Starting phenix.real_space_refine on Sun Jun 15 18:13:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7c_29806/06_2025/8g7c_29806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7c_29806/06_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_29806/06_2025/8g7c_29806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7c_29806/06_2025/8g7c_29806.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7c_29806/06_2025/8g7c_29806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7c_29806/06_2025/8g7c_29806.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.25, per 1000 atoms: 0.64 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: 4.27 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.60 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: 5.97 Time building geometry restraints manager: 5.08 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 620 or resid 1301 through 1303)) selection = (chain 'B' and (resid 14 through 620 or resid 1301 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.310 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.650 ------------------------------------------------------------------------------- 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 : 15.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), 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 TRP 0.026 0.002 TRP D 436 HIS 0.008 0.002 HIS D 69 PHE 0.031 0.002 PHE D 400 TYR 0.025 0.002 TYR F 31 ARG 0.026 0.001 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01326 ( 12) link_NAG-ASN : angle 7.48924 ( 36) hydrogen bonds : bond 0.13268 ( 560) hydrogen bonds : angle 7.83025 ( 1449) SS BOND : bond 0.00637 ( 24) SS BOND : angle 1.30402 ( 48) covalent geometry : bond 0.00388 (17916) covalent geometry : angle 0.72911 (24378) *********************** 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 : 2.062 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: 0.7487 (pp) REVERT: A 351 TYR cc_start: 0.4192 (m-10) cc_final: 0.3600 (m-80) REVERT: A 418 ILE cc_start: 0.8171 (mm) cc_final: 0.7846 (mm) 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: 0.7002 (mttp) 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: 0.9110 (tt) REVERT: D 515 PHE cc_start: 0.8053 (m-80) cc_final: 0.7628 (m-10) REVERT: E 81 LEU cc_start: 0.6735 (tp) cc_final: 0.6111 (tp) REVERT: G 73 ASP cc_start: 0.5535 (p0) cc_final: 0.4575 (p0) 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: 0.2777 time to fit residues: 87.3931 Evaluate side-chains 142 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 196 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** 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 = 0.4578 r_free = 0.4578 target = 0.166357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.131666 restraints weight = 60378.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.130119 restraints weight = 43705.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.130369 restraints weight = 37087.480| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1058 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= 0.127 Angle : 0.666 16.033 24462 Z= 0.331 Chirality : 0.047 0.339 2697 Planarity : 0.005 0.054 3150 Dihedral : 6.068 52.322 2646 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2175 helix: -1.93 (0.43), residues: 126 sheet: 0.18 (0.20), residues: 692 loop : -1.16 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 36 HIS 0.004 0.001 HIS A 66 PHE 0.023 0.002 PHE D 400 TYR 0.017 0.001 TYR A 351 ARG 0.006 0.001 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01276 ( 12) link_NAG-ASN : angle 6.11005 ( 36) hydrogen bonds : bond 0.03749 ( 560) hydrogen bonds : angle 6.54662 ( 1449) SS BOND : bond 0.00357 ( 24) SS BOND : angle 1.07000 ( 48) covalent geometry : bond 0.00279 (17916) covalent geometry : angle 0.62277 (24378) *********************** 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 