Starting phenix.real_space_refine on Wed Aug 5 21:36:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrb_38601/08_2026/8xrb_38601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrb_38601/08_2026/8xrb_38601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xrb_38601/08_2026/8xrb_38601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrb_38601/08_2026/8xrb_38601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xrb_38601/08_2026/8xrb_38601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrb_38601/08_2026/8xrb_38601.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 7446 2.51 5 N 2035 2.21 5 O 2351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11904 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3930 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 19, 'TRANS': 477} Chain: "B" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3909 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 19, 'TRANS': 474} Chain breaks: 1 Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3883 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 19, 'TRANS': 471} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.17, per 1000 atoms: 0.18 Number of scatterers: 11904 At special positions: 0 Unit cell: (91.8, 86.7, 149.6, 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 2351 8.00 N 2035 7.00 C 7446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.04 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.02 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.04 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 701 " - " ASN A 28 " " NAG A 702 " - " ASN A 290 " " NAG A 703 " - " ASN A 16 " " NAG B 701 " - " ASN B 28 " " NAG B 702 " - " ASN B 290 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 290 " " NAG D 1 " - " ASN A 169 " " NAG E 1 " - " ASN B 169 " " NAG F 1 " - " ASN C 169 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 446.2 milliseconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 33 sheets defined 27.5% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.716A pdb=" N LEU A 75 " --> pdb=" O CYS A 72 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.959A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 389 removed outlier: 3.940A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 457 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 488 through 491 removed outlier: 3.723A pdb=" N LYS A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.757A pdb=" N GLU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.589A pdb=" N LEU B 75 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 76 " --> pdb=" O ASP B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 76' Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.565A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 368 through 388 Processing helix chain 'B' and resid 404 through 457 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.845A pdb=" N SER B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.714A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 75 " --> pdb=" O CYS C 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.640A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 369 through 388 Processing helix chain 'C' and resid 404 through 456 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.507A pdb=" N MET C 479 " --> pdb=" O ASP C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 363 removed outlier: 3.508A pdb=" N GLN A 7 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 8 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 468 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.565A pdb=" N GLY A 11 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA5, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA6, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.249A pdb=" N LEU A 46 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 48 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.587A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.607A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.969A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.898A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.701A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 362 through 363 removed outlier: 3.648A pdb=" N GLY B 11 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 7 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 8 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B 468 