Starting phenix.real_space_refine on Sun Mar 17 10:54:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7c_29806/03_2024/8g7c_29806.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7c_29806/03_2024/8g7c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7c_29806/03_2024/8g7c_29806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7c_29806/03_2024/8g7c_29806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7c_29806/03_2024/8g7c_29806.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7c_29806/03_2024/8g7c_29806.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.62, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 6.67 Conformation dependent library (CDL) restraints added in 3.2 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: 2.37 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: 6.30 Time building geometry restraints manager: 7.24 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: 99.97 - 106.79: 490 106.79 - 113.61: 9560 113.61 - 120.43: 6549 120.43 - 127.25: 7609 127.25 - 134.07: 170 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 2.440 nonbonded pdb=" NH2 ARG B 328 " pdb=" OE1 GLN B 580 " model vdw 2.083 2.520 nonbonded pdb=" O ASP D 80 " pdb=" OH TYR D 265 " model vdw 2.087 2.440 nonbonded pdb=" N SER D 375 " pdb=" O ALA D 435 " model vdw 2.113 2.520 nonbonded pdb=" OG1 THR D 553 " pdb=" OD1 ASP D 586 " model vdw 2.122 2.440 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 2.900 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: 12.420 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 48.210 Find NCS groups from input model: 1.220 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.260 ------------------------------------------------------------------------------- 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 17916 Z= 0.248 Angle : 0.729 11.424 24378 Z= 0.386 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.935 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: 0.2669 time to fit residues: 83.2364 Evaluate side-chains 142 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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: 2.9990 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 196 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 39 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17916 Z= 0.207 Angle : 0.620 10.525 24378 Z= 0.319 Chirality : 0.046 0.316 2697 Planarity : 0.005 0.054 3150 Dihedral : 6.299 56.262 2646 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2175 helix: -1.87 (0.46), residues: 120 sheet: 0.13 (0.20), residues: 693 loop : -1.19 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 36 HIS 0.005 0.001 HIS A 66 PHE 0.021 0.002 PHE D 400 TYR 0.018 0.002 TYR A 473 ARG 0.005 0.001 ARG D 457 *********************** 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 192 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.961 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 440 ASN cc_start: 0.7983 (m-40) cc_final: 0.7627 (m-40) REVERT: B 101 ILE cc_start: 0.8804 (pt) cc_final: 0.8580 (pt) REVERT: D 202 LYS cc_start: 0.7665 (mttp) cc_final: 0.6995 (mttm) REVERT: D 392 PHE cc_start: 0.7087 (m-80) cc_final: 0.6809 (m-80) REVERT: E 81 LEU cc_start: 0.7436 (tp) cc_final: 0.6971 (tp) REVERT: G 83 MET cc_start: 0.5296 (pmm) cc_final: 0.4780 (tpp) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.2724 time to fit residues: 81.7656 Evaluate side-chains 141 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 50.0000 chunk 60 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 0.0770 chunk 196 optimal weight: 0.0470 chunk 212 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 overall best weight: 3.