Starting phenix.real_space_refine on Tue Jun 10 18:24:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrb_38601/06_2025/8xrb_38601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrb_38601/06_2025/8xrb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xrb_38601/06_2025/8xrb_38601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrb_38601/06_2025/8xrb_38601.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrb_38601/06_2025/8xrb_38601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrb_38601/06_2025/8xrb_38601.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.14, per 1000 atoms: 0.60 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: 2.96 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.69 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: 4.56 Time building geometry restraints manager: 3.36 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 501 or resid 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.540 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP A 422 HIS 0.006 0.001 HIS B 356 PHE 0.013 0.001 PHE C 440 TYR 0.011 0.001 TYR A 492 ARG 0.006 0.000 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 10) link_NAG-ASN : angle 2.34351 ( 30) link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 0.80434 ( 9) hydrogen bonds : bond 0.16476 ( 449) hydrogen bonds : angle 6.87541 ( 1359) SS BOND : bond 0.00499 ( 18) SS BOND : angle 2.09234 ( 36) covalent geometry : bond 0.00339 (12157) covalent geometry : angle 0.56708 (16442) *********************** 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 : 1.252 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: 1.3593 time to fit residues: 564.4013 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 : 1.281 ------------------------------------------------------------------------------- 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 124 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3670 r_free = 0.3670 target = 0.120323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106532 restraints weight = 15644.586| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.87 r_work: 0.3357 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12188 Z= 0.260 Angle : 0.643 11.572 16517 Z= 0.339 Chirality : 0.047 0.279 1803 Planarity : 0.004 0.037 2131 Dihedral : 10.069 108.145 1956 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 7.16 % Allowed : 26.66 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1472 helix: 2.52 (0.27), residues: 376 sheet: -0.06 (0.30), residues: 335 loop : -1.55 (0.19), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 127 HIS 0.009 0.002 HIS B 356 PHE 0.018 0.002 PHE C 468 TYR 0.018 0.002 TYR A 364 ARG 0.005 0.001 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 10) link_NAG-ASN : angle 2.86388 ( 30) link_BETA1-4 : bond 0.00522 ( 3) link_BETA1-4 : angle 0.72578 ( 9) hydrogen bonds : bond 0.07013 ( 449) hydrogen bonds : angle 5.02266 ( 1359) SS BOND : bond 0.00670 ( 18) SS BOND : angle 2.36059 ( 36) covalent geometry : bond 0.00634 (12157) covalent geometry : angle 0.62279 (16442) *********************** 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 448 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 355 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.8013 (m-30) cc_final: 0.7778 (m-30) REVERT: A 462 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6900 (mt-10) REVERT: A 468 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6428 (p90) REVERT: B 480 ASN cc_start: 0.7565 (m110) cc_final: 0.7336 (m110) REVERT: C 88 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7473 (tm-30) REVERT: C 458 ASP cc_start: 0.7750 (t0) cc_final: 0.7454 (t0) REVERT: C 495 GLU cc_start: 0.7285 (tp30) cc_final: 0.6935 (tp30) outliers start: 93 outliers final: 56 residues processed: 411 average time/residue: 1.3306 time to fit residues: 588.5702 Evaluate side-chains 410 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 353 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 196 GLN 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 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 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 117 GLU Chi-restraints excluded: chain B residue 125 ASP 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 118 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 123 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106757 restraints weight = 15853.451| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.87 r_work: 0.3361 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12188 Z= 0.212 Angle : 0.611 11.101 16517 Z= 0.322 Chirality : 0.046 0.267 1803 Planarity : 0.004 0.050 2131 Dihedral : 9.094 109.611 1906 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.70 % Allowed : 26.89 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1472 helix: 2.66 (0.27), residues: 376 sheet: -0.03 (0.30), residues: 335 loop : -1.59 (0.19), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.009 0.001 HIS C 356 PHE 0.017 0.002 PHE C 468 TYR 0.014 0.002 TYR A 364 ARG 0.005 0.001 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 10) link_NAG-ASN : angle 2.82664 ( 30) link_BETA1-4 : bond 0.00415 ( 3) link_BETA1-4 : angle 0.81889 ( 9) hydrogen bonds : bond 0.06690 ( 449) hydrogen bonds : angle 4.74891 ( 1359) SS BOND : bond 0.00547 ( 18) SS BOND : angle 2.30447 ( 36) covalent geometry : bond 0.00514 (12157) covalent geometry : angle 0.59054 (16442) *********************** 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 439 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 352 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 THR cc_start: 0.8557 (t) cc_final: 0.8352 (t) REVERT: A 468 