Starting phenix.real_space_refine on Sun Aug 24 06:23:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7c_29806/08_2025/8g7c_29806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7c_29806/08_2025/8g7c_29806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7c_29806/08_2025/8g7c_29806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7c_29806/08_2025/8g7c_29806.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7c_29806/08_2025/8g7c_29806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7c_29806/08_2025/8g7c_29806.cif" } resolution = 4.1 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= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 11142 2.51 5 N 2910 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17466 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4792 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 32, 'TRANS': 571} Chain breaks: 1 Chain: "B" Number of atoms: 4792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4792 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 32, 'TRANS': 571} Chain breaks: 1 Chain: "D" Number of atoms: 4792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4792 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 32, 'TRANS': 571} Chain breaks: 1 Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.57, per 1000 atoms: 0.20 Number of scatterers: 17466 At special positions: 0 Unit cell: (157.589, 166.443, 129.259, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3342 8.00 N 2910 7.00 C 11142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.06 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 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 NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 616 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 729.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 40 sheets defined 7.4% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.209A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.622A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.216A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.619A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.334A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.603A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.622A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.619A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 removed outlier: 4.221A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.776A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.609A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.627A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.584A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.749A pdb=" N PHE A 43 " --> pdb=" O ARG D 567 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.208A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.583A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.751A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.814A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.779A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.719A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.095A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AB6, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.425A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.772A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.923A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.451A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.594A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.789A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 30 removed outlier: 7.803A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.187A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 68 through 70 Processing sheet with id=AC7, first strand: chain 'D' and resid 84 through 85 removed outlier: 12.836A pdb=" N PHE D 135 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 12.801A pdb=" N THR D 240 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 10.828A pdb=" N ASN D 137 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N LEU D 242 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU D 244 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.551A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER D 172 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 