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AB6, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB8, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.850A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.511A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 100 removed outlier: 8.095A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.603A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'B' and resid 288 through 289 removed outlier: 4.165A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 362 through 363 removed outlier: 4.092A pdb=" N GLN C 7 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 8 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 468 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.245A pdb=" N GLU C 19 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.097A pdb=" N LEU C 46 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 48 " --> pdb=" O CYS C 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.824A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.495A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 98 through 100 removed outlier: 7.973A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 136 through 141 removed outlier: 5.238A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.595A pdb=" N ILE C 289 " --> pdb=" O CYS C 282 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 295 through 296 485 hydrogen bonds defined for protein. 1359 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: 1.89 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3938 1.35 - 1.47: 2871 1.47 - 1.59: 5240 1.59 - 1.72: 0 1.72 - 1.84: 108 Bond restraints: 12157 Sorted by residual: bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C CYS C 306 " pdb=" N PRO C 307 " ideal model delta sigma weight residual 1.331 1.371 -0.039 1.21e-02 6.83e+03 1.05e+01 bond pdb=" CB CYS B 278 " pdb=" SG CYS B 278 " ideal model delta sigma weight residual 1.808 1.755 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" CA GLU C 305 " pdb=" CB GLU C 305 " ideal model delta sigma weight residual 1.530 1.553 -0.024 1.57e-02 4.06e+03 2.29e+00 ... (remaining 12152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 16195 2.03 - 4.06: 217 4.06 - 6.09: 25 6.09 - 8.12: 4 8.12 - 10.15: 1 Bond angle restraints: 16442 Sorted by residual: angle pdb=" C ARG A 457 " pdb=" CA ARG A 457 " pdb=" CB ARG A 457 " ideal model delta sigma weight residual 117.23 109.77 7.46 1.36e+00 5.41e-01 3.01e+01 angle pdb=" N CYS B 47 " pdb=" CA CYS B 47 " pdb=" C CYS B 47 " ideal model delta sigma weight residual 108.24 114.76 -6.52 1.32e+00 5.74e-01 2.44e+01 angle pdb=" CA ARG A 457 " pdb=" C ARG A 457 " pdb=" N ASP A 458 " ideal model delta sigma weight residual 119.98 116.77 3.21 8.50e-01 1.38e+00 1.42e+01 angle pdb=" C ASP C 488 " pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 119.78 124.28 -4.50 1.24e+00 6.50e-01 1.31e+01 angle pdb=" N PRO C 307 " pdb=" CA PRO C 307 " pdb=" C PRO C 307 " ideal model delta sigma weight residual 111.33 116.38 -5.05 1.43e+00 4.89e-01 1.25e+01 ... (remaining 16437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.38: 6537 24.38 - 48.76: 774 48.76 - 73.15: 142 73.15 - 97.53: 20 97.53 - 121.91: 3 Dihedral angle restraints: 7476 sinusoidal: 3238 harmonic: 4238 Sorted by residual: dihedral pdb=" CB CYS B 282 " pdb=" SG CYS B 282 " pdb=" SG CYS B 306 " pdb=" CB CYS B 306 " ideal model delta sinusoidal sigma weight residual 93.00 17.80 75.20 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS A 95 " pdb=" SG CYS A 95 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 18.58 74.42 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual 93.00 26.36 66.64 1 1.00e+01 1.00e-02 5.79e+01 ... (remaining 7473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1351 0.044 - 0.089: 328 0.089 - 0.133: 120 0.133 - 0.178: 3 0.178 - 0.222: 1 Chirality restraints: 1803 Sorted by residual: chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 28 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA CYS B 47 " pdb=" N CYS B 47 " pdb=" C CYS B 47 " pdb=" CB CYS B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ASP A 458 " pdb=" N ASP A 458 " pdb=" C ASP A 458 " pdb=" CB ASP A 458 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 1800 not shown) Planarity restraints: 2141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 420 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" CG ASP A 420 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP A 420 