Starting phenix.real_space_refine on Fri Sep 11 21:50:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wth_21896/09_2026/6wth_21896.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wth_21896/09_2026/6wth_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6wth_21896/09_2026/6wth_21896.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wth_21896/09_2026/6wth_21896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wth_21896/09_2026/6wth_21896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wth_21896/09_2026/6wth_21896.map" model { file = "/net/cci-nas-00/data/ceres_data/6wth_21896/09_2026/6wth_21896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wth_21896/09_2026/6wth_21896.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.63, per 1000 atoms: 0.22 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: 0.97 Conformation dependent library (CDL) restraints added in 516.8 milliseconds 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: 0.30 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: 2.34 Time building geometry restraints manager: 1.27 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: 6771 11.34 - 22.68: 280 22.68 - 34.02: 74 34.02 - 45.36: 15 45.36 - 56.70: 1 Dihedral angle restraints: 7141 sinusoidal: 2418 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 7138 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: 6.050 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 6.813 56.696 3986 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG B 388 TYR 0.008 0.001 TYR C 425 PHE 0.005 0.001 PHE A 297 TRP 0.005 0.001 TRP B 462 HIS 0.002 0.000 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (11972) covalent geometry : angle 0.56155 / 0.28 (16309) SS BOND : bond 0.01870 / 1.23 ( 25) SS BOND : angle 0.58241 / 0.36 ( 50) hydrogen bonds : bond 0.23561 / 15.13 ( 457) hydrogen bonds : angle 8.90039 / 6.19 ( 1296) link_BETA1-4 : bond 0.05311 / 2.42 ( 3) link_BETA1-4 : angle 9.55475 / 5.05 ( 9) link_NAG-ASN : bond 0.00137 / 0.06 ( 7) link_NAG-ASN : angle 1.05777 / 0.63 ( 21) *********************** 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 : 0.515 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: 0.1252 time to fit residues: 33.2812 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 : 0.400 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN A 255 HIS A 336 GLN A 532 ASN B 403 HIS ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 358 HIS C 426 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.119263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100476 restraints weight = 19528.837| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.55 r_work: 0.3275 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12007 Z= 0.173 Angle : 0.548 9.098 16389 Z= 0.276 Chirality : 0.040 0.182 1884 Planarity : 0.003 0.035 2128 Dihedral : 3.807 42.094 1697 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.77 % Allowed : 7.27 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.22), residues: 1163 helix: -0.88 (0.27), residues: 295 sheet: -1.76 (0.25), residues: 299 loop : -1.32 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 90 TYR 0.014 0.001 TYR C 508 PHE 0.013 0.001 PHE B 208 TRP 0.010 0.001 TRP B 462 HIS 0.005 0.001 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (11972) covalent geometry : angle 0.53821 / 0.27 (16309) SS BOND : bond 0.00355 / 0.22 ( 25) SS BOND : angle 1.64889 / 0.99 ( 50) hydrogen bonds : bond 0.04161 / 2.74 ( 457) hydrogen bonds : angle 5.41385 / 3.74 ( 1296) link_BETA1-4 : bond 0.00628 / 0.32 ( 3) link_BETA1-4 : angle 1.29459 / 0.69 ( 9) link_NAG-ASN : bond 0.00538 / 0.26 ( 7) link_NAG-ASN : angle 1.55542 / 0.94 ( 21) *********************** 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 122 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.8515 (tt0) cc_final: 0.8153 (tm-30) REVERT: B 510 SER cc_start: 0.9085 (m) cc_final: 0.8556 (p) REVERT: C 231 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8332 (ttpp) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.0931 time to fit residues: 16.9041 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 368 VAL 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 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 72 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101718 restraints weight = 19738.492| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.57 r_work: 0.3292 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12007 Z= 0.094 Angle : 0.449 7.233 16389 Z= 0.227 Chirality : 0.037 0.145 1884 Planarity : 0.003 0.033 2128 Dihedral : 3.629 42.977 1697 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.96 % Allowed : 7.46 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.23), residues: 1163 helix: 0.21 (0.30), residues: 294 sheet: -1.33 (0.25), residues: 312 loop : -1.02 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 90 TYR 0.016 0.001 TYR C 389 PHE 0.009 0.001 PHE C 219 TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (11972) covalent geometry : angle 0.44573 / 0.23 (16309) SS BOND : bond 0.00265 / 0.18 ( 25) SS