311 through 318 removed outlier: 5.380A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AD2, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.686A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.722A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.835A pdb=" N ARG E 38 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.293A pdb=" N GLY G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE G 34 " --> pdb=" O CYS G 50 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.293A pdb=" N GLY G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.261A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG F 38 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLY F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.261A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1449 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: 3.20 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5572 1.34 - 1.46: 4692 1.46 - 1.59: 7571 1.59 - 1.71: 0 1.71 - 1.84: 81 Bond restraints: 17916 Sorted by residual: bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 NAG D1302 " pdb=" O5 NAG D1302 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" N CYS D 391 " pdb=" CA CYS D 391 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.33e-02 5.65e+03 6.61e+00 bond pdb=" N LEU D 390 " pdb=" CA LEU D 390 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.44e+00 ... (remaining 17911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 23899 2.28 - 4.57: 428 4.57 - 6.85: 39 6.85 - 9.14: 7 9.14 - 11.42: 5 Bond angle restraints: 24378 Sorted by residual: angle pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta sigma weight residual 110.38 116.41 -6.03 1.38e+00 5.25e-01 1.91e+01 angle pdb=" N ILE A 569 " pdb=" CA ILE A 569 " pdb=" C ILE A 569 " ideal model delta sigma weight residual 113.71 109.77 3.94 9.50e-01 1.11e+00 1.72e+01 angle pdb=" C1 NAG D1302 " pdb=" O5 NAG D1302 " pdb=" C5 NAG D1302 " ideal model delta sigma weight residual 113.21 124.63 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C TRP F 104 " pdb=" N TYR F 105 " pdb=" CA TYR F 105 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C VAL B 615 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 121.66 115.24 6.42 1.92e+00 2.71e-01 1.12e+01 ... (remaining 24373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 9730 17.17 - 34.35: 745 34.35 - 51.52: 171 51.52 - 68.69: 31 68.69 - 85.87: 12 Dihedral angle restraints: 10689 sinusoidal: 4326 harmonic: 6363 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 172.51 -79.51 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 37.64 55.36 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual 93.00 43.48 49.52 1 1.00e+01 1.00e-02 3.37e+01 ... (remaining 10686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2650 0.125 - 0.250: 45 0.250 - 0.376: 0 0.376 - 0.501: 1 0.501 - 0.626: 1 Chirality restraints: 2697 Sorted by residual: chirality pdb=" C1 NAG D1301 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D1301 " pdb=" O5 NAG D1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 282 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2694 not shown) Planarity restraints: 3162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 282 " 0.048 2.00e-02 2.50e+03 4.58e-02 2.63e+01 pdb=" CG ASN D 282 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN D 282 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN D 282 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG D1302 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.015 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" CG ASN B 616 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" CG ASN B 616 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.021 2.00e-02 2.50e+03 ... (remaining 3159 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 260 2.64 - 3.21: 15782 3.21 - 3.77: 25447 3.77 - 4.34: 35616 4.34 - 4.90: 57537 Nonbonded interactions: 134642 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.076 3.040 nonbonded pdb=" NH2 ARG B 328 " pdb=" OE1 GLN B 580 " model vdw 2.083 3.120 nonbonded pdb=" O ASP D 80 " pdb=" OH TYR D 265 " model vdw 2.087 3.040 nonbonded pdb=" N SER D 375 " pdb=" O ALA D 435 " model vdw 2.113 3.120 nonbonded pdb=" OG1 THR D 553 " pdb=" OD1 ASP D 586 " model vdw 2.122 3.040 ... (remaining 134637 