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 422 ASN A 487 ASN A 532 ASN B 422 ASN D 121 ASN D 137 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN E 39 GLN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17916 Z= 0.425 Angle : 0.803 11.755 24378 Z= 0.422 Chirality : 0.051 0.290 2697 Planarity : 0.006 0.083 3150 Dihedral : 6.801 55.273 2646 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 0.21 % Allowed : 5.16 % Favored : 94.63 % 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: -1.49 (0.17), residues: 2175 helix: -2.05 (0.45), residues: 118 sheet: -0.08 (0.19), residues: 679 loop : -1.42 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 436 HIS 0.009 0.002 HIS A 66 PHE 0.040 0.003 PHE A 86 TYR 0.024 0.003 TYR B 423 ARG 0.008 0.001 ARG D 509 *********************** 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 197 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 1.911 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: 0.0299 (mpp) cc_final: -0.0086 (mpp) REVERT: A 439 ASN cc_start: 0.7279 (p0) cc_final: 0.7073 (p0) REVERT: A 440 ASN cc_start: 0.8531 (m-40) cc_final: 0.7986 (m-40) REVERT: A 582 LEU cc_start: 0.8190 (pt) cc_final: 0.7761 (tp) REVERT: B 96 GLU cc_start: 0.6664 (tt0) cc_final: 0.6362 (tt0) REVERT: D 202 LYS cc_start: 0.7758 (mttp) cc_final: 0.7193 (mttm) REVERT: D 392 PHE cc_start: 0.7649 (m-80) cc_final: 0.7410 (m-10) REVERT: G 83 MET cc_start: 0.5568 (pmm) cc_final: 0.5155 (tpp) outliers start: 4 outliers final: 2 residues processed: 197 average time/residue: 0.2536 time to fit residues: 80.5509 Evaluate side-chains 135 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 388 ASN E 39 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17916 Z= 0.172 Angle : 0.622 9.083 24378 Z= 0.321 Chirality : 0.047 0.307 2697 Planarity : 0.005 0.075 3150 Dihedral : 5.948 44.941 2646 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: -1.30 (0.17), residues: 2175 helix: -1.74 (0.45), residues: 124 sheet: -0.00 (0.19), residues: 670 loop : -1.26 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 353 HIS 0.003 0.001 HIS D 207 PHE 0.022 0.002 PHE A 392 TYR 0.018 0.001 TYR B 265 ARG 0.005 0.000 ARG D 509 *********************** 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 194 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.921 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 100 ILE cc_start: 0.6882 (mt) cc_final: 0.6614 (mt) REVERT: A 153 MET cc_start: 0.0359 (mpp) cc_final: -0.0719 (mpp) REVERT: A 242 LEU cc_start: 0.8224 (mm) cc_final: 0.7766 (mt) REVERT: A 582 LEU cc_start: 0.8199 (pt) cc_final: 0.7834 (tp) REVERT: B 574 ASP cc_start: 0.8356 (p0) cc_final: 0.8055 (p0) REVERT: D 202 LYS cc_start: 0.7612 (mttp) cc_final: 0.6949 (mttm) REVERT: E 81 LEU cc_start: 0.7310 (tp) cc_final: 0.7058 (tp) REVERT: G 73 ASP cc_start: 0.5622 (p0) cc_final: 0.4875 (p0) REVERT: G 81 LEU cc_start: 0.7378 (pp) cc_final: 0.7136 (pp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2594 time to fit residues: 80.0313 Evaluate side-chains 134 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 50.0000 chunk 187 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 388 ASN E 39 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17916 Z= 0.205 Angle : 0.609 9.699 24378 Z= 0.315 Chirality : 0.047 0.405 2697 Planarity : 0.005 0.058 3150 Dihedral : 5.778 45.079 2646 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: -1.23 (0.17), residues: 2175 helix: -1.67 (0.46), residues: 124 sheet: 0.05 (0.19), residues: 681 loop : -1.22 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 353 HIS 0.004 0.001 HIS A 66 PHE 0.029 0.002 PHE A 135 TYR 0.016 0.001 TYR B 266 ARG 0.007 0.000 ARG B 328 *********************** 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 165 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.930 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: 0.0894 (mpp) cc_final: -0.0204 (mpp) REVERT: A 418 ILE cc_start: 0.8697 (mm) cc_final: 0.8384 (tp) REVERT: A 582 LEU cc_start: 0.8211 (pt) cc_final: 0.7819 (tp) REVERT: B 574 ASP cc_start: 0.8395 (p0) cc_final: 0.8092 (p0) REVERT: D 153 MET cc_start: 0.2064 (pmm) cc_final: -0.0744 (tmm) REVERT: D 202 LYS cc_start: 0.7549 (mttp) cc_final: 0.6970 (mttm) REVERT: D 392 PHE cc_start: 0.7408 (m-10) cc_final: 0.7181 (m-10) REVERT: E 81 LEU cc_start: 0.7440 (tp) cc_final: 0.7237 (tp) REVERT: G 73 ASP cc_start: 0.5581 (p0) cc_final: 0.4210 (p0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2579 time to fit residues: 69.1409 Evaluate side-chains 122 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 506 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17916 Z= 0.368 Angle : 0.725 8.919 24378 Z= 0.379 Chirality : 0.049 