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 420 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 458 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ASP C 458 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP C 458 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN C 459 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 293 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 294 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 294 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 294 " -0.021 5.00e-02 4.00e+02 ... (remaining 2138 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 698 2.73 - 3.27: 10599 3.27 - 3.82: 18838 3.82 - 4.36: 22489 4.36 - 4.90: 39703 Nonbonded interactions: 92327 Sorted by model distance: nonbonded pdb=" OG1 THR A 131 " pdb=" O LYS A 156 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASN B 358 " pdb=" N ASP B 359 " model vdw 2.201 3.120 nonbonded pdb=" O SER C 142 " pdb=" OG SER C 142 " model vdw 2.244 3.040 nonbonded pdb=" NE2 GLN A 360 " pdb=" OD2 ASP A 476 " model vdw 2.245 3.120 nonbonded pdb=" OE2 GLU A 39 " pdb=" OG1 THR A 41 " model vdw 2.248 3.040 ... (remaining 92322 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 6 through 327 or resid 333 through 501 or resid 702)) selection = (chain 'B' and (resid 6 through 327 or resid 333 through 501 or resid 702)) selection = (chain 'C' and resid 6 through 701) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.120 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12188 Z= 0.160 Angle : 0.583 10.150 16517 Z= 0.306 Chirality : 0.043 0.222 1803 Planarity : 0.004 0.038 2131 Dihedral : 19.636 121.908 4718 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.62 % Allowed : 31.43 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.22), residues: 1472 helix: 2.64 (0.27), residues: 372 sheet: 0.16 (0.33), residues: 307 loop : -1.40 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 91 TYR 0.011 0.001 TYR A 492 PHE 0.013 0.001 PHE C 440 TRP 0.012 0.001 TRP A 422 HIS 0.006 0.001 HIS B 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (12157) covalent geometry : angle 0.56708 / 0.30 (16442) SS BOND : bond 0.00499 / 0.26 ( 18) SS BOND : angle 2.09234 / 1.55 ( 36) hydrogen bonds : bond 0.16476 / 11.91 ( 449) hydrogen bonds : angle 6.87541 / 4.86 ( 1359) link_BETA1-4 : bond 0.00360 / 0.18 ( 3) link_BETA1-4 : angle 0.80434 / 0.48 ( 9) link_NAG-ASN : bond 0.00370 / 0.26 ( 10) link_NAG-ASN : angle 2.34351 / 1.43 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 295 PHE cc_start: 0.8793 (m-80) cc_final: 0.8406 (m-80) REVERT: C 495 GLU cc_start: 0.6953 (tp30) cc_final: 0.6752 (tp30) outliers start: 60 outliers final: 52 residues processed: 387 average time/residue: 0.4951 time to fit residues: 206.5573 Evaluate side-chains 385 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 333 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.1825 > 50:) chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN B 197 ASN B 210 ASN B 356 HIS C 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.120971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107211 restraints weight = 15724.072| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.86 r_work: 0.3365 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12188 Z= 0.232 Angle : 0.621 10.895 16517 Z= 0.328 Chirality : 0.046 0.267 1803 Planarity : 0.004 0.037 2131 Dihedral : 10.052 109.074 1956 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 7.09 % Allowed : 26.58 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1472 helix: 2.58 (0.27), residues: 376 sheet: 0.08 (0.31), residues: 325 loop : -1.53 (0.19), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 91 TYR 0.017 0.002 TYR A 364 PHE 0.017 0.002 PHE C 440 TRP 0.009 0.002 TRP B 127 HIS 0.008 0.002 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (12157) covalent geometry : angle 0.60271 / 0.32 (16442) SS BOND : bond 0.00610 / 0.37 ( 18) SS BOND : angle 2.20543 / 1.45 ( 36) hydrogen bonds : bond 0.06751 / 4.49 ( 449) hydrogen bonds : angle 4.99628 / 3.51 ( 1359) link_BETA1-4 : bond 0.00380 / 0.19 ( 3) link_BETA1-4 : angle 0.72521 / 0.40 ( 9) link_NAG-ASN : bond 0.00312 / 0.21 ( 10) link_NAG-ASN : angle 2.73266 / 1.60 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 348 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.8000 (m-30) cc_final: 0.7767 (m-30) REVERT: A 420 ASP cc_start: 0.7918 (m-30) cc_final: 0.7691 (m-30) REVERT: A 462 