834 51.171 1907 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.42 % Allowed : 8.67 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1163 helix: 0.48 (0.31), residues: 296 sheet: -1.23 (0.25), residues: 322 loop : -0.88 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS C 276 PHE 0.011 0.001 PHE C 219 TYR 0.012 0.001 TYR A 447 ARG 0.004 0.000 ARG C 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 7) link_NAG-ASN : angle 1.51790 ( 21) link_BETA1-4 : bond 0.00277 ( 3) link_BETA1-4 : angle 1.33783 ( 9) hydrogen bonds : bond 0.03296 ( 457) hydrogen bonds : angle 4.86684 ( 1296) SS BOND : bond 0.00273 ( 25) SS BOND : angle 1.17693 ( 50) covalent geometry : bond 0.00315 (11972) covalent geometry : angle 0.49897 (16309) *********************** 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 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7649 (tppt) REVERT: B 323 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: B 341 GLU cc_start: 0.8482 (tt0) cc_final: 0.8171 (tm-30) REVERT: B 510 SER cc_start: 0.9089 (m) cc_final: 0.8682 (p) REVERT: C 231 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8245 (ttpp) outliers start: 26 outliers final: 19 residues processed: 113 average time/residue: 0.1976 time to fit residues: 34.5644 Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 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 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.112858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093890 restraints weight = 19755.030| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.51 r_work: 0.3165 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12007 Z= 0.220 Angle : 0.583 6.860 16389 Z= 0.288 Chirality : 0.041 0.144 1884 Planarity : 0.003 0.040 2128 Dihedral : 4.947 53.502 1907 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.89 % Allowed : 8.95 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1163 helix: 0.73 (0.31), residues: 290 sheet: -1.11 (0.25), residues: 325 loop : -0.81 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS A 255 PHE 0.011 0.001 PHE C 261 TYR 0.016 0.001 TYR C 389 ARG 0.003 0.000 ARG C 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 7) link_NAG-ASN : angle 1.76313 ( 21) link_BETA1-4 : bond 0.00187 ( 3) link_BETA1-4 : angle 1.47972 ( 9) hydrogen bonds : bond 0.03578 ( 457) hydrogen bonds : angle 4.90480 ( 1296) SS BOND : bond 0.00380 ( 25) SS BOND : angle 1.39209 ( 50) covalent geometry : bond 0.00518 (11972) covalent geometry : angle 0.57506 (16309) *********************** 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 116 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7696 (tppt) REVERT: B 111 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8562 (mp) REVERT: B 323 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: B 341 GLU cc_start: 0.8541 (tt0) cc_final: 0.8230 (tm-30) REVERT: B 422 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8456 (m-30) REVERT: B 510 SER cc_start: 0.9084 (m) cc_final: 0.8659 (p) REVERT: C 231 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8259 (ttpp) outliers start: 31 outliers final: 23 residues processed: 108 average time/residue: 0.2197 time to fit residues: 35.8062 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE 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 111 LEU Chi-restraints excluded: chain B residue 152 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 422 ASP Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 81 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 117 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 418 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095027 restraints weight = 19477.679| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.37 r_work: 0.3172 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12007 Z= 0.128 Angle : 0.504 7.999 16389 Z= 0.252 Chirality : 0.038 0.186 1884 Planarity : 0.003 0.040 2128 Dihedral : 4.498 52.469 1905 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.70 % Allowed : 9.41 % 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: 0.93 (0.31), residues: 296 sheet: -0.92 (0.26), residues: 325 loop : -0.64 (0.28), residues: 542 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 0.016 0.001 TYR C 389 ARG 0.010 0.000 ARG B 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 7) link_NAG-ASN : angle 1.51319 ( 21) link_BETA1-4 : bond 0.00278 ( 3) link_BETA1-4 : angle 1.33759 ( 9) hydrogen bonds : bond 0.03139 ( 457) hydrogen bonds : angle 4.73078 ( 1296) SS BOND : bond 