0.336 2697 Planarity : 0.005 0.060 3150 Dihedral : 6.234 44.769 2646 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.09 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: -1.47 (0.17), residues: 2175 helix: -1.69 (0.48), residues: 116 sheet: -0.19 (0.19), residues: 675 loop : -1.36 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP D 436 HIS 0.010 0.002 HIS D 207 PHE 0.041 0.003 PHE D 275 TYR 0.020 0.002 TYR B 279 ARG 0.006 0.001 ARG D 457 *********************** 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 165 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8120 (m-30) cc_final: 0.7854 (m-30) REVERT: A 153 MET cc_start: 0.0741 (mpp) cc_final: -0.2187 (tpp) REVERT: A 197 ILE cc_start: 0.9352 (pt) cc_final: 0.8800 (pt) REVERT: B 177 MET cc_start: 0.5756 (mmp) cc_final: 0.2168 (ttt) REVERT: B 574 ASP cc_start: 0.8421 (p0) cc_final: 0.8120 (p0) REVERT: D 202 LYS cc_start: 0.7780 (mttp) cc_final: 0.7283 (mttm) REVERT: D 265 TYR cc_start: 0.7248 (p90) cc_final: 0.6683 (p90) REVERT: D 392 PHE cc_start: 0.7612 (m-10) cc_final: 0.7299 (m-80) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2525 time to fit residues: 66.7863 Evaluate side-chains 116 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 ASN E 39 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 17916 Z= 0.362 Angle : 0.710 8.283 24378 Z= 0.374 Chirality : 0.049 0.305 2697 Planarity : 0.005 0.060 3150 Dihedral : 6.411 47.779 2646 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.91 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 2175 helix: -1.83 (0.45), residues: 124 sheet: -0.36 (0.19), residues: 670 loop : -1.51 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 436 HIS 0.009 0.002 HIS D 245 PHE 0.034 0.003 PHE A 275 TYR 0.038 0.002 TYR D 38 ARG 0.006 0.001 ARG A 246 *********************** 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 158 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8039 (m-30) cc_final: 0.7808 (m-30) REVERT: A 153 MET cc_start: -0.0945 (mpp) cc_final: -0.3034 (mmm) REVERT: B 265 TYR cc_start: 0.8500 (p90) cc_final: 0.8183 (p90) REVERT: B 574 ASP cc_start: 0.8472 (p0) cc_final: 0.8122 (p0) REVERT: D 202 LYS cc_start: 0.8025 (mttp) cc_final: 0.7467 (mttm) REVERT: D 265 TYR cc_start: 0.7125 (p90) cc_final: 0.6489 (p90) REVERT: D 392 PHE cc_start: 0.7652 (m-10) cc_final: 0.7383 (m-80) REVERT: G 73 ASP cc_start: 0.6001 (p0) cc_final: 0.5561 (p0) REVERT: G 114 PHE cc_start: 0.0121 (m-80) cc_final: -0.0276 (m-80) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2640 time to fit residues: 67.5731 Evaluate side-chains 109 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 19 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 189 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN E 39 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17916 Z= 0.204 Angle : 0.627 9.341 24378 Z= 0.326 Chirality : 0.047 0.302 2697 Planarity : 0.004 0.056 3150 Dihedral : 6.001 47.218 2646 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 0.05 % Allowed : 1.36 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.17), residues: 2175 helix: -1.55 (0.48), residues: 116 sheet: -0.26 (0.20), residues: 658 loop : -1.38 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP D 436 HIS 0.004 0.001 HIS D 207 PHE 0.026 0.002 PHE A 275 TYR 0.018 0.002 TYR A 91 ARG 0.004 0.000 ARG D 457 *********************** 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 156 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8047 (m-30) cc_final: 0.7790 (m-30) REVERT: A 153 MET cc_start: -0.1151 (mpp) cc_final: -0.1931 (tpp) REVERT: B 177 MET cc_start: 0.6084 (mmp) cc_final: 0.2459 (ttt) REVERT: B 265 TYR cc_start: 0.8432 (p90) cc_final: 0.8224 (p90) REVERT: B 574 ASP cc_start: 0.8388 (p0) cc_final: 0.8043 (p0) REVERT: D 202 LYS cc_start: 0.7875 (mttp) cc_final: 0.7298 (mttm) REVERT: D 392 PHE cc_start: 0.7603 (m-10) cc_final: 0.7328 (m-80) REVERT: E 81 LEU cc_start: 0.7616 (tp) cc_final: 0.7395 (tp) REVERT: G 73 ASP cc_start: 0.6006 (p0) cc_final: 0.4774 (p0) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.2620 time to fit residues: 65.4904 Evaluate side-chains 113 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 175 