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6968 (mt-10) REVERT: B 480 ASN cc_start: 0.7550 (m110) cc_final: 0.7320 (m110) REVERT: C 458 ASP cc_start: 0.7721 (t0) cc_final: 0.7447 (t0) REVERT: C 495 GLU cc_start: 0.7226 (tp30) cc_final: 0.6880 (tp30) outliers start: 92 outliers final: 55 residues processed: 404 average time/residue: 0.4851 time to fit residues: 211.6631 Evaluate side-chains 402 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 347 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 106 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 33 optimal weight: 0.0570 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN B 197 ASN B 210 ASN B 356 HIS B 459 ASN B 480 ASN C 480 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108180 restraints weight = 15876.970| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.89 r_work: 0.3387 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12188 Z= 0.139 Angle : 0.552 9.988 16517 Z= 0.292 Chirality : 0.043 0.248 1803 Planarity : 0.004 0.036 2131 Dihedral : 9.021 110.817 1910 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.39 % Allowed : 27.04 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1472 helix: 2.81 (0.27), residues: 376 sheet: 0.03 (0.30), residues: 317 loop : -1.47 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 91 TYR 0.010 0.001 TYR A 364 PHE 0.013 0.001 PHE C 468 TRP 0.009 0.001 TRP B 422 HIS 0.008 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (12157) covalent geometry : angle 0.53411 / 0.29 (16442) SS BOND : bond 0.00423 / 0.23 ( 18) SS BOND : angle 1.87255 / 1.21 ( 36) hydrogen bonds : bond 0.06090 / 4.06 ( 449) hydrogen bonds : angle 4.65487 / 3.27 ( 1359) link_BETA1-4 : bond 0.00320 / 0.16 ( 3) link_BETA1-4 : angle 0.79711 / 0.44 ( 9) link_NAG-ASN : bond 0.00380 / 0.26 ( 10) link_NAG-ASN : angle 2.62661 / 1.55 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 350 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 THR cc_start: 0.8520 (t) cc_final: 0.8313 (t) REVERT: A 468 PHE cc_start: 0.6954 (OUTLIER) cc_final: 0.5987 (p90) REVERT: B 480 ASN cc_start: 0.7589 (m-40) cc_final: 0.7178 (m110) REVERT: C 458 ASP cc_start: 0.7791 (t0) cc_final: 0.7399 (t0) REVERT: C 495 GLU cc_start: 0.7269 (tp30) cc_final: 0.6903 (tp30) outliers start: 83 outliers final: 54 residues processed: 393 average time/residue: 0.4633 time to fit residues: 197.6208 Evaluate side-chains 403 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 348 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 492 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 23 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 0.0470 chunk 106 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 145 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN B 197 ASN B 210 ASN B 356 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107767 restraints weight = 15757.740| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.88 r_work: 0.3377 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12188 Z= 0.167 Angle : 0.566 10.139 16517 Z= 0.300 Chirality : 0.044 0.242 1803 Planarity : 0.004 0.037 2131 Dihedral : 8.431 110.798 1895 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.63 % Allowed : 26.66 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.22), residues: 1472 helix: 2.85 (0.27), residues: 376 sheet: 0.29 (0.30), residues: 313 loop : -1.45 (0.19), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 91 TYR 0.012 0.002 TYR A 364 PHE 0.015 0.002 PHE C 468 TRP 0.008 0.001 TRP B 422 HIS 0.009 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (12157) covalent geometry : angle 0.54754 / 0.29 (16442) SS BOND : bond 0.00525 / 0.29 ( 18) SS BOND : angle 2.01173 / 1.29 ( 36) hydrogen bonds : bond 0.06159 / 4.08 ( 449) hydrogen bonds : angle 4.60103 / 3.23 ( 1359) link_BETA1-4 : bond 0.00385 / 0.19 ( 3) link_BETA1-4 : angle 0.80961 / 0.44 ( 9) link_NAG-ASN : bond 0.00368 / 0.26 ( 10) link_NAG-ASN : angle 2.59759 / 1.51 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 346 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 THR cc_start: 0.8534 (t) cc_final: 0.8313 (t) REVERT: A 420 ASP cc_start: 0.7919 (m-30) cc_final: 0.7675 (m-30) REVERT: A 468 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6121 (p90) REVERT: C 458 ASP cc_start: 0.7884 (t0) cc_final: 0.7479 (t0) REVERT: C 495 GLU cc_start: 0.7413 (tp30) cc_final: 0.7191 (tp30) outliers start: 86 outliers final: 55 residues processed: 391 average time/residue: 