200 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 1.834 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 242 LEU cc_start: 0.8242 (mt) cc_final: 0.8041 (mt) REVERT: A 440 ASN cc_start: 0.8212 (m-40) cc_final: 0.7856 (m-40) REVERT: B 81 ASN cc_start: 0.8961 (p0) cc_final: 0.8726 (p0) REVERT: B 101 ILE cc_start: 0.8723 (pt) cc_final: 0.8520 (pt) REVERT: B 287 ASP cc_start: 0.7855 (t0) cc_final: 0.6764 (p0) REVERT: B 574 ASP cc_start: 0.8511 (p0) cc_final: 0.8198 (p0) REVERT: D 364 ASP cc_start: 0.7616 (p0) cc_final: 0.7398 (p0) REVERT: E 81 LEU cc_start: 0.7632 (tp) cc_final: 0.7256 (tp) REVERT: E 83 MET cc_start: 0.2351 (ttm) cc_final: 0.1993 (ptm) REVERT: G 73 ASP cc_start: 0.6674 (p0) cc_final: 0.6223 (m-30) REVERT: G 80 TYR cc_start: 0.8095 (m-80) cc_final: 0.7523 (m-80) REVERT: G 83 MET cc_start: 0.6037 (pmm) cc_final: 0.5409 (tpp) REVERT: F 83 MET cc_start: 0.1626 (mpp) cc_final: 0.0401 (mpp) outliers start: 2 outliers final: 1 residues processed: 200 average time/residue: 0.2707 time to fit residues: 84.9007 Evaluate side-chains 147 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 50 optimal weight: 0.2980 chunk 208 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 147 optimal weight: 0.0670 chunk 187 optimal weight: 30.0000 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 422 ASN A 437 ASN A 532 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 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** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.167406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.133913 restraints weight = 59910.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.131005 restraints weight = 43340.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.131260 restraints weight = 39415.179| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17952 Z= 0.111 Angle : 0.637 15.458 24462 Z= 0.314 Chirality : 0.046 0.346 2697 Planarity : 0.004 0.057 3150 Dihedral : 5.800 57.124 2646 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2175 helix: -1.91 (0.43), residues: 125 sheet: 0.30 (0.20), residues: 688 loop : -1.09 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 353 HIS 0.004 0.001 HIS D 69 PHE 0.019 0.001 PHE G 114 TYR 0.018 0.001 TYR A 351 ARG 0.005 0.000 ARG D 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01163 ( 12) link_NAG-ASN : angle 6.03348 ( 36) hydrogen bonds : bond 0.03402 ( 560) hydrogen bonds : angle 6.27196 ( 1449) SS BOND : bond 0.00303 ( 24) SS BOND : angle 1.23989 ( 48) covalent geometry : bond 0.00244 (17916) covalent geometry : angle 0.59246 (24378) *********************** 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 198 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8255 (mt) cc_final: 0.7975 (mt) REVERT: A 353 TRP cc_start: 0.5797 (m-10) cc_final: 0.5294 (m-10) REVERT: A 440 ASN cc_start: 0.8283 (m-40) cc_final: 0.7926 (m-40) REVERT: B 102 ARG cc_start: 0.7869 (mmp-170) cc_final: 0.7353 (mmp80) REVERT: B 106 PHE cc_start: 0.8814 (m-80) cc_final: 0.8587 (m-80) REVERT: B 176 LEU cc_start: 0.7923 (mt) cc_final: 0.7251 (pp) REVERT: B 287 ASP cc_start: 0.7593 (t0) cc_final: 0.6605 (p0) REVERT: B 574 ASP cc_start: 0.8630 (p0) cc_final: 0.8256 (p0) REVERT: G 29 LEU cc_start: 0.5709 (mm) cc_final: 0.5508 (mm) REVERT: G 83 MET cc_start: 0.6085 (pmm) cc_final: 0.5463 (tpp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2797 time to fit residues: 87.3360 Evaluate side-chains 143 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 126 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 115 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 487 ASN B 49 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 448 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.157361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.119740 restraints weight = 58454.