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 'A' and resid 14 through 1303) selection = (chain 'B' and resid 14 through 1303) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.120 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 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 : 0.004 0.091 17952 Z= 0.185 Angle : 0.785 18.558 24462 Z= 0.398 Chirality : 0.052 0.626 2697 Planarity : 0.006 0.089 3150 Dihedral : 12.952 85.865 6555 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.78 % Favored : 95.08 % Rotamer: Outliers : 0.10 % Allowed : 0.47 % Favored : 99.43 % 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 aren not related in a simple way. whole: -1.27 (0.17), residues: 2175 helix: -1.94 (0.44), residues: 121 sheet: 0.09 (0.20), residues: 670 loop : -1.26 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 509 TYR 0.025 0.002 TYR F 31 PHE 0.031 0.002 PHE D 400 TRP 0.026 0.002 TRP D 436 HIS 0.008 0.002 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00388 (17916) covalent geometry : angle 0.72911 (24378) SS BOND : bond 0.00637 ( 24) SS BOND : angle 1.30402 ( 48) hydrogen bonds : bond 0.13268 ( 560) hydrogen bonds : angle 7.83025 ( 1449) link_NAG-ASN : bond 0.01326 ( 12) link_NAG-ASN : angle 7.48924 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.6977 (t0) cc_final: 0.6635 (m-30) REVERT: A 216 LEU cc_start: 0.8073 (mm) cc_final: 0.7490 (pp) REVERT: A 351 TYR cc_start: 0.4192 (m-10) cc_final: 0.3599 (m-80) REVERT: A 418 ILE cc_start: 0.8171 (mm) cc_final: 0.7845 (mm) REVERT: B 101 ILE cc_start: 0.8853 (pt) cc_final: 0.8583 (pt) REVERT: B 574 ASP cc_start: 0.8143 (p0) cc_final: 0.7805 (p0) REVERT: D 202 LYS cc_start: 0.7618 (mttp) cc_final: 0.6890 (mtpp) REVERT: D 237 ARG cc_start: 0.7431 (mmm-85) cc_final: 0.7153 (mmm160) REVERT: D 276 LEU cc_start: 0.9358 (tp) cc_final: 0.9109 (tt) REVERT: D 515 PHE cc_start: 0.8053 (m-80) cc_final: 0.7783 (m-10) REVERT: E 81 LEU cc_start: 0.6735 (tp) cc_final: 0.6094 (tp) REVERT: G 73 ASP cc_start: 0.5535 (p0) cc_final: 0.4558 (p0) REVERT: G 80 TYR cc_start: 0.5774 (m-80) cc_final: 0.5374 (m-80) REVERT: F 83 MET cc_start: 0.2325 (mpp) cc_final: 0.2101 (mmt) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.1104 time to fit residues: 35.0199 Evaluate side-chains 141 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 40.0000 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 394 ASN A 487 ASN B 137 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.155465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.117998 restraints weight = 59893.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116183 restraints weight = 41118.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.116283 restraints weight = 41454.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.116637 restraints weight = 36854.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.116749 restraints weight = 33168.636| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.198 17952 Z= 0.374 Angle : 0.954 16.690 24462 Z= 0.489 Chirality : 0.055 0.300 2697 Planarity : 0.007 0.059 3150 Dihedral : 7.257 58.937 2646 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.23 % Favored : 91.63 % Rotamer: Outliers : 0.42 % Allowed : 6.05 % Favored : 93.53 % 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 aren not related in a simple way. whole: -1.68 (0.17), residues: 2175 helix: -2.56 (0.40), residues: 117 sheet: -0.20 (0.20), residues: 659 loop : -1.51 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 403 TYR 0.027 0.003 TYR B 279 PHE 0.042 0.004 PHE A 194 TRP 0.066 0.003 TRP G 36 HIS 0.012 0.003 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00846 (17916) covalent geometry : angle 0.91542 (24378) SS BOND : bond 0.00691 ( 24) SS BOND : angle 1.71812 ( 48) hydrogen bonds : bond 0.05858 ( 560) hydrogen bonds : angle 7.72844 ( 1449) link_NAG-ASN : bond 0.01067 ( 12) link_NAG-ASN : angle 6.82851 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8349 (mp0) cc_final: 0.7876 (mm-30) REVERT: A 418 ILE cc_start: 0.8766 (mm) cc_final: 0.8555 (tp) REVERT: A 440 ASN cc_start: 0.8508 (m-40) cc_final: 0.8204 (m-40) REVERT: A 582 LEU cc_start: 0.8236 (pt) cc_final: 0.7705 (tp) REVERT: D 191 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6978 (mp0) REVERT: D 202 LYS cc_start: 0.7666 (mttp) cc_final: 