0.00277 ( 25) SS BOND : angle 1.10876 ( 50) covalent geometry : bond 0.00298 (11972) covalent geometry : angle 0.49742 (16309) *********************** 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 116 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7784 (tppt) REVERT: B 323 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8402 (mp10) REVERT: B 510 SER cc_start: 0.9114 (m) cc_final: 0.8742 (p) outliers start: 29 outliers final: 24 residues processed: 108 average time/residue: 0.2257 time to fit residues: 37.1625 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 321 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.090896 restraints weight = 20285.845| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.58 r_work: 0.3120 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 12007 Z= 0.369 Angle : 0.725 7.209 16389 Z= 0.356 Chirality : 0.046 0.171 1884 Planarity : 0.004 0.041 2128 Dihedral : 5.270 51.298 1905 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.08 % Allowed : 9.79 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1163 helix: 0.69 (0.30), residues: 291 sheet: -1.03 (0.26), residues: 325 loop : -0.91 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 462 HIS 0.005 0.001 HIS B 110 PHE 0.017 0.002 PHE C 261 TYR 0.018 0.002 TYR C 389 ARG 0.006 0.001 ARG B 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 7) link_NAG-ASN : angle 2.16831 ( 21) link_BETA1-4 : bond 0.00191 ( 3) link_BETA1-4 : angle 1.73320 ( 9) hydrogen bonds : bond 0.04143 ( 457) hydrogen bonds : angle 5.07333 ( 1296) SS BOND : bond 0.00535 ( 25) SS BOND : angle 1.54231 ( 50) covalent geometry : bond 0.00874 (11972) covalent geometry : angle 0.71592 (16309) *********************** 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 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 323 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8321 (mp10) REVERT: B 510 SER cc_start: 0.9085 (m) cc_final: 0.8672 (p) REVERT: C 363 PHE cc_start: 0.8455 (m-80) cc_final: 0.8252 (m-80) outliers start: 33 outliers final: 24 residues processed: 102 average time/residue: 0.2639 time to fit residues: 43.2536 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE 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 111 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 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 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 139 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 154 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094960 restraints weight = 19844.484| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.57 r_work: 0.3186 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12007 Z= 0.132 Angle : 0.531 8.975 16389 Z= 0.264 Chirality : 0.039 0.185 1884 Planarity : 0.003 0.039 2128 Dihedral : 4.547 44.740 1904 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.24 % Allowed : 10.72 % Favored : 87.05 % 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: 1.01 (0.31), residues: 295 sheet: -0.90 (0.26), residues: 326 loop : -0.71 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 470 HIS 0.004 0.001 HIS C 276 PHE 0.009 0.001 PHE C 459 TYR 0.019 0.001 TYR C 389 ARG 0.008 0.000 ARG B 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 7) link_NAG-ASN : angle 1.66346 ( 21) link_BETA1-4 : bond 0.00273 ( 3) link_BETA1-4 : angle 1.37522 ( 9) hydrogen bonds : bond 0.03249 ( 457) hydrogen bonds : angle 4.80433 ( 1296) SS BOND : bond 0.00300 ( 25) SS BOND : angle 1.18359 ( 50) covalent geometry : bond 0.00306 (11972) covalent geometry : angle 0.52398 (16309) *********************** 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 to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7752 (tppt) REVERT: B 322 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7788 (tt0) REVERT: B 323 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8372 (mp10) REVERT: B 510 SER cc_start: 0.9074 (m) cc_final: 0.8659 (p) outliers start: 24 outliers final: 21 residues processed: 101 average time/residue: 0.2042 time to fit residues: 32.1329 Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 114 optimal weight: 0.0770 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** 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 = 0.3583 r_free = 0.3583 target = 0.113299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094229 restraints weight = 19914.411| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.57 r_work: 0.3175 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12007 Z= 