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.118125 restraints weight = 37604.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.118689 restraints weight = 34939.720| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17952 Z= 0.271 Angle : 0.832 13.848 24462 Z= 0.428 Chirality : 0.052 0.309 2697 Planarity : 0.006 0.090 3150 Dihedral : 6.440 43.717 2646 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.54 % Favored : 92.37 % Rotamer: Outliers : 0.16 % Allowed : 5.01 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2175 helix: -2.01 (0.44), residues: 118 sheet: 0.09 (0.20), residues: 664 loop : -1.36 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP D 436 HIS 0.010 0.002 HIS A 66 PHE 0.038 0.003 PHE A 86 TYR 0.029 0.003 TYR G 94 ARG 0.011 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00961 ( 12) link_NAG-ASN : angle 6.30364 ( 36) hydrogen bonds : bond 0.05123 ( 560) hydrogen bonds : angle 7.11256 ( 1449) SS BOND : bond 0.00413 ( 24) SS BOND : angle 1.55081 ( 48) covalent geometry : bond 0.00584 (17916) covalent geometry : angle 0.79403 (24378) *********************** 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 192 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0051 (mpp) cc_final: -0.0277 (mpp) REVERT: A 350 VAL cc_start: 0.5375 (t) cc_final: 0.4932 (t) REVERT: A 440 ASN cc_start: 0.8487 (m-40) cc_final: 0.8214 (m-40) REVERT: A 582 LEU cc_start: 0.8411 (pt) cc_final: 0.7969 (tp) REVERT: B 177 MET cc_start: 0.6212 (mmp) cc_final: 0.2246 (ttt) REVERT: B 574 ASP cc_start: 0.8685 (p0) cc_final: 0.8441 (m-30) REVERT: D 191 GLU cc_start: 0.7653 (mt-10) cc_final: 0.6842 (mp0) REVERT: D 202 LYS cc_start: 0.7539 (mtpp) cc_final: 0.7110 (mttm) REVERT: D 392 PHE cc_start: 0.7567 (m-10) cc_final: 0.7225 (m-80) REVERT: D 439 ASN cc_start: 0.6881 (m-40) cc_final: 0.6661 (t0) REVERT: E 81 LEU cc_start: 0.7439 (tp) cc_final: 0.7207 (tp) REVERT: G 73 ASP cc_start: 0.8273 (m-30) cc_final: 0.7067 (m-30) REVERT: G 80 TYR cc_start: 0.8506 (m-80) cc_final: 0.7810 (m-80) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.2552 time to fit residues: 78.2815 Evaluate side-chains 132 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** B 137 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN E 3 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.159253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.122079 restraints weight = 60119.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.120748 restraints weight = 38329.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.121462 restraints weight = 34637.080| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17952 Z= 0.146 Angle : 0.682 15.833 24462 Z= 0.342 Chirality : 0.048 0.442 2697 Planarity : 0.005 0.080 3150 Dihedral : 5.735 38.552 2646 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2175 helix: -1.80 (0.45), residues: 118 sheet: 0.03 (0.19), residues: 679 loop : -1.25 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 436 HIS 0.004 0.001 HIS A 66 PHE 0.018 0.002 PHE A 400 TYR 0.021 0.002 TYR F 94 ARG 0.003 0.000 ARG D 457 Details of bonding type rmsd link_NAG-ASN : bond 0.01091 ( 12) link_NAG-ASN : angle 5.91652 ( 36) hydrogen bonds : bond 0.03847 ( 560) hydrogen bonds : angle 6.53857 ( 1449) SS BOND : bond 0.00332 ( 24) SS BOND : angle 1.38196 ( 48) covalent geometry : bond 0.00330 (17916) covalent geometry : angle 0.64079 (24378) *********************** 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 190 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.760 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 153 MET cc_start: 0.0011 (mpp) cc_final: -0.1710 (mmt) REVERT: A 440 ASN cc_start: 0.8581 (m-40) cc_final: 0.8302 (m-40) REVERT: A 582 LEU cc_start: 0.8376 (pt) cc_final: 0.8170 (tp) REVERT: B 81 ASN cc_start: 0.8901 (p0) cc_final: 0.8609 (p0) REVERT: B 102 ARG cc_start: 0.8098 (mmp-170) cc_final: 