0.7101 (mttm) REVERT: D 439 ASN cc_start: 0.6947 (m-40) cc_final: 0.6651 (t0) REVERT: D 495 TYR cc_start: 0.3996 (OUTLIER) cc_final: 0.1045 (m-10) REVERT: D 515 PHE cc_start: 0.8706 (m-10) cc_final: 0.8461 (m-10) REVERT: E 81 LEU cc_start: 0.7522 (tp) cc_final: 0.7218 (tp) REVERT: E 83 MET cc_start: 0.2586 (ttm) cc_final: 0.2223 (ttm) REVERT: G 29 LEU cc_start: 0.6904 (mm) cc_final: 0.6564 (mm) REVERT: G 77 ASN cc_start: 0.7264 (m-40) cc_final: 0.6880 (p0) REVERT: F 83 MET cc_start: 0.1794 (mpp) cc_final: 0.0516 (mmt) outliers start: 8 outliers final: 3 residues processed: 197 average time/residue: 0.1055 time to fit residues: 32.8384 Evaluate side-chains 131 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 192 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 144 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 439 ASN A 532 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 422 ASN D 121 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 388 ASN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.159590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.124659 restraints weight = 60586.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.123808 restraints weight = 40393.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.124127 restraints weight = 34824.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.124519 restraints weight = 31991.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.124616 restraints weight = 29433.791| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17952 Z= 0.133 Angle : 0.698 17.379 24462 Z= 0.350 Chirality : 0.048 0.331 2697 Planarity : 0.005 0.076 3150 Dihedral : 6.199 48.625 2646 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % 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 aren not related in a simple way. whole: -1.39 (0.17), residues: 2175 helix: -2.02 (0.44), residues: 118 sheet: -0.03 (0.19), residues: 674 loop : -1.33 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 357 TYR 0.020 0.001 TYR B 351 PHE 0.026 0.002 PHE D 400 TRP 0.041 0.002 TRP D 436 HIS 0.004 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00290 (17916) covalent geometry : angle 0.65283 (24378) SS BOND : bond 0.00352 ( 24) SS BOND : angle 1.48920 ( 48) hydrogen bonds : bond 0.03944 ( 560) hydrogen bonds : angle 6.82639 ( 1449) link_NAG-ASN : bond 0.01272 ( 12) link_NAG-ASN : angle 6.31186 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8188 (mp0) cc_final: 0.7551 (mm-30) REVERT: A 439 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.6749 (p0) REVERT: A 582 LEU cc_start: 0.8205 (pt) cc_final: 0.7849 (tp) REVERT: B 102 ARG cc_start: 0.7916 (mmp-170) cc_final: 0.7383 (mmp80) REVERT: B 574 ASP cc_start: 0.8660 (p0) cc_final: 0.8264 (p0) REVERT: D 191 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6296 (mp0) REVERT: D 202 LYS cc_start: 0.7609 (mttp) cc_final: 0.6901 (mttm) REVERT: D 265 TYR cc_start: 0.7283 (p90) cc_final: 0.6978 (p90) REVERT: D 392 PHE cc_start: 0.7671 (m-80) cc_final: 0.7450 (m-80) REVERT: E 81 LEU cc_start: 0.7416 (tp) cc_final: 0.7125 (tp) outliers start: 3 outliers final: 0 residues processed: 191 average time/residue: 0.0965 time to fit residues: 30.4352 Evaluate side-chains 130 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 150 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 163 optimal weight: 0.0170 chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 overall best weight: 2.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.156132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.119907 restraints weight = 59633.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.117422 restraints weight = 36805.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.118043 restraints weight = 36603.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.118186 restraints weight = 34752.