0.170 Angle : 0.546 7.975 16389 Z= 0.271 Chirality : 0.040 0.181 1884 Planarity : 0.003 0.038 2128 Dihedral : 4.376 30.586 1902 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.61 % Allowed : 10.53 % 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: -0.47 (0.25), residues: 1163 helix: 1.09 (0.31), residues: 294 sheet: -0.82 (0.26), residues: 326 loop : -0.68 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 470 HIS 0.003 0.001 HIS C 276 PHE 0.009 0.001 PHE C 219 TYR 0.019 0.001 TYR C 389 ARG 0.008 0.000 ARG B 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 7) link_NAG-ASN : angle 1.73961 ( 21) link_BETA1-4 : bond 0.00208 ( 3) link_BETA1-4 : angle 1.44975 ( 9) hydrogen bonds : bond 0.03298 ( 457) hydrogen bonds : angle 4.74170 ( 1296) SS BOND : bond 0.00322 ( 25) SS BOND : angle 1.27720 ( 50) covalent geometry : bond 0.00400 (11972) covalent geometry : angle 0.53858 (16309) *********************** 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 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7729 (tppt) REVERT: B 322 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7800 (tt0) REVERT: B 323 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8402 (mp10) REVERT: B 510 SER cc_start: 0.9090 (m) cc_final: 0.8671 (p) outliers start: 28 outliers final: 23 residues processed: 97 average time/residue: 0.2067 time to fit residues: 31.2451 Evaluate side-chains 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 187 HIS Chi-restraints excluded: chain B residue 191 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 124 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.092741 restraints weight = 19916.336| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.55 r_work: 0.3153 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12007 Z= 0.247 Angle : 0.614 7.569 16389 Z= 0.302 Chirality : 0.042 0.181 1884 Planarity : 0.003 0.039 2128 Dihedral : 4.666 31.121 1902 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.33 % Allowed : 11.00 % 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: -0.67 (0.24), residues: 1163 helix: 0.91 (0.31), residues: 296 sheet: -0.87 (0.26), residues: 326 loop : -0.84 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 470 HIS 0.005 0.001 HIS B 110 PHE 0.012 0.001 PHE C 261 TYR 0.023 0.001 TYR C 425 ARG 0.008 0.000 ARG B 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 7) link_NAG-ASN : angle 1.98779 ( 21) link_BETA1-4 : bond 0.00126 ( 3) link_BETA1-4 : angle 1.54888 ( 9) hydrogen bonds : bond 0.03609 ( 457) hydrogen bonds : angle 4.86480 ( 1296) SS BOND : bond 0.00401 ( 25) SS BOND : angle 1.42893 ( 50) covalent geometry : bond 0.00580 (11972) covalent geometry : angle 0.60535 (16309) ********************** 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 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7742 (tppt) REVERT: B 323 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: B 510 SER cc_start: 0.9091 (m) cc_final: 0.8663 (p) outliers start: 25 outliers final: 23 residues processed: 95 average time/residue: 0.2003 time to fit residues: 29.5304 Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 187 HIS Chi-restraints excluded: chain B residue 191 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 56 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094337 restraints weight = 19901.951| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.48 r_work: 0.3172 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12007 Z= 0.188 Angle : 0.561 7.529 16389 Z= 0.277 Chirality : 0.040 0.183 1884 Planarity : 0.003 0.039 2128 Dihedral : 4.497 30.799 1902 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.42 % Allowed : 11.00 % Favored : 86.58 % 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: -0.59 (0.24), residues: 1163 helix: 0.94 (0.31), residues: 300 sheet: -0.81 (0.26), residues: 326 loop : -0.79 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 470 HIS 0.004 0.001 HIS B 110 PHE 0.010 0.001 PHE C 261 TYR 0.019 0.001 TYR C 425 ARG 0.008 0.000 ARG B 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 7) link_NAG-ASN : angle 1.85559 ( 21) link_BETA1-4 : bond 0.00130 ( 3) link_BETA1-4 : angle 1.45123 ( 9) hydrogen bonds : bond 0.03369 ( 457) hydrogen bonds : angle 4.78884 ( 1296) SS BOND : bond 0.00328 ( 25) SS BOND : angle 1.31067 ( 50) covalent geometry : bond 0.00443 (11972) covalent geometry : angle 0.55269 (16309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6694.80 seconds wall clock time: 118 minutes 39.04 seconds (7119.04 seconds total)