0.7598 (mmp80) REVERT: B 176 LEU cc_start: 0.7976 (mt) cc_final: 0.7194 (pp) REVERT: B 574 ASP cc_start: 0.8626 (p0) cc_final: 0.8313 (m-30) REVERT: D 191 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6686 (mp0) REVERT: D 202 LYS cc_start: 0.7478 (mtpp) cc_final: 0.6910 (mttm) REVERT: D 392 PHE cc_start: 0.7405 (m-10) cc_final: 0.7201 (m-10) REVERT: D 414 GLN cc_start: 0.4807 (pm20) cc_final: 0.4320 (pm20) REVERT: E 83 MET cc_start: 0.0561 (ptt) cc_final: -0.0217 (ptt) REVERT: G 73 ASP cc_start: 0.8175 (m-30) cc_final: 0.7763 (m-30) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.2880 time to fit residues: 86.1489 Evaluate side-chains 131 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 84 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN D 121 ASN D 137 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN G 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.150765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.113150 restraints weight = 59492.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.111546 restraints weight = 38731.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.111852 restraints weight = 38584.114| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 17952 Z= 0.346 Angle : 0.915 15.732 24462 Z= 0.473 Chirality : 0.054 0.351 2697 Planarity : 0.007 0.070 3150 Dihedral : 6.827 43.999 2646 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.69 % Favored : 91.22 % Rotamer: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2175 helix: -1.98 (0.46), residues: 110 sheet: -0.42 (0.19), residues: 669 loop : -1.57 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP D 436 HIS 0.012 0.003 HIS D 207 PHE 0.042 0.004 PHE B 559 TYR 0.025 0.003 TYR B 28 ARG 0.030 0.001 ARG D 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00967 ( 12) link_NAG-ASN : angle 6.30871 ( 36) hydrogen bonds : bond 0.05624 ( 560) hydrogen bonds : angle 7.45513 ( 1449) SS BOND : bond 0.00448 ( 24) SS BOND : angle 1.63730 ( 48) covalent geometry : bond 0.00793 (17916) covalent geometry : angle 0.88076 (24378) *********************** 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 164 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.1554 (mpp) cc_final: -0.2393 (tpp) REVERT: A 440 ASN cc_start: 0.8666 (m-40) cc_final: 0.8398 (m110) REVERT: B 177 MET cc_start: 0.6254 (mmp) cc_final: 0.2494 (ttt) REVERT: D 191 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7433 (mp0) REVERT: D 202 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7306 (mttm) REVERT: D 265 TYR cc_start: 0.7345 (p90) cc_final: 0.6852 (p90) REVERT: D 392 PHE cc_start: 0.7684 (m-10) cc_final: 0.7397 (m-80) REVERT: D 515 PHE cc_start: 0.8720 (m-80) cc_final: 0.8369 (m-10) REVERT: E 78 THR cc_start: 0.2720 (t) cc_final: 0.0956 (t) REVERT: G 73 ASP cc_start: 0.8339 (m-30) cc_final: 0.7985 (m-30) outliers start: 3 outliers final: 1 residues processed: 163 average time/residue: 0.2592 time to fit residues: 68.2212 Evaluate side-chains 106 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 47 optimal weight: 9.9990 chunk 166 optimal weight: 0.0030 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 45 optimal weight: 0.0870 chunk 167 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.6068 ------------------------------------------------------------------------------- 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** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.155806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.119043 restraints weight = 58950.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.117880 restraints weight = 38431.