BOND : angle 0.82821 / 0.53 ( 50) hydrogen bonds : bond 0.03358 / 2.24 ( 457) hydrogen bonds : angle 4.88031 / 3.37 ( 1296) link_BETA1-4 : bond 0.00482 / 0.25 ( 3) link_BETA1-4 : angle 1.04347 / 0.59 ( 9) link_NAG-ASN : bond 0.00191 / 0.09 ( 7) link_NAG-ASN : angle 1.11285 / 0.67 ( 21) *********************** 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 125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.8425 (tt0) cc_final: 0.8076 (tm-30) REVERT: B 510 SER cc_start: 0.9063 (m) cc_final: 0.8561 (p) REVERT: C 231 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8280 (ttpp) outliers start: 21 outliers final: 13 residues processed: 119 average time/residue: 0.0855 time to fit residues: 15.5085 Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 428 SER 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 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 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.112519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093386 restraints weight = 20032.317| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.55 r_work: 0.3152 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 12007 Z= 0.302 Angle : 0.684 8.226 16389 Z= 0.337 Chirality : 0.045 0.187 1884 Planarity : 0.004 0.041 2128 Dihedral : 4.767 53.063 1697 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.42 % Allowed : 8.29 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.23), residues: 1163 helix: 0.29 (0.30), residues: 289 sheet: -1.25 (0.25), residues: 315 loop : -1.03 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 324 TYR 0.018 0.002 TYR C 508 PHE 0.015 0.002 PHE A 226 TRP 0.016 0.002 TRP B 462 HIS 0.007 0.001 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.30 (11972) covalent geometry : angle 0.67645 / 0.33 (16309) SS BOND : bond 0.00474 / 0.31 ( 25) SS BOND : angle 1.38462 / 0.84 ( 50) hydrogen bonds : bond 0.04060 / 2.70 ( 457) hydrogen bonds : angle 5.07321 / 3.53 ( 1296) link_BETA1-4 : bond 0.00267 / 0.13 ( 3) link_BETA1-4 : angle 1.47153 / 0.79 ( 9) link_NAG-ASN : bond 0.00317 / 0.14 ( 7) link_NAG-ASN : angle 1.96289 / 1.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 GLU cc_start: 0.8570 (tt0) cc_final: 0.8206 (tm-30) REVERT: B 510 SER cc_start: 0.9078 (m) cc_final: 0.8596 (p) REVERT: C 231 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8313 (ttpp) outliers start: 26 outliers final: 17 residues processed: 111 average time/residue: 0.0889 time to fit residues: 15.3812 Evaluate side-chains 101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 256 CYS 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 Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.115046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.096196 restraints weight = 19708.643| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.53 r_work: 0.3206 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2909 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= 0.136 Angle : 0.507 6.847 16389 Z= 0.254 Chirality : 0.038 0.172 1884 Planarity : 0.003 0.041 2128 Dihedral : 4.291 51.772 1697 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.96 % Allowed : 8.95 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.24), residues: 1163 helix: 0.52 (0.30), residues: 308 sheet: -1.00 (0.25), residues: 322 loop : -0.81 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 410 TYR 0.016 0.001 TYR C 389 PHE 0.010 0.001 PHE C 219 TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11972) covalent geometry : angle 0.50180 / 0.25 (16309) SS BOND : bond 0.00370 / 0.20 ( 25) SS BOND : angle 1.05172 / 0.65 ( 50) hydrogen bonds : bond 0.03254 / 2.17 ( 457) hydrogen bonds : angle 4.76186 / 3.30 ( 1296) link_BETA1-4 : bond 0.00404 / 0.20 ( 3) link_BETA1-4 : angle 1.15836 / 0.63 ( 9) link_NAG-ASN : bond 0.00119 / 0.05 ( 7) link_NAG-ASN : angle 1.46628 / 0.87 ( 21) *********************** 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 114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8388 (mp10) REVERT: B 341 GLU cc_start: 0.8486 (tt0) cc_final: 0.8164 (tm-30) REVERT: B 510 SER cc_start: 0.9083 (m) cc_final: 0.8660 (p) REVERT: C 231 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8280 (ttpp) outliers start: 21 outliers final: 16 residues processed: 109 average time/residue: 0.0962 time to fit residues: 16.1559 Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR 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 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 357 MET Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 119 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.112098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093152 restraints weight = 20067.117| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.53 r_work: 0.3155 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3213 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= 0.236 Angle : 0.611 8.393 16389 Z= 0.301 Chirality : 0.042 0.156 1884 Planarity : 0.003 0.042 2128 Dihedral : 4.680 54.020 1697 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.05 % Allowed : 