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6398 (p90) REVERT: B 480 ASN cc_start: 0.7613 (m-40) cc_final: 0.7224 (m110) REVERT: C 88 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7439 (tm-30) REVERT: C 126 ARG cc_start: 0.7837 (ptm-80) cc_final: 0.7507 (ptm-80) REVERT: C 457 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7509 (mtp85) REVERT: C 458 ASP cc_start: 0.7832 (t0) cc_final: 0.7425 (t0) REVERT: C 495 GLU cc_start: 0.7299 (tp30) cc_final: 0.6986 (tp30) outliers start: 87 outliers final: 58 residues processed: 399 average time/residue: 1.2695 time to fit residues: 546.5002 Evaluate side-chains 404 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 344 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 238 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 THR 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 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 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 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 340 ILE 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 474 CYS 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 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 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 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 457 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 77 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107784 restraints weight = 15605.981| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.86 r_work: 0.3377 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12188 Z= 0.147 Angle : 0.555 10.452 16517 Z= 0.294 Chirality : 0.043 0.249 1803 Planarity : 0.004 0.061 2131 Dihedral : 8.537 110.967 1898 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.78 % Allowed : 26.43 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1472 helix: 2.82 (0.27), residues: 376 sheet: 0.13 (0.30), residues: 323 loop : -1.48 (0.19), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.009 0.001 HIS C 356 PHE 0.013 0.001 PHE C 468 TYR 0.011 0.001 TYR A 364 ARG 0.005 0.000 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 10) link_NAG-ASN : angle 2.67664 ( 30) link_BETA1-4 : bond 0.00366 ( 3) link_BETA1-4 : angle 0.81587 ( 9) hydrogen bonds : bond 0.06105 ( 449) hydrogen bonds : angle 4.58200 ( 1359) SS BOND : bond 0.00513 ( 18) SS BOND : angle 1.92781 ( 36) covalent geometry : bond 0.00341 (12157) covalent geometry : angle 0.53621 (16442) *********************** 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 427 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 339 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 THR cc_start: 0.8546 (t) cc_final: 0.8328 (t) REVERT: A 420 ASP cc_start: 0.7896 (m-30) cc_final: 0.7658 (m-30) REVERT: A 468 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6356 (p90) REVERT: B 480 ASN cc_start: 0.7582 (m-40) cc_final: 0.7262 (m110) REVERT: C 88 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 126 ARG cc_start: 0.7806 (ptm-80) cc_final: 0.7449 (ptm-80) REVERT: C 457 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7422 (mtp85) REVERT: C 458 ASP cc_start: 0.7851 (t0) cc_final: 0.7349 (t0) REVERT: C 489 TYR cc_start: 0.7978 (t80) cc_final: 0.7699 (t80) REVERT: C 495 GLU cc_start: 0.7327 (tp30) cc_final: 0.7108 (tp30) outliers start: 88 outliers final: 56 residues processed: 384 average time/residue: 1.2828 time to fit residues: 530.5052 Evaluate side-chains 402 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 344 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU 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 271 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 LEU 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 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 313 GLU 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 459 ASN 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 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 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 394 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 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 Chi-restraints excluded: chain C residue 496 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 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 = 0.3696 r_free = 0.3696 target = 0.122105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108213 restraints weight = 15755.882| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.88 r_work: 0.3379 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12188 Z= 0.147 Angle : 0.561 10.254 16517 Z= 0.296 Chirality : 0.043 0.239 1803 Planarity : 0.004 0.055 2131 Dihedral : 8.247 111.256 1894 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.32 % Allowed : 27.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1472 helix: 2.83 (0.27), residues: 377 sheet: 0.19 (0.30), residues: 325 loop : -1.46 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.009 0.001 HIS C 356 PHE 0.013 0.001 PHE C 468 TYR 0.018 0.002 TYR B 492 ARG 0.007 0.000 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 10) link_NAG-ASN : angle 2.63928 ( 30) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 0.83282 ( 9) hydrogen bonds : bond 0.05985 ( 449) hydrogen bonds : angle 4.48210 ( 1359) SS BOND : bond 0.00457 ( 18) SS BOND : angle 2.07640 ( 36) covalent geometry : bond 0.00347 (12157) covalent geometry : angle 0.54193 (16442) *********************** 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 428 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 346 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 THR cc_start: 0.8518 (t) cc_final: 0.8311 (t) REVERT: A 435 