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17916 Z= 0.341 Angle : 0.730 9.264 24378 Z= 0.382 Chirality : 0.050 0.295 2697 Planarity : 0.005 0.067 3150 Dihedral : 6.503 48.483 2646 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.83 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.74 (0.17), residues: 2175 helix: -1.61 (0.48), residues: 116 sheet: -0.49 (0.20), residues: 670 loop : -1.51 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP D 436 HIS 0.009 0.002 HIS A 49 PHE 0.036 0.003 PHE A 275 TYR 0.039 0.002 TYR D 38 ARG 0.007 0.001 ARG D 357 *********************** 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 151 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8099 (m-30) cc_final: 0.7851 (m-30) REVERT: A 153 MET cc_start: -0.1691 (mpp) cc_final: -0.2491 (tpp) REVERT: B 129 LYS cc_start: 0.8200 (tppt) cc_final: 0.7260 (tptm) REVERT: B 177 MET cc_start: 0.6247 (mmp) cc_final: 0.2564 (ttt) REVERT: B 265 TYR cc_start: 0.8554 (p90) cc_final: 0.8213 (p90) REVERT: B 574 ASP cc_start: 0.8417 (p0) cc_final: 0.8042 (p0) REVERT: D 202 LYS cc_start: 0.7988 (mttp) cc_final: 0.7421 (mttm) REVERT: D 265 TYR cc_start: 0.7165 (p90) cc_final: 0.6472 (p90) REVERT: D 392 PHE cc_start: 0.7859 (m-10) cc_final: 0.7610 (m-80) REVERT: G 73 ASP cc_start: 0.6152 (p0) cc_final: 0.5887 (p0) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2604 time to fit residues: 64.2847 Evaluate side-chains 108 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.0000 chunk 125 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 142 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 198 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 136 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17916 Z= 0.204 Angle : 0.629 9.185 24378 Z= 0.327 Chirality : 0.047 0.294 2697 Planarity : 0.005 0.054 3150 Dihedral : 6.132 50.812 2646 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.56 (0.17), residues: 2175 helix: -1.52 (0.48), residues: 116 sheet: -0.31 (0.20), residues: 655 loop : -1.41 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 436 HIS 0.004 0.001 HIS A 66 PHE 0.024 0.002 PHE A 275 TYR 0.020 0.001 TYR A 351 ARG 0.016 0.001 ARG D 357 ********************** 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 169 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.840 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 88 ASP cc_start: 0.8032 (m-30) cc_final: 0.7768 (m-30) REVERT: A 153 MET cc_start: -0.1595 (mpp) cc_final: -0.1917 (tpp) REVERT: B 129 LYS cc_start: 0.8092 (tppt) cc_final: 0.7427 (tttt) REVERT: B 177 MET cc_start: 0.6232 (mmp) cc_final: 0.2730 (ttt) REVERT: B 265 TYR cc_start: 0.8468 (p90) cc_final: 0.8243 (p90) REVERT: B 574 ASP cc_start: 0.8376 (p0) cc_final: 0.7980 (p0) REVERT: B 582 LEU cc_start: 0.7840 (mt) cc_final: 0.7636 (mt) REVERT: D 202 LYS cc_start: 0.7860 (mttp) cc_final: 0.7226 (mttm) REVERT: D 265 TYR cc_start: 0.6990 (p90) cc_final: 0.6236 (p90) REVERT: D 392 PHE cc_start: 0.7582 (m-10) cc_final: 0.7319 (m-80) REVERT: E 81 LEU cc_start: 0.7473 (tp) cc_final: 0.7255 (tp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2586 time to fit residues: 69.6974 Evaluate side-chains 117 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.151101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.114869 restraints weight = 58465.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113577 restraints weight = 37302.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.114005 restraints weight = 35669.636| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17916 Z= 0.268 Angle : 0.655 9.252 24378 Z= 0.341 Chirality : 0.047 0.299 2697 Planarity : 0.005 0.056 3150 Dihedral : 6.235 53.577 2646 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.49 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.61 (0.17), residues: 2175 helix: -1.30 (0.51), residues: 110 sheet: -0.40 (0.20), residues: 667 loop : -1.44 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP D 436 HIS 0.005 0.001 HIS A 66 PHE 0.028 0.002 PHE A 275 TYR 0.022 0.002 TYR A 351 ARG 0.016 0.001 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3165.69 seconds wall clock time: 58 minutes 36.70 seconds (3516.70 seconds total)