0.4937 time to fit residues: 208.2756 Evaluate side-chains 405 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 349 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 492 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN B 197 ASN B 210 ASN B 459 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.122557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108597 restraints weight = 15831.151| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.89 r_work: 0.3389 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12188 Z= 0.136 Angle : 0.554 9.708 16517 Z= 0.291 Chirality : 0.043 0.231 1803 Planarity : 0.004 0.035 2131 Dihedral : 8.214 111.676 1894 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.86 % Allowed : 27.20 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.22), residues: 1472 helix: 2.90 (0.27), residues: 376 sheet: 0.33 (0.30), residues: 315 loop : -1.43 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 91 TYR 0.019 0.001 TYR B 492 PHE 0.012 0.001 PHE C 468 TRP 0.009 0.001 TRP A 422 HIS 0.008 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12157) covalent geometry : angle 0.53641 / 0.29 (16442) SS BOND : bond 0.00455 / 0.25 ( 18) SS BOND : angle 1.90137 / 1.27 ( 36) hydrogen bonds : bond 0.05836 / 3.87 ( 449) hydrogen bonds : angle 4.48458 / 3.15 ( 1359) link_BETA1-4 : bond 0.00361 / 0.18 ( 3) link_BETA1-4 : angle 0.83931 / 0.47 ( 9) link_NAG-ASN : bond 0.00412 / 0.28 ( 10) link_NAG-ASN : angle 2.53715 / 1.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 345 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: A 291 THR cc_start: 0.8506 (t) cc_final: 0.8300 (t) REVERT: A 435 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: A 468 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6070 (p90) REVERT: B 368 LYS cc_start: 0.7810 (mptt) cc_final: 0.7587 (mptt) REVERT: B 458 ASP cc_start: 0.7162 (t0) cc_final: 0.6922 (t0) REVERT: C 457 ARG cc_start: 0.7469 (mtm-85) cc_final: 0.7046 (mtm-85) REVERT: C 458 ASP cc_start: 0.7924 (t0) cc_final: 0.7514 (t0) REVERT: C 489 TYR cc_start: 0.8138 (t80) cc_final: 0.7848 (t80) outliers start: 76 outliers final: 50 residues processed: 383 average time/residue: 0.4763 time to fit residues: 197.2576 Evaluate side-chains 398 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 492 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 210 ASN B 356 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.120346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106514 restraints weight = 15904.661| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.88 r_work: 0.3360 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 12188 Z= 0.247 Angle : 0.628 10.539 16517 Z= 0.331 Chirality : 0.046 0.236 1803 Planarity : 0.004 0.038 2131 Dihedral : 7.909 110.711 1888 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.93 % Allowed : 28.20 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1472 helix: 2.75 (0.27), residues: 376 sheet: 0.27 (0.30), residues: 327 loop : -1.54 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 91 TYR 0.016 0.002 TYR C 492 PHE 0.019 0.002 PHE C 468 TRP 0.012 0.002 TRP A 81 HIS 0.010 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.25 (12157) covalent geometry : angle 0.60802 / 0.32 (16442) SS BOND : bond 0.00686 / 0.41 ( 18) SS BOND : angle 2.45258 / 1.63 ( 36) hydrogen bonds : bond 0.06574 / 4.34 ( 449) hydrogen bonds : angle 4.55710 / 3.20 ( 1359) link_BETA1-4 : bond 0.00369 / 0.19 ( 3) link_BETA1-4 : angle 0.84721 / 0.46 ( 9) link_NAG-ASN : bond 0.00329 / 0.23 ( 10) link_NAG-ASN : angle 2.68524 / 1.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 344 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 THR cc_start: 0.8541 (t) cc_final: 0.8337 (t) REVERT: A 462 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6862 (mt-10) REVERT: A 468 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6439 (p90) REVERT: B 368 LYS cc_start: 0.7857 (mptt) cc_final: 0.7609 (mptt) REVERT: C 126 ARG cc_start: 0.7823 (ptm-80) cc_final: 0.7490 (ptm-80) REVERT: C 458 ASP cc_start: 0.7974 (t0) cc_final: 0.7588 (t0) outliers start: 77 outliers final: 51 residues processed: 383 average time/residue: 0.4775 time to fit residues: 197.6773 Evaluate side-chains 395 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 343 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 492 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 137 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 