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: A 468 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6339 (p90) REVERT: B 458 ASP cc_start: 0.7173 (t0) cc_final: 0.6943 (t0) REVERT: C 88 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 126 ARG cc_start: 0.7796 (ptm-80) cc_final: 0.7472 (ptm-80) REVERT: C 457 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7444 (mtp85) REVERT: C 458 ASP cc_start: 0.7894 (t0) cc_final: 0.7375 (t0) REVERT: C 495 GLU cc_start: 0.7381 (tp30) cc_final: 0.7028 (tm-30) outliers start: 82 outliers final: 57 residues processed: 387 average time/residue: 1.2831 time to fit residues: 534.6393 Evaluate side-chains 390 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 330 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU 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 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 8 ILE 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 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 340 ILE 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 446 LYS Chi-restraints excluded: chain B residue 454 MET 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 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 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 457 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 114 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN B 16 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106922 restraints weight = 15788.730| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.87 r_work: 0.3367 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12188 Z= 0.214 Angle : 0.609 10.639 16517 Z= 0.321 Chirality : 0.045 0.235 1803 Planarity : 0.004 0.059 2131 Dihedral : 7.865 111.051 1888 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.01 % Allowed : 28.04 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1472 helix: 2.73 (0.27), residues: 377 sheet: 0.23 (0.30), residues: 325 loop : -1.46 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 422 HIS 0.010 0.001 HIS C 356 PHE 0.018 0.002 PHE C 468 TYR 0.020 0.002 TYR A 354 ARG 0.007 0.001 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 10) link_NAG-ASN : angle 2.70286 ( 30) link_BETA1-4 : bond 0.00386 ( 3) link_BETA1-4 : angle 0.85874 ( 9) hydrogen bonds : bond 0.06427 ( 449) hydrogen bonds : angle 4.51583 ( 1359) SS BOND : bond 0.00616 ( 18) SS BOND : angle 2.35658 ( 36) covalent geometry : bond 0.00521 (12157) covalent geometry : angle 0.58880 (16442) *********************** 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 414 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 336 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 THR cc_start: 0.8548 (t) cc_final: 0.8336 (t) REVERT: A 468 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6543 (p90) REVERT: B 458 ASP cc_start: 0.7257 (t0) cc_final: 0.7023 (t0) REVERT: C 88 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 126 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.7499 (ptm-80) REVERT: C 457 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7517 (mtp85) REVERT: C 458 ASP cc_start: 0.7958 (t0) cc_final: 0.7420 (t0) REVERT: C 495 GLU cc_start: 0.7475 (tp30) cc_final: 0.7224 (tm-30) REVERT: C 499 ASN cc_start: 0.8325 (m-40) cc_final: 0.7951 (m110) outliers start: 78 outliers final: 58 residues processed: 378 average time/residue: 1.3008 time to fit residues: 530.2084 Evaluate side-chains 394 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU 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 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 8 ILE 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 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 313 GLU 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 454 MET 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 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 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 457 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 Chi-restraints excluded: chain C residue 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN B 16 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107827 restraints weight = 15795.549| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.88 r_work: 0.3378 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12188 Z= 0.163 Angle : 0.582 10.204 16517 Z= 0.307 Chirality : 0.044 0.227 1803 Planarity : 0.004 0.059 2131 Dihedral : 7.762 111.960 1888 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.86 % Allowed : 28.43 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1472 helix: 2.77 (0.27), residues: 377 sheet: 0.24 (0.31), residues: 326 loop : -1.49 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.010 0.001 HIS C 356 PHE 0.014 0.001 PHE C 468 TYR 0.015 0.002 TYR A 354 ARG 0.006 0.000 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 10) link_NAG-ASN : angle 2.64071 ( 30) link_BETA1-4 : bond 0.00385 ( 3) link_BETA1-4 : angle 0.87474 ( 9) hydrogen bonds : bond 0.06114 ( 449) hydrogen bonds : angle 4.46052 ( 1359) SS BOND : bond 0.00566 ( 18) SS BOND : angle 2.12405 ( 36) covalent geometry : bond 0.00388 (12157) covalent geometry : angle 0.56286 (16442) *********************** 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 413 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 337 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 THR cc_start: 0.8532 (t) cc_final: 0.8328 (t) REVERT: A 420 ASP cc_start: 0.7908 (m-30) cc_final: 0.7696 (m-30) REVERT: A 468 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6430 (p90) REVERT: B 247 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8461 (t) REVERT: B 368 LYS cc_start: 0.7849 (mptt) cc_final: 0.7637 (mptt) REVERT: B 458 ASP cc_start: 0.7283 (t0) cc_final: 0.6881 (t0) REVERT: B 495 GLU cc_start: 0.7828 (tp30) cc_final: 0.7428 (tp30) REVERT: C 88 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7449 (tm-30) REVERT: C 457 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7430 (mtp85) REVERT: C 458 ASP cc_start: 0.7949 (t0) cc_final: 0.7413 (t0) outliers start: 76 outliers final: 61 residues processed: 377 average time/residue: 1.2734 time to fit residues: 517.1293 Evaluate side-chains 397 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 59 ASP 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 410 LEU Chi-restraints excluded: chain A residue 448 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 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 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 247 SER 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 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 454 MET Chi-restraints excluded: chain B residue 459 ASN 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 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 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 457 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 Chi-restraints excluded: chain C residue 496 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN B 210 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.120949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107133 restraints weight = 15941.451| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.88 r_work: 0.3368 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12188 Z= 0.200 Angle : 0.609 10.221 16517 Z= 0.321 Chirality : 0.045 0.222 1803 Planarity : 0.004 0.059 2131 Dihedral : 7.759 112.073 1888 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.09 % Allowed : 28.43 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1472 helix: 2.77 (0.27), residues: 376 sheet: 0.30 (0.31), residues: 316 loop : -1.48 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.010 0.001 HIS C 356 PHE 0.016 0.002 PHE C 468 TYR 0.016 0.002 TYR A 354 ARG 0.009 0.001 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 10) link_NAG-ASN : angle 2.65562 ( 30) link_BETA1-4 : bond 0.00367 ( 3) link_BETA1-4 : angle 0.88097 ( 9) hydrogen bonds : bond 0.06290 ( 449) hydrogen bonds : angle 4.46584 ( 1359) SS BOND : bond 0.00613 ( 18) SS BOND : angle 2.38853 ( 36) covalent geometry : bond 0.00487 (12157) covalent geometry : angle 0.58909 (16442) *********************** 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 412 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 333 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5713 (pp20) REVERT: A 420 ASP cc_start: 0.7932 (m-30) cc_final: 0.7710 (m-30) REVERT: A 468 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6491 (p90) REVERT: B 247 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8479 (t) REVERT: B 368 LYS cc_start: 0.7851 (mptt) cc_final: 0.7633 (mptt) REVERT: B 458 ASP cc_start: 0.7326 (t0) cc_final: 0.6922 (t0) REVERT: C 88 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 457 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7502 (mtp85) REVERT: C 458 ASP cc_start: 0.7953 (t0) cc_final: 0.7438 (t0) outliers start: 79 outliers final: 61 residues processed: 372 average time/residue: 1.3096 time to fit residues: 523.7583 Evaluate side-chains 398 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 333 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU 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 240 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 279 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 448 LEU Chi-restraints excluded: chain A residue 454 MET 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 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 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 CYS 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 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 454 MET 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 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 375 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 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 Chi-restraints excluded: chain C residue 496 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 116 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 5 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 499 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108244 restraints weight = 15991.695| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.89 r_work: 0.3386 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12188 Z= 0.140 Angle : 0.576 9.577 16517 Z= 0.301 Chirality : 0.043 0.211 1803 Planarity : 0.004 0.065 2131 Dihedral : 7.586 113.031 1887 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.16 % Allowed : 29.66 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1472 helix: 2.84 (0.27), residues: 376 sheet: 0.36 (0.31), residues: 316 loop : -1.43 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.009 0.001 HIS C 356 PHE 0.013 0.001 PHE C 440 TYR 0.013 0.001 TYR A 354 ARG 0.009 0.001 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 10) link_NAG-ASN : angle 2.53388 ( 30) link_BETA1-4 : bond 0.00356 ( 3) link_BETA1-4 : angle 0.91051 ( 9) hydrogen bonds : bond 0.05816 ( 449) hydrogen bonds : angle 4.36433 ( 1359) SS BOND : bond 0.00501 ( 18) SS BOND : angle 1.94810 ( 36) covalent geometry : bond 0.00325 (12157) covalent geometry : angle 0.55909 (16442) *********************** 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 405 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5703 (pp20) REVERT: A 420 ASP cc_start: 0.7871 (m-30) cc_final: 0.7653 (m-30) REVERT: A 435 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: A 468 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6345 (p90) REVERT: B 349 ASP cc_start: 0.7473 (t0) cc_final: 0.7214 (t0) REVERT: B 368 LYS cc_start: 0.7847 (mptt) cc_final: 0.7630 (mptt) REVERT: B 458 ASP cc_start: 0.7341 (t0) cc_final: 0.6961 (t0) REVERT: C 88 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7482 (tm-30) REVERT: C 295 PHE cc_start: 0.8695 (m-80) cc_final: 0.8388 (m-80) REVERT: C 457 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7392 (mtp85) REVERT: C 458 ASP cc_start: 0.7955 (t0) cc_final: 0.7427 (t0) outliers start: 67 outliers final: 55 residues processed: 368 average time/residue: 1.2880 time to fit residues: 510.0114 Evaluate side-chains 387 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 328 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 110 LEU 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 279 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 435 GLU Chi-restraints excluded: chain A residue 448 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 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 356 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 454 MET 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 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 281 LYS 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 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 457 ARG 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 122 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108206 restraints weight = 15723.622| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.88 r_work: 0.3387 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12188 Z= 0.146 Angle : 0.595 9.443 16517 Z= 0.311 Chirality : 0.043 0.206 1803 Planarity : 0.004 0.064 2131 Dihedral : 7.475 112.965 1885 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.70 % Allowed : 30.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1472 helix: 2.82 (0.27), residues: 376 sheet: 0.28 (0.30), residues: 339 loop : -1.45 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.009 0.001 HIS C 356 PHE 0.012 0.001 PHE C 440 TYR 0.018 0.002 TYR C 492 ARG 0.010 0.001 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 10) link_NAG-ASN : angle 2.50789 ( 30) link_BETA1-4 : bond 0.00351 ( 3) link_BETA1-4 : angle 0.89690 ( 9) hydrogen bonds : bond 0.05829 ( 449) hydrogen bonds : angle 4.34164 ( 1359) SS BOND : bond 0.00497 ( 18) SS BOND : angle 2.17734 ( 36) covalent geometry : bond 0.00341 (12157) covalent geometry : angle 0.57762 (16442) ********************** 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 390 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5696 (pp20) REVERT: A 420 ASP cc_start: 0.7886 (m-30) cc_final: 0.7676 (m-30) REVERT: A 435 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: A 468 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6309 (p90) REVERT: B 349 ASP cc_start: 0.7436 (t0) cc_final: 0.7180 (t0) REVERT: B 368 LYS cc_start: 0.7838 (mptt) cc_final: 0.7620 (mptt) REVERT: B 458 ASP cc_start: 0.7362 (t0) cc_final: 0.6979 (t0) REVERT: C 88 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 126 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.7481 (ptm-80) REVERT: C 457 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7316 (mtp85) REVERT: C 458 ASP cc_start: 0.7953 (t0) cc_final: 0.7411 (t0) outliers start: 61 outliers final: 49 residues processed: 359 average time/residue: 1.3128 time to fit residues: 506.8198 Evaluate side-chains 387 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 334 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 110 LEU 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 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 435 GLU Chi-restraints excluded: chain A residue 448 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 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 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 454 MET 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 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 375 ILE 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 457 ARG 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 101 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 499 ASN B 197 ASN B 210 ASN B 356 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN C 499 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108121 restraints weight = 15782.596| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.88 r_work: 0.3385 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12188 Z= 0.152 Angle : 0.603 9.291 16517 Z= 0.314 Chirality : 0.044 0.201 1803 Planarity : 0.004 0.065 2131 Dihedral : 7.412 113.050 1883 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.31 % Allowed : 30.89 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1472 helix: 2.77 (0.27), residues: 376 sheet: 0.39 (0.30), residues: 329 loop : -1.45 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.010 0.001 HIS C 356 PHE 0.012 0.001 PHE C 468 TYR 0.023 0.002 TYR B 449 ARG 0.009 0.001 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 10) link_NAG-ASN : angle 2.48568 ( 30) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 0.89961 ( 9) hydrogen bonds : bond 0.05872 ( 449) hydrogen bonds : angle 4.33775 ( 1359) SS BOND : bond 0.00502 ( 18) SS BOND : angle 2.30112 ( 36) covalent geometry : bond 0.00357 (12157) covalent geometry : angle 0.58469 (16442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11882.06 seconds wall clock time: 202 minutes 48.18 seconds (12168.18 seconds total)