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.118558 restraints weight = 29730.114| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17952 Z= 0.192 Angle : 0.715 16.452 24462 Z= 0.359 Chirality : 0.048 0.294 2697 Planarity : 0.005 0.063 3150 Dihedral : 6.014 36.127 2646 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.08 % Favored : 92.83 % Rotamer: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.93 % 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 aren not related in a simple way. whole: -1.41 (0.17), residues: 2175 helix: -1.95 (0.44), residues: 119 sheet: -0.05 (0.19), residues: 672 loop : -1.34 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 457 TYR 0.020 0.002 TYR G 80 PHE 0.023 0.002 PHE B 559 TRP 0.023 0.002 TRP G 36 HIS 0.006 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00437 (17916) covalent geometry : angle 0.67256 (24378) SS BOND : bond 0.00328 ( 24) SS BOND : angle 1.20437 ( 48) hydrogen bonds : bond 0.04270 ( 560) hydrogen bonds : angle 6.75152 ( 1449) link_NAG-ASN : bond 0.00991 ( 12) link_NAG-ASN : angle 6.23917 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8317 (mp0) cc_final: 0.7711 (mm-30) REVERT: A 197 ILE cc_start: 0.9280 (pt) cc_final: 0.8624 (pt) REVERT: A 582 LEU cc_start: 0.8225 (pt) cc_final: 0.7900 (tp) REVERT: B 102 ARG cc_start: 0.7908 (mmp-170) cc_final: 0.7473 (mmp80) REVERT: B 574 ASP cc_start: 0.8716 (p0) cc_final: 0.8281 (p0) REVERT: D 191 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6537 (mp0) REVERT: D 202 LYS cc_start: 0.7575 (mttp) cc_final: 0.7043 (mttt) REVERT: D 265 TYR cc_start: 0.7331 (p90) cc_final: 0.6944 (p90) REVERT: D 392 PHE cc_start: 0.7763 (m-80) cc_final: 0.7432 (m-80) REVERT: G 73 ASP cc_start: 0.7201 (p0) cc_final: 0.5868 (p0) REVERT: G 80 TYR cc_start: 0.8460 (m-80) cc_final: 0.7756 (m-80) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.0946 time to fit residues: 25.6592 Evaluate side-chains 132 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 193 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 42 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** 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 = 0.4450 r_free = 0.4450 target = 0.155669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.118864 restraints weight = 58864.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.118099 restraints weight = 40846.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118028 restraints weight = 34257.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.118452 restraints weight = 33069.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.118717 restraints weight = 29597.069| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17952 Z= 0.170 Angle : 0.681 16.487 24462 Z= 0.343 Chirality : 0.048 0.315 2697 Planarity : 0.005 0.059 3150 Dihedral : 5.781 37.887 2646 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % 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 aren not related in a simple way. whole: -1.43 (0.17), residues: 2175 helix: -1.84 (0.46), residues: 110 sheet: -0.12 (0.20), residues: 652 loop : -1.33 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 457 TYR 0.022 0.002 TYR A 423 PHE 0.022 0.002 PHE A 392 TRP 0.049 0.002 TRP D 436 HIS 0.007 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00386 (17916) covalent geometry : angle 0.63953 (24378) SS BOND : bond 0.00354 ( 24) SS BOND : angle 1.40094 ( 48) hydrogen bonds : bond 0.03951 ( 560) hydrogen bonds : angle 6.58337 ( 1449) link_NAG-ASN : bond 0.01023 ( 12) link_NAG-ASN : angle 5.95442 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0815 (mpp) cc_final: -0.2456 (mmm) REVERT: A 191 GLU cc_start: 0.8269 (mp0) cc_final: 0.7529 (mm-30) REVERT: B 102 ARG cc_start: 0.8068 (mmp-170) cc_final: 0.7590 (mmp80) REVERT: B 574 ASP cc_start: 0.8699 (p0) cc_final: 0.8257 (p0) REVERT: D 191 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6516 (mp0) REVERT: D 202 LYS cc_start: 0.7648 (mttp) cc_final: 0.7056 (mttm) REVERT: D 265 TYR cc_start: 0.7262 (p90) cc_final: 0.7011 (p90) REVERT: D 392 PHE cc_start: 0.7790 (m-80) cc_final: 0.7392 (m-80) REVERT: G 73 ASP cc_start: 0.7051 (p0) cc_final: 0.6121 (p0) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0998 time to fit residues: 26.9114 Evaluate side-chains 122 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 152 optimal weight: 0.2980 chunk 109 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.154827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.117253 restraints weight = 57658.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.115417 restraints weight = 36716.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115912 restraints weight = 35846.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.116207 restraints weight = 32101.