32 optimal weight: 0.0000 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 145 optimal weight: 0.0970 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN B 197 ASN B 210 ASN B 459 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.122018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108081 restraints weight = 15794.883| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.88 r_work: 0.3383 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12188 Z= 0.146 Angle : 0.573 9.838 16517 Z= 0.302 Chirality : 0.043 0.223 1803 Planarity : 0.004 0.036 2131 Dihedral : 7.643 112.103 1885 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.16 % Allowed : 28.51 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1472 helix: 2.86 (0.27), residues: 376 sheet: 0.30 (0.31), residues: 326 loop : -1.48 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 457 TYR 0.014 0.001 TYR C 492 PHE 0.013 0.001 PHE C 468 TRP 0.010 0.001 TRP B 422 HIS 0.009 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (12157) covalent geometry : angle 0.55539 / 0.30 (16442) SS BOND : bond 0.00563 / 0.31 ( 18) SS BOND : angle 1.98843 / 1.31 ( 36) hydrogen bonds : bond 0.05989 / 3.96 ( 449) hydrogen bonds : angle 4.46052 / 3.14 ( 1359) link_BETA1-4 : bond 0.00283 / 0.14 ( 3) link_BETA1-4 : angle 0.85567 / 0.47 ( 9) link_NAG-ASN : bond 0.00391 / 0.28 ( 10) link_NAG-ASN : angle 2.57159 / 1.52 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 336 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: A 328 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5741 (pp20) REVERT: A 468 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6133 (p90) REVERT: B 368 LYS cc_start: 0.7845 (mptt) cc_final: 0.7594 (mptt) REVERT: C 126 ARG cc_start: 0.7819 (ptm-80) cc_final: 0.7481 (ptm-80) REVERT: C 458 ASP cc_start: 0.7967 (t0) cc_final: 0.7565 (t0) REVERT: C 489 TYR cc_start: 0.8009 (t80) cc_final: 0.7714 (t80) outliers start: 67 outliers final: 50 residues processed: 373 average time/residue: 0.4832 time to fit residues: 194.7190 Evaluate side-chains 389 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 128 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 356 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.122201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108310 restraints weight = 15781.494| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.88 r_work: 0.3385 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12188 Z= 0.142 Angle : 0.569 9.567 16517 Z= 0.299 Chirality : 0.043 0.215 1803 Planarity : 0.004 0.042 2131 Dihedral : 7.418 112.462 1883 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.01 % Allowed : 29.66 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1472 helix: 2.86 (0.27), residues: 376 sheet: 0.43 (0.31), residues: 316 loop : -1.47 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 137 TYR 0.019 0.001 TYR C 492 PHE 0.012 0.001 PHE C 440 TRP 0.008 0.001 TRP B 422 HIS 0.009 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12157) covalent geometry : angle 0.55246 / 0.29 (16442) SS BOND : bond 0.00514 / 0.28 ( 18) SS BOND : angle 1.87365 / 1.24 ( 36) hydrogen bonds : bond 0.05844 / 3.86 ( 449) hydrogen bonds : angle 4.38397 / 3.09 ( 1359) link_BETA1-4 : bond 0.00372 / 0.19 ( 3) link_BETA1-4 : angle 0.88620 / 0.50 ( 9) link_NAG-ASN : bond 0.00379 / 0.27 ( 10) link_NAG-ASN : angle 2.51267 / 1.48 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 340 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5698 (pp20) REVERT: A 468 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6118 (p90) REVERT: C 458 ASP cc_start: 0.7926 (t0) cc_final: 0.7559 (t0) REVERT: C 489 TYR cc_start: 0.7903 (t80) cc_final: 0.7396 (t80) outliers start: 65 outliers final: 46 residues processed: 373 average time/residue: 0.5203 time to fit residues: 209.5398 Evaluate side-chains 391 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 343 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN B 197 ASN B 356 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107537 restraints weight = 15859.414| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.89 r_work: 0.3380 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12188 Z= 0.177 Angle : 0.611 9.626 16517 Z= 0.320 Chirality : 0.044 0.212 1803 Planarity : 0.004 0.046 2131 Dihedral : 7.396 112.391 1881 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.55 % Allowed : 30.43 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1472 