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.118344 restraints weight = 35484.338| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4910 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= 0.136 Angle : 0.685 16.570 24462 Z= 0.348 Chirality : 0.048 0.346 2697 Planarity : 0.005 0.060 3150 Dihedral : 5.796 40.380 2646 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2175 helix: -1.75 (0.46), residues: 111 sheet: -0.12 (0.20), residues: 669 loop : -1.37 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP D 436 HIS 0.004 0.001 HIS A 66 PHE 0.020 0.002 PHE A 275 TYR 0.021 0.002 TYR B 351 ARG 0.005 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.01140 ( 12) link_NAG-ASN : angle 5.69659 ( 36) hydrogen bonds : bond 0.03794 ( 560) hydrogen bonds : angle 6.71499 ( 1449) SS BOND : bond 0.00355 ( 24) SS BOND : angle 1.47980 ( 48) covalent geometry : bond 0.00299 (17916) covalent geometry : angle 0.64729 (24378) *********************** 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 175 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.1646 (mpp) cc_final: -0.2142 (tpp) REVERT: A 440 ASN cc_start: 0.8784 (m-40) cc_final: 0.8537 (m-40) REVERT: B 81 ASN cc_start: 0.8877 (p0) cc_final: 0.8614 (p0) REVERT: B 102 ARG cc_start: 0.7493 (mmp-170) cc_final: 0.7130 (mmp80) REVERT: B 176 LEU cc_start: 0.7959 (mt) cc_final: 0.7736 (mt) REVERT: B 177 MET cc_start: 0.6191 (mmp) cc_final: 0.2496 (ttt) REVERT: B 574 ASP cc_start: 0.8120 (p0) cc_final: 0.7863 (m-30) REVERT: B 618 THR cc_start: 0.6660 (p) cc_final: 0.5376 (t) REVERT: D 191 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6843 (mp0) REVERT: D 202 LYS cc_start: 0.7614 (mtpp) cc_final: 0.7073 (mttm) REVERT: D 265 TYR cc_start: 0.6990 (p90) cc_final: 0.6565 (p90) REVERT: D 385 THR cc_start: 0.7914 (p) cc_final: 0.7680 (p) REVERT: D 386 LYS cc_start: 0.8274 (mmmt) cc_final: 0.8020 (mmmt) REVERT: D 392 PHE cc_start: 0.7546 (m-10) cc_final: 0.7189 (m-80) REVERT: D 515 PHE cc_start: 0.8498 (m-80) cc_final: 0.8281 (m-10) REVERT: G 73 ASP cc_start: 0.8286 (m-30) cc_final: 0.7762 (m-30) REVERT: G 114 PHE cc_start: 0.0241 (m-80) cc_final: 0.0008 (m-80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2712 time to fit residues: 75.8798 Evaluate side-chains 125 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 87 optimal weight: 5.9990 chunk 178 optimal weight: 0.0030 chunk 188 optimal weight: 0.5980 chunk 153 optimal weight: 6.9990 chunk 182 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 204 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 overall best weight: 1.2992 ------------------------------------------------------------------------------- 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 A 165 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.154574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.117760 restraints weight = 59505.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.117554 restraints weight = 41399.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.117124 restraints weight = 36022.498| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17952 Z= 0.148 Angle : 0.674 15.333 24462 Z= 0.342 Chirality : 0.047 0.336 2697 Planarity : 0.005 0.060 3150 Dihedral : 5.607 38.312 2646 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.15 % Rotamer: Outliers : 0.05 % Allowed : 0.68 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2175 helix: -1.67 (0.47), residues: 110 sheet: -0.06 (0.20), residues: 682 loop : -1.31 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP D 436 HIS 0.004 0.001 HIS A 66 PHE 0.020 0.002 PHE B 490 TYR 0.019 0.001 TYR D 423 ARG 0.005 0.000 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.01026 ( 12) link_NAG-ASN : angle 5.60619 ( 36) hydrogen bonds : bond 0.03724 ( 560) hydrogen bonds : angle 6.59307 ( 1449) SS BOND : bond 0.00274 ( 24) SS BOND : angle 1.25812 ( 48) covalent geometry : bond 0.00335 (17916) covalent geometry : angle 0.63783 (24378) *********************** 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 164 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.2139 (mpp) cc_final: -0.2628 (tpp) REVERT: A 440 ASN cc_start: 0.8815 (m-40) cc_final: 0.8551 (m-40) REVERT: A 452 LEU cc_start: 0.8495 (mm) cc_final: 0.7867 (mm) REVERT: B 177 MET cc_start: 0.6262 (mmp) cc_final: 0.2583 (ttt) REVERT: B 574 ASP cc_start: 0.8174 (p0) cc_final: 0.7857 (m-30) REVERT: D 96 GLU cc_start: 0.7035 (tt0) cc_final: 0.6227 (tp30) REVERT: D 191 GLU cc_start: 0.7627 (mt-10) cc_final: 0.6925 (mp0) REVERT: D 202 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7171 (mttm) REVERT: D 265 TYR cc_start: 0.6982 (p90) cc_final: 0.6577 (p90) REVERT: D 392 PHE cc_start: 0.7589 (m-10) cc_final: 0.7267 (m-10) REVERT: D 439 ASN cc_start: 0.6745 (t0) cc_final: 0.6503 (t0) REVERT: D 515 PHE cc_start: 0.8623 (m-80) cc_final: 0.8387 (m-10) REVERT: G 73 ASP cc_start: 0.8220 (m-30) cc_final: 0.7566 (m-30) REVERT: G 114 PHE cc_start: -0.0007 (m-80) cc_final: -0.0287 (m-80) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.2755 time to fit residues: 73.0451 Evaluate side-chains 120 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 164 optimal weight: 0.0000 chunk 126 optimal weight: 0.0060 chunk 213 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.155757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.118204 restraints weight = 59162.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.117647 restraints weight = 37407.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.117869 restraints weight = 33453.279| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17952 Z= 0.123 Angle : 0.648 14.782 24462 Z= 0.326 Chirality : 0.047 0.335 2697 Planarity : 0.004 0.058 3150 Dihedral : 5.395 38.070 2646 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2175 helix: -1.65 (0.46), residues: 110 sheet: -0.03 (0.20), residues: 681 loop : -1.22 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 436 HIS 0.004 0.001 HIS A 66 PHE 0.025 0.002 PHE D 400 TYR 0.024 0.001 TYR G 80 ARG 0.005 0.000 ARG D 403 Details of bonding type rmsd link_NAG-ASN : bond 0.01072 ( 12) link_NAG-ASN : angle 5.48132 ( 36) hydrogen bonds : bond 0.03466 ( 560) hydrogen bonds : angle 6.42883 ( 1449) SS BOND : bond 0.00267 ( 24) SS BOND : angle 1.06346 ( 48) covalent geometry : bond 0.00278 (17916) covalent geometry : angle 0.61257 (24378) *********************** 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 168 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.1935 (mpp) cc_final: -0.2419 (tpp) REVERT: A 440 ASN cc_start: 0.8822 (m-40) cc_final: 0.8576 (m-40) REVERT: A 452 LEU cc_start: 0.8596 (mm) cc_final: 0.8082 (mm) REVERT: B 81 ASN cc_start: 0.8910 (p0) cc_final: 0.8679 (p0) REVERT: B 176 LEU cc_start: 0.8010 (mt) cc_final: 0.7747 (mt) REVERT: B 177 MET cc_start: 0.6316 (mmp) cc_final: 0.2696 (ttt) REVERT: B 574 ASP cc_start: 0.8186 (p0) cc_final: 0.7862 (m-30) REVERT: B 618 THR cc_start: 0.5898 (p) cc_final: 0.5139 (t) REVERT: D 96 GLU cc_start: 0.6870 (tt0) cc_final: 0.6164 (tp30) REVERT: D 191 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6901 (mp0) REVERT: D 202 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7132 (mttm) REVERT: D 265 TYR cc_start: 0.7016 (p90) cc_final: 0.6629 (p90) REVERT: D 392 PHE cc_start: 0.7543 (m-10) cc_final: 0.7214 (m-80) REVERT: E 82 GLN cc_start: 0.4222 (tp40) cc_final: 0.3306 (tm-30) REVERT: G 73 ASP cc_start: 0.8200 (m-30) cc_final: 0.7648 (m-30) REVERT: G 80 TYR cc_start: 0.8422 (m-80) cc_final: 0.8117 (m-10) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2466 time to fit residues: 66.9621 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 : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 214 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 189 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 121 optimal weight: 0.0070 chunk 210 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.0802 ------------------------------------------------------------------------------- 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** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.155092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.119486 restraints weight = 59337.