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.116200 restraints weight = 29345.496| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17952 Z= 0.209 Angle : 0.717 16.346 24462 Z= 0.364 Chirality : 0.048 0.310 2697 Planarity : 0.005 0.059 3150 Dihedral : 5.890 39.005 2646 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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 aren not related in a simple way. whole: -1.48 (0.17), residues: 2175 helix: -1.76 (0.47), residues: 110 sheet: -0.17 (0.20), residues: 672 loop : -1.38 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 457 TYR 0.025 0.002 TYR D 38 PHE 0.032 0.002 PHE A 135 TRP 0.051 0.002 TRP D 436 HIS 0.005 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00466 (17916) covalent geometry : angle 0.67807 (24378) SS BOND : bond 0.00323 ( 24) SS BOND : angle 1.29214 ( 48) hydrogen bonds : bond 0.04244 ( 560) hydrogen bonds : angle 6.70509 ( 1449) link_NAG-ASN : bond 0.00940 ( 12) link_NAG-ASN : angle 5.93932 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0739 (mpp) cc_final: -0.1474 (tpp) REVERT: A 242 LEU cc_start: 0.8394 (mm) cc_final: 0.8153 (mt) REVERT: B 574 ASP cc_start: 0.8688 (p0) cc_final: 0.8179 (p0) REVERT: D 191 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6734 (mp0) REVERT: D 202 LYS cc_start: 0.7718 (mttp) cc_final: 0.7072 (mttm) REVERT: D 265 TYR cc_start: 0.7221 (p90) cc_final: 0.6871 (p90) REVERT: G 73 ASP cc_start: 0.7505 (p0) cc_final: 0.6355 (p0) REVERT: G 80 TYR cc_start: 0.8373 (m-10) cc_final: 0.8109 (m-80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1001 time to fit residues: 25.6615 Evaluate side-chains 111 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 147 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 172 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 105 optimal weight: 0.0870 chunk 182 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 184 optimal weight: 0.1980 chunk 206 optimal weight: 20.0000 overall best weight: 0.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 188 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.156376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121213 restraints weight = 58230.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.117746 restraints weight = 38170.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.118758 restraints weight = 40361.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.118674 restraints weight = 35297.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.118893 restraints weight = 31834.754| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17952 Z= 0.123 Angle : 0.662 16.242 24462 Z= 0.330 Chirality : 0.048 0.326 2697 Planarity : 0.005 0.057 3150 Dihedral : 5.505 37.587 2646 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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 aren not related in a simple way. whole: -1.36 (0.17), residues: 2175 helix: -1.74 (0.46), residues: 110 sheet: -0.15 (0.20), residues: 659 loop : -1.25 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 38 TYR 0.028 0.002 TYR G 94 PHE 0.026 0.002 PHE G 37 TRP 0.060 0.002 TRP D 436 HIS 0.003 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00267 (17916) covalent geometry : angle 0.62110 (24378) SS BOND : bond 0.00280 ( 24) SS BOND : angle 0.99718 ( 48) hydrogen bonds : bond 0.03542 ( 560) hydrogen bonds : angle 6.38733 ( 1449) link_NAG-ASN : bond 0.01126 ( 12) link_NAG-ASN : angle 5.92112 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8076 (m-80) cc_final: 0.7698 (m-10) REVERT: A 153 MET cc_start: -0.1133 (mpp) cc_final: -0.2565 (mmm) REVERT: A 191 GLU cc_start: 0.8133 (mp0) cc_final: 0.7660 (mm-30) REVERT: A 242 LEU cc_start: 0.8442 (mm) cc_final: 0.8144 (mt) REVERT: A 495 TYR cc_start: 0.6424 (m-10) cc_final: 0.6175 (m-10) REVERT: B 81 ASN cc_start: 0.8908 (p0) cc_final: 0.8695 (p0) REVERT: B 574 ASP cc_start: 0.8657 (p0) cc_final: 0.8069 (p0) REVERT: D 191 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6481 (mp0) REVERT: D 202 LYS cc_start: 0.7529 (mttp) cc_final: 0.6872 (mttm) REVERT: D 265 TYR cc_start: 0.7073 (p90) cc_final: 0.6749 (p90) REVERT: E 83 MET cc_start: 0.0767 (ptt) cc_final: 0.0267 (ptt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0936 time to fit residues: 24.7929 Evaluate side-chains 117 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 187 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 132 optimal weight: 0.0970 chunk 1 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.152216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.114394 restraints weight = 57943.