helix: 2.77 (0.27), residues: 375 sheet: 0.38 (0.30), residues: 327 loop : -1.50 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 137 TYR 0.017 0.002 TYR C 492 PHE 0.014 0.002 PHE C 468 TRP 0.008 0.001 TRP B 422 HIS 0.010 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (12157) covalent geometry : angle 0.59181 / 0.31 (16442) SS BOND : bond 0.00568 / 0.32 ( 18) SS BOND : angle 2.40159 / 1.72 ( 36) hydrogen bonds : bond 0.06085 / 4.03 ( 449) hydrogen bonds : angle 4.39984 / 3.10 ( 1359) link_BETA1-4 : bond 0.00377 / 0.19 ( 3) link_BETA1-4 : angle 0.88732 / 0.50 ( 9) link_NAG-ASN : bond 0.00361 / 0.26 ( 10) link_NAG-ASN : angle 2.53759 / 1.50 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5717 (pp20) REVERT: A 468 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6208 (p90) REVERT: B 246 GLU cc_start: 0.7696 (tp30) cc_final: 0.7481 (tp30) REVERT: C 126 ARG cc_start: 0.7828 (ptm-80) cc_final: 0.7460 (ptm-80) REVERT: C 458 ASP cc_start: 0.7934 (t0) cc_final: 0.7556 (t0) outliers start: 59 outliers final: 46 residues processed: 358 average time/residue: 0.5152 time to fit residues: 198.7980 Evaluate side-chains 385 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 337 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 109 optimal weight: 0.0470 chunk 143 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 356 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108823 restraints weight = 15828.291| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.89 r_work: 0.3395 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12188 Z= 0.131 Angle : 0.588 9.726 16517 Z= 0.308 Chirality : 0.043 0.206 1803 Planarity : 0.004 0.039 2131 Dihedral : 7.321 113.010 1881 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.39 % Allowed : 30.28 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.22), residues: 1472 helix: 2.77 (0.27), residues: 375 sheet: 0.31 (0.31), residues: 321 loop : -1.43 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 137 TYR 0.022 0.001 TYR C 492 PHE 0.012 0.001 PHE C 440 TRP 0.010 0.001 TRP A 422 HIS 0.009 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12157) covalent geometry : angle 0.56974 / 0.30 (16442) SS BOND : bond 0.00467 / 0.25 ( 18) SS BOND : angle 2.22150 / 1.45 ( 36) hydrogen bonds : bond 0.05679 / 3.76 ( 449) hydrogen bonds : angle 4.32504 / 3.05 ( 1359) link_BETA1-4 : bond 0.00364 / 0.18 ( 3) link_BETA1-4 : angle 0.90914 / 0.52 ( 9) link_NAG-ASN : bond 0.00401 / 0.28 ( 10) link_NAG-ASN : angle 2.44027 / 1.46 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 335 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5690 (pp20) REVERT: A 468 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.5904 (p90) REVERT: C 458 ASP cc_start: 0.7919 (t0) cc_final: 0.7550 (t0) outliers start: 57 outliers final: 44 residues processed: 364 average time/residue: 0.4875 time to fit residues: 191.6117 Evaluate side-chains 374 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 356 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 196 GLN A 499 ASN B 197 ASN B 356 HIS ** C 355 HIS ** 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 = 0.3688 r_free = 0.3688 target = 0.121432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107530 restraints weight = 15892.098| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.88 r_work: 0.3372 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12188 Z= 0.195 Angle : 0.638 11.113 16517 Z= 0.334 Chirality : 0.045 0.201 1803 Planarity : 0.004 0.054 2131 Dihedral : 7.357 112.620 1881 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.01 % Allowed : 31.05 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1472 helix: 2.66 (0.27), residues: 376 sheet: 0.37 (0.30), residues: 327 loop : -1.51 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 91 TYR 0.023 0.002 TYR C 492 PHE 0.016 0.002 PHE C 468 TRP 0.009 0.001 TRP B 422 HIS 0.010 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (12157) covalent geometry : angle 0.61917 / 0.33 (16442) SS BOND : bond 0.00605 / 0.34 ( 18) SS BOND : angle 2.55885 / 1.72 ( 36) hydrogen bonds : bond 0.06149 / 4.07 ( 449) hydrogen bonds : angle 4.40113 / 3.10 ( 1359) link_BETA1-4 : bond 0.00362 / 0.18 ( 3) link_BETA1-4 : angle 0.87920 / 0.49 ( 9) link_NAG-ASN : bond 0.00343 / 0.24 ( 10) link_NAG-ASN : angle 2.50118 / 1.49 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4619.52 seconds wall clock time: 78 minutes 58.57 seconds (4738.57 seconds total)