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.116733 restraints weight = 45170.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.117002 restraints weight = 42204.404| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17952 Z= 0.132 Angle : 0.654 14.702 24462 Z= 0.330 Chirality : 0.047 0.331 2697 Planarity : 0.004 0.055 3150 Dihedral : 5.398 38.166 2646 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2175 helix: -1.60 (0.47), residues: 110 sheet: 0.05 (0.20), residues: 676 loop : -1.19 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 436 HIS 0.004 0.001 HIS A 66 PHE 0.026 0.002 PHE A 464 TYR 0.014 0.001 TYR A 265 ARG 0.005 0.000 ARG D 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01014 ( 12) link_NAG-ASN : angle 5.41332 ( 36) hydrogen bonds : bond 0.03536 ( 560) hydrogen bonds : angle 6.40280 ( 1449) SS BOND : bond 0.00266 ( 24) SS BOND : angle 1.03383 ( 48) covalent geometry : bond 0.00303 (17916) covalent geometry : angle 0.61903 (24378) ********************** 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 161 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.1896 (mpp) cc_final: -0.2212 (tpp) REVERT: A 440 ASN cc_start: 0.8836 (m-40) cc_final: 0.8580 (m-40) REVERT: A 452 LEU cc_start: 0.8535 (mm) cc_final: 0.7750 (mm) REVERT: B 177 MET cc_start: 0.6361 (mmp) cc_final: 0.2813 (ttt) REVERT: B 574 ASP cc_start: 0.8139 (p0) cc_final: 0.7822 (m-30) REVERT: D 96 GLU cc_start: 0.7066 (tt0) cc_final: 0.6372 (tp30) REVERT: D 191 GLU cc_start: 0.7604 (mt-10) cc_final: 0.6931 (mp0) REVERT: D 202 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7215 (mttm) REVERT: D 258 TRP cc_start: 0.4666 (m100) cc_final: 0.3989 (m-10) REVERT: D 265 TYR cc_start: 0.6966 (p90) cc_final: 0.6623 (p90) REVERT: D 392 PHE cc_start: 0.7540 (m-10) cc_final: 0.7262 (m-10) REVERT: D 439 ASN cc_start: 0.7001 (t0) cc_final: 0.6756 (t0) REVERT: G 73 ASP cc_start: 0.8251 (m-30) cc_final: 0.7629 (m-30) REVERT: G 80 TYR cc_start: 0.8446 (m-80) cc_final: 0.8149 (m-80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2558 time to fit residues: 67.5723 Evaluate side-chains 114 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 100 optimal weight: 20.0000 chunk 21 optimal weight: 0.0470 chunk 130 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 83 optimal weight: 0.0470 chunk 126 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** 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 = 0.4463 r_free = 0.4463 target = 0.156326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.120406 restraints weight = 58888.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.119324 restraints weight = 42142.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.119110 restraints weight = 37841.219| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17952 Z= 0.114 Angle : 0.637 14.257 24462 Z= 0.319 Chirality : 0.047 0.333 2697 Planarity : 0.004 0.053 3150 Dihedral : 5.194 37.518 2646 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2175 helix: -1.58 (0.47), residues: 110 sheet: 0.09 (0.20), residues: 644 loop : -1.11 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 436 HIS 0.003 0.001 HIS A 66 PHE 0.017 0.001 PHE D 275 TYR 0.013 0.001 TYR A 265 ARG 0.006 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01050 ( 12) link_NAG-ASN : angle 5.25257 ( 36) hydrogen bonds : bond 0.03325 ( 560) hydrogen bonds : angle 6.17461 ( 1449) SS BOND : bond 0.00288 ( 24) SS BOND : angle 0.86880 ( 48) covalent geometry : bond 0.00257 (17916) covalent geometry : angle 0.60392 (24378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5811.06 seconds wall clock time: 101 minutes 48.20 seconds (6108.20 seconds total)