9.60 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.24), residues: 1163 helix: 0.87 (0.31), residues: 290 sheet: -1.00 (0.26), residues: 318 loop : -0.76 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 410 TYR 0.015 0.001 TYR C 389 PHE 0.011 0.001 PHE C 219 TRP 0.011 0.001 TRP B 462 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (11972) covalent geometry : angle 0.60396 / 0.30 (16309) SS BOND : bond 0.00422 / 0.27 ( 25) SS BOND : angle 1.27081 / 0.77 ( 50) hydrogen bonds : bond 0.03661 / 2.44 ( 457) hydrogen bonds : angle 4.83537 / 3.36 ( 1296) link_BETA1-4 : bond 0.00300 / 0.15 ( 3) link_BETA1-4 : angle 1.35373 / 0.72 ( 9) link_NAG-ASN : bond 0.00247 / 0.11 ( 7) link_NAG-ASN : angle 1.88205 / 1.12 ( 21) *********************** 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 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: B 341 GLU cc_start: 0.8560 (tt0) cc_final: 0.8255 (tm-30) REVERT: B 510 SER cc_start: 0.9106 (m) cc_final: 0.8634 (p) REVERT: C 231 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8315 (ttpp) outliers start: 22 outliers final: 19 residues processed: 101 average time/residue: 0.0900 time to fit residues: 14.0982 Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR 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 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 99 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.111999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093711 restraints weight = 19482.654| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.34 r_work: 0.3150 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12007 Z= 0.173 Angle : 0.543 8.415 16389 Z= 0.269 Chirality : 0.040 0.173 1884 Planarity : 0.003 0.039 2128 Dihedral : 4.496 54.052 1697 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.61 % Allowed : 9.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.24), residues: 1163 helix: 0.82 (0.31), residues: 302 sheet: -0.87 (0.26), residues: 325 loop : -0.63 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 410 TYR 0.017 0.001 TYR C 389 PHE 0.010 0.001 PHE C 219 TRP 0.010 0.001 TRP B 470 HIS 0.004 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (11972) covalent geometry : angle 0.53656 / 0.27 (16309) SS BOND : bond 0.00352 / 0.22 ( 25) SS BOND : angle 1.12503 / 0.69 ( 50) hydrogen bonds : bond 0.03336 / 2.23 ( 457) hydrogen bonds : angle 4.72782 / 3.28 ( 1296) link_BETA1-4 : bond 0.00310 / 0.16 ( 3) link_BETA1-4 : angle 1.25438 / 0.68 ( 9) link_NAG-ASN : bond 0.00136 / 0.06 ( 7) link_NAG-ASN : angle 1.66067 / 0.99 ( 21) *********************** 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 112 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8355 (mp10) REVERT: B 422 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: B 510 SER cc_start: 0.9140 (m) cc_final: 0.8774 (p) outliers start: 28 outliers final: 20 residues processed: 105 average time/residue: 0.0904 time to fit residues: 14.8478 Evaluate side-chains 101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 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 422 ASP Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 107 optimal weight: 0.0570 chunk 71 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094432 restraints weight = 19512.923| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.33 r_work: 0.3166 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3282 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= 0.146 Angle : 0.518 7.940 16389 Z= 0.257 Chirality : 0.039 0.188 1884 Planarity : 0.003 0.038 2128 Dihedral : 4.388 53.111 1697 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.14 % Allowed : 10.34 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1163 helix: 1.08 (0.31), residues: 296 sheet: -0.77 (0.26), residues: 326 loop : -0.55 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 410 TYR 0.017 0.001 TYR C 389 PHE 0.009 0.001 PHE C 219 TRP 0.010 0.001 TRP B 470 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11972) covalent geometry : angle 0.51219 / 0.26 (16309) SS BOND : bond 0.00314 / 0.20 ( 25) SS BOND : angle 1.05715 / 0.65 ( 50) hydrogen bonds : bond 0.03177 / 2.13 ( 457) hydrogen bonds : angle 4.62283 / 3.21 ( 1296) link_BETA1-4 : bond 0.00271 / 0.13 ( 3) link_BETA1-4 : angle 1.25342 / 0.68 ( 9) link_NAG-ASN : bond 0.00123 / 0.06 ( 7) link_NAG-ASN : angle 1.60878 / 0.95 ( 21) *********************** 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 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 GLN cc_start: 0.8025 (mp10) cc_final: 0.7664 (mp10) REVERT: B 323 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8372 (mp10) REVERT: B 510 SER cc_start: 0.9124 (m) cc_final: 0.8735 (p) outliers start: 23 outliers final: 20 residues processed: 98 average time/residue: 0.0894 time to fit residues: 13.7930 Evaluate side-chains 101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 425 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN B 417 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095912 restraints weight = 19658.471| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.56 