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.113131 restraints weight = 37210.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.113596 restraints weight = 34151.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113751 restraints weight = 32620.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113723 restraints weight = 29934.213| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17952 Z= 0.210 Angle : 0.735 15.083 24462 Z= 0.372 Chirality : 0.050 0.535 2697 Planarity : 0.005 0.072 3150 Dihedral : 5.883 40.985 2646 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.14 % Favored : 91.77 % Rotamer: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.17), residues: 2175 helix: -1.70 (0.48), residues: 109 sheet: -0.22 (0.20), residues: 649 loop : -1.35 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 38 TYR 0.040 0.002 TYR D 38 PHE 0.033 0.003 PHE B 559 TRP 0.062 0.003 TRP D 436 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00484 (17916) covalent geometry : angle 0.69540 (24378) SS BOND : bond 0.00316 ( 24) SS BOND : angle 1.61340 ( 48) hydrogen bonds : bond 0.04339 ( 560) hydrogen bonds : angle 6.75824 ( 1449) link_NAG-ASN : bond 0.01194 ( 12) link_NAG-ASN : angle 5.98888 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8000 (m-30) cc_final: 0.7750 (m-30) REVERT: A 153 MET cc_start: -0.1560 (mpp) cc_final: -0.2002 (tpp) REVERT: A 191 GLU cc_start: 0.8198 (mp0) cc_final: 0.7620 (mm-30) REVERT: B 574 ASP cc_start: 0.8746 (p0) cc_final: 0.8172 (p0) REVERT: D 191 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6476 (mp0) REVERT: D 202 LYS cc_start: 0.7910 (mttp) cc_final: 0.7316 (mttm) REVERT: D 265 TYR cc_start: 0.7172 (p90) cc_final: 0.6769 (p90) REVERT: G 73 ASP cc_start: 0.7577 (p0) cc_final: 0.5913 (p0) REVERT: G 80 TYR cc_start: 0.8482 (m-80) cc_final: 0.7903 (m-80) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.0917 time to fit residues: 24.2298 Evaluate side-chains 110 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 4 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 209 optimal weight: 50.0000 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 165 ASN A 188 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.154351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.118436 restraints weight = 58248.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115358 restraints weight = 37327.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.116061 restraints weight = 37900.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116412 restraints weight = 31156.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.116558 restraints weight = 28490.115| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17952 Z= 0.127 Angle : 0.663 15.612 24462 Z= 0.332 Chirality : 0.048 0.416 2697 Planarity : 0.004 0.056 3150 Dihedral : 5.511 40.235 2646 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 aren not related in a simple way. whole: -1.38 (0.17), residues: 2175 helix: -1.72 (0.46), residues: 110 sheet: -0.16 (0.20), residues: 649 loop : -1.26 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 38 TYR 0.019 0.001 TYR G 94 PHE 0.026 0.002 PHE G 114 TRP 0.067 0.002 TRP D 436 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00290 (17916) covalent geometry : angle 0.62526 (24378) SS BOND : bond 0.00276 ( 24) SS BOND : angle 1.24058 ( 48) hydrogen bonds : bond 0.03552 ( 560) hydrogen bonds : angle 6.43852 ( 1449) link_NAG-ASN : bond 0.01181 ( 12) link_NAG-ASN : angle 5.63384 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7921 (m-30) cc_final: 0.7691 (m-30) REVERT: A 153 MET cc_start: -0.1354 (mpp) cc_final: -0.1714 (tpp) REVERT: A 191 GLU cc_start: 0.8170 (mp0) cc_final: 0.7758 (mm-30) REVERT: B 81 ASN cc_start: 0.8934 (p0) cc_final: 0.8669 (p0) REVERT: B 574 ASP cc_start: 0.8729 (p0) cc_final: 0.8232 (p0) REVERT: D 191 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6430 (mp0) REVERT: D 202 LYS cc_start: 0.7770 (mttp) cc_final: 0.7037 (mttm) REVERT: D 258 TRP cc_start: 0.4483 (m100) cc_final: 0.3671 (m-10) REVERT: D 265 TYR cc_start: 0.7119 (p90) cc_final: 0.6667 (p90) REVERT: G 73 ASP cc_start: 0.7338 (p0) cc_final: 0.6624 (p0) REVERT: G 80 TYR cc_start: 0.8517 (m-80) cc_final: 0.8177 (m-80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0962 time to fit residues: 26.1133 Evaluate side-chains 119 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 197 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 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 = 0.4414 r_free = 0.4414 target = 0.153003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.116577 restraints weight = 58016.