r_work: 0.3202 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3312 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= 0.132 Angle : 0.500 8.205 16389 Z= 0.248 Chirality : 0.038 0.182 1884 Planarity : 0.003 0.038 2128 Dihedral : 4.299 52.490 1697 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.24 % Allowed : 10.53 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1163 helix: 0.95 (0.31), residues: 309 sheet: -0.66 (0.26), residues: 326 loop : -0.54 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 410 TYR 0.015 0.001 TYR C 389 PHE 0.009 0.001 PHE C 219 TRP 0.010 0.001 TRP B 470 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11972) covalent geometry : angle 0.49388 / 0.25 (16309) SS BOND : bond 0.00304 / 0.19 ( 25) SS BOND : angle 0.96912 / 0.60 ( 50) hydrogen bonds : bond 0.03084 / 2.07 ( 457) hydrogen bonds : angle 4.55201 / 3.16 ( 1296) link_BETA1-4 : bond 0.00297 / 0.15 ( 3) link_BETA1-4 : angle 1.23984 / 0.67 ( 9) link_NAG-ASN : bond 0.00115 / 0.05 ( 7) link_NAG-ASN : angle 1.55058 / 0.92 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 GLN cc_start: 0.8013 (mp10) cc_final: 0.7445 (mp10) REVERT: B 323 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: B 510 SER cc_start: 0.9133 (m) cc_final: 0.8708 (p) REVERT: C 299 MET cc_start: 0.8627 (ttt) cc_final: 0.8310 (ttt) REVERT: C 389 TYR cc_start: 0.9167 (t80) cc_final: 0.8909 (t80) outliers start: 24 outliers final: 18 residues processed: 104 average time/residue: 0.0861 time to fit residues: 14.1656 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 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 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 97 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 0.0030 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 HIS A 532 ASN B 417 ASN ** 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 = 0.3615 r_free = 0.3615 target = 0.115421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096619 restraints weight = 19917.646| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.58 r_work: 0.3211 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12007 Z= 0.111 Angle : 0.484 8.185 16389 Z= 0.242 Chirality : 0.038 0.184 1884 Planarity : 0.003 0.037 2128 Dihedral : 4.121 51.760 1696 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.05 % Allowed : 10.62 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1163 helix: 1.03 (0.31), residues: 309 sheet: -0.58 (0.26), residues: 326 loop : -0.50 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 410 TYR 0.016 0.001 TYR C 389 PHE 0.009 0.001 PHE C 219 TRP 0.010 0.001 TRP C 431 HIS 0.004 0.000 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (11972) covalent geometry : angle 0.47905 / 0.24 (16309) SS BOND : bond 0.00277 / 0.17 ( 25) SS BOND : angle 0.90956 / 0.57 ( 50) hydrogen bonds : bond 0.02938 / 1.98 ( 457) hydrogen bonds : angle 4.49429 / 3.12 ( 1296) link_BETA1-4 : bond 0.00328 / 0.16 ( 3) link_BETA1-4 : angle 1.21401 / 0.66 ( 9) link_NAG-ASN : bond 0.00124 / 0.06 ( 7) link_NAG-ASN : angle 1.48678 / 0.88 ( 21) ********************** 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 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 GLN cc_start: 0.7905 (mp10) cc_final: 0.7306 (mp10) REVERT: B 323 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8415 (mp10) REVERT: B 510 SER cc_start: 0.9101 (m) cc_final: 0.8648 (p) REVERT: C 389 TYR cc_start: 0.9137 (t80) cc_final: 0.8899 (t80) outliers start: 22 outliers final: 17 residues processed: 101 average time/residue: 0.0890 time to fit residues: 14.0014 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 152 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 110 optimal weight: 0.0010 chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 532 ASN B 160 HIS C 280 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093968 restraints weight = 19929.195| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.57 r_work: 0.3170 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12007 Z= 0.206 Angle : 0.554 8.191 16389 Z= 0.275 Chirality : 0.040 0.185 1884 Planarity : 0.003 0.039 2128 Dihedral : 4.418 53.581 1696 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.05 % Allowed : 10.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1163 helix: 1.06 (0.31), residues: 301 sheet: -0.63 (0.26), residues: 326 loop : -0.60 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 410 TYR 0.016 0.001 TYR C 389 PHE 0.011 0.001 PHE C 219 TRP 0.009 0.001 TRP B 470 HIS 0.004 0.001 HIS C 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (11972) covalent geometry : angle 0.54771 / 0.27 (16309) SS BOND : bond 0.00385 / 0.24 ( 25) SS BOND : angle 1.11692 / 0.69 ( 50) hydrogen bonds : bond 0.03335 / 2.23 ( 457) hydrogen bonds : angle 4.61476 / 3.20 ( 1296) link_BETA1-4 : bond 0.00240 / 0.11 ( 3) link_BETA1-4 : angle 1.33824 / 0.72 ( 9) link_NAG-ASN : bond 0.00152 / 0.07 ( 7) link_NAG-ASN : angle 1.76150 / 1.05 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.98 seconds wall clock time: 52 minutes 53.36 seconds (3173.36 seconds total)