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.115697 restraints weight = 40541.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.115590 restraints weight = 34846.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.116024 restraints weight = 33107.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116173 restraints weight = 29876.424| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17952 Z= 0.156 Angle : 0.672 14.864 24462 Z= 0.338 Chirality : 0.048 0.366 2697 Planarity : 0.005 0.054 3150 Dihedral : 5.561 39.820 2646 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.99 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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 aren not related in a simple way. whole: -1.47 (0.17), residues: 2175 helix: -1.68 (0.47), residues: 110 sheet: -0.30 (0.20), residues: 641 loop : -1.28 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 38 TYR 0.017 0.002 TYR G 94 PHE 0.022 0.002 PHE A 464 TRP 0.057 0.002 TRP D 436 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00360 (17916) covalent geometry : angle 0.63500 (24378) SS BOND : bond 0.00317 ( 24) SS BOND : angle 1.28215 ( 48) hydrogen bonds : bond 0.03777 ( 560) hydrogen bonds : angle 6.45818 ( 1449) link_NAG-ASN : bond 0.01024 ( 12) link_NAG-ASN : angle 5.63418 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8030 (m-30) cc_final: 0.7780 (m-30) REVERT: A 191 GLU cc_start: 0.8140 (mp0) cc_final: 0.7697 (mm-30) REVERT: B 81 ASN cc_start: 0.8923 (p0) cc_final: 0.8721 (p0) REVERT: B 574 ASP cc_start: 0.8752 (p0) cc_final: 0.8229 (p0) REVERT: D 191 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6442 (mp0) REVERT: D 202 LYS cc_start: 0.7854 (mttp) cc_final: 0.7181 (mttm) REVERT: D 258 TRP cc_start: 0.4473 (m100) cc_final: 0.3589 (m-10) REVERT: D 265 TYR cc_start: 0.7085 (p90) cc_final: 0.6677 (p90) REVERT: G 73 ASP cc_start: 0.7592 (p0) cc_final: 0.6920 (p0) REVERT: G 80 TYR cc_start: 0.8257 (m-80) cc_final: 0.7796 (m-80) REVERT: F 6 GLU cc_start: 0.1683 (tp30) cc_final: 0.0508 (tp30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0986 time to fit residues: 27.1341 Evaluate side-chains 113 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 141 optimal weight: 0.0070 chunk 153 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 165 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.153521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.117353 restraints weight = 58589.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.116442 restraints weight = 41809.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116343 restraints weight = 35414.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.116702 restraints weight = 33480.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.117283 restraints weight = 30326.850| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17952 Z= 0.132 Angle : 0.655 14.721 24462 Z= 0.328 Chirality : 0.047 0.359 2697 Planarity : 0.004 0.055 3150 Dihedral : 5.465 40.342 2646 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.17), residues: 2175 helix: -1.66 (0.47), residues: 110 sheet: -0.25 (0.20), residues: 636 loop : -1.24 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 38 TYR 0.018 0.001 TYR A 453 PHE 0.022 0.002 PHE A 275 TRP 0.066 0.002 TRP D 436 HIS 0.003 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00303 (17916) covalent geometry : angle 0.61907 (24378) SS BOND : bond 0.00285 ( 24) SS BOND : angle 1.13958 ( 48) hydrogen bonds : bond 0.03550 ( 560) hydrogen bonds : angle 6.34039 ( 1449) link_NAG-ASN : bond 0.01068 ( 12) link_NAG-ASN : angle 5.50337 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.70 seconds wall clock time: 46 minutes 11.91 seconds (2771.91 seconds total)