Starting phenix.real_space_refine on Sat Jan 18 07:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xg1_38311/01_2025/8xg1_38311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xg1_38311/01_2025/8xg1_38311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xg1_38311/01_2025/8xg1_38311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xg1_38311/01_2025/8xg1_38311.map" model { file = "/net/cci-nas-00/data/ceres_data/8xg1_38311/01_2025/8xg1_38311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xg1_38311/01_2025/8xg1_38311.cif" } resolution = 2.53 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= 0.026 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 75 5.16 5 C 7495 2.51 5 N 2009 2.21 5 O 2362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11941 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 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: 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: "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: 7.90, per 1000 atoms: 0.66 Number of scatterers: 11941 At special positions: 0 Unit cell: (87.55, 87.55, 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 75 16.00 O 2362 8.00 N 2009 7.00 C 7495 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 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=2.03 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 BETA1-3 " GAL D 1 " - " NAG D 2 " " GAL E 1 " - " NAG E 2 " " GAL F 1 " - " NAG F 2 " BETA1-4 " NAG D 2 " - " GAL D 3 " " NAG E 2 " - " GAL E 3 " " NAG F 2 " - " GAL F 3 " BETA2-6 " GAL D 3 " - " SIA D 4 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL E 3 " - " SIA E 4 " " GAL F 3 " - " SIA F 4 " NAG-ASN " NAG A 601 " - " ASN A 16 " " NAG A 602 " - " ASN A 28 " " NAG A 603 " - " ASN A 169 " " NAG B 601 " - " ASN B 16 " " NAG B 602 " - " ASN B 28 " " NAG B 603 " - " ASN B 169 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 169 " Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 32 sheets defined 27.1% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.915A pdb=" N ASP A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 387 Processing helix chain 'A' and resid 404 through 457 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.806A pdb=" N ASN A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.723A pdb=" N LEU B 75 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 3.736A 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 110 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.688A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 368 through 387 Processing helix chain 'B' and resid 405 through 457 removed outlier: 3.586A pdb=" N GLU B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.718A pdb=" N SER B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 3.610A 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 102 through 111 Processing helix chain 'C' and resid 187 through 196 removed outlier: 3.546A pdb=" N LEU C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 389 removed outlier: 3.910A pdb=" N MET C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.780A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 445 " --> pdb=" O HIS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 488 through 502 removed outlier: 3.862A pdb=" N TYR C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU C 494 " --> pdb=" O PRO C 490 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 366 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.483A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.414A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS A 115 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG A 263 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 113 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.945A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.551A pdb=" N ALA A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N LYS A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.527A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.651A pdb=" N GLY B 361 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.404A pdb=" N GLU B 19 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB5, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 49 removed outlier: 7.763A pdb=" N LEU B 46 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR B 280 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS B 48 " --> pdb=" O THR B 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.658A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.607A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N HIS B 115 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG B 263 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 113 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.607A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.333A pdb=" N ALA B 138 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N LYS B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 364 removed outlier: 3.584A pdb=" N GLY C 361 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AC6, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC7, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AC8, first strand: chain 'C' and resid 48 through 49 removed outlier: 5.903A pdb=" N LYS C 48 " --> pdb=" O THR C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.763A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.752A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS C 115 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG C 263 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 113 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.752A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 8.005A 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: 4.386A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (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 287 through 288 499 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 3.69 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: 3873 1.35 - 1.47: 2965 1.47 - 1.59: 5256 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 12208 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C6 GAL E 3 " pdb=" O6 GAL E 3 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 12203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.06: 16498 6.06 - 12.12: 6 12.12 - 18.19: 5 18.19 - 24.25: 4 24.25 - 30.31: 1 Bond angle restraints: 16514 Sorted by residual: angle pdb=" C2 GAL F 1 " pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 107.49 137.80 -30.31 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C5 GAL D 3 " pdb=" C6 GAL D 3 " pdb=" O6 GAL D 3 " ideal model delta sigma weight residual 109.08 133.08 -24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sigma weight residual 107.29 130.01 -22.72 3.00e+00 1.11e-01 5.74e+01 angle pdb=" C5 NAG E 2 " pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 111.70 89.43 22.27 3.00e+00 1.11e-01 5.51e+01 angle pdb=" C5 GAL F 3 " pdb=" C6 GAL F 3 " pdb=" O6 GAL F 3 " ideal model delta sigma weight residual 109.08 130.86 -21.78 3.00e+00 1.11e-01 5.27e+01 ... (remaining 16509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 6575 22.40 - 44.80: 806 44.80 - 67.21: 213 67.21 - 89.61: 27 89.61 - 112.01: 8 Dihedral angle restraints: 7629 sinusoidal: 3414 harmonic: 4215 Sorted by residual: dihedral pdb=" CB CYS A 47 " pdb=" SG CYS A 47 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual -86.00 -8.76 -77.24 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 72 " pdb=" CB CYS A 72 " ideal model delta sinusoidal sigma weight residual -86.00 -137.37 51.37 1 1.00e+01 1.00e-02 3.61e+01 dihedral pdb=" CB CYS C 60 " pdb=" SG CYS C 60 " pdb=" SG CYS C 72 " pdb=" CB CYS C 72 " ideal model delta sinusoidal sigma weight residual 93.00 134.38 -41.38 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 7626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 1815 0.214 - 0.427: 1 0.427 - 0.641: 1 0.641 - 0.855: 1 0.855 - 1.068: 1 Chirality restraints: 1819 Sorted by residual: chirality pdb=" C2 SIA E 4 " pdb=" O6 GAL E 3 " pdb=" C1 SIA E 4 " pdb=" O6 SIA E 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.70 0.20 2.00e-02 2.50e+03 9.91e+01 chirality pdb=" C2 SIA F 4 " pdb=" O6 GAL F 3 " pdb=" C1 SIA F 4 " pdb=" O6 SIA F 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.65 0.15 2.00e-02 2.50e+03 5.91e+01 chirality pdb=" C2 SIA D 4 " pdb=" O6 GAL D 3 " pdb=" C1 SIA D 4 " pdb=" O6 SIA D 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.65 0.15 2.00e-02 2.50e+03 5.58e+01 ... (remaining 1816 not shown) Planarity restraints: 2119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 458 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C ASP A 458 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP A 458 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A 459 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 306 " 0.028 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 307 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 489 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 490 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " -0.022 5.00e-02 4.00e+02 ... (remaining 2116 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1047 2.74 - 3.28: 10559 3.28 - 3.82: 19229 3.82 - 4.36: 23223 4.36 - 4.90: 40736 Nonbonded interactions: 94794 Sorted by model distance: nonbonded pdb=" O SER B 443 " pdb=" ND2 ASN B 447 " model vdw 2.199 3.120 nonbonded pdb=" OE1 GLU C 39 " pdb=" OG1 THR C 291 " model vdw 2.208 3.040 nonbonded pdb=" O SER C 142 " pdb=" OG SER C 142 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASN A 484 " pdb=" OG1 THR A 486 " model vdw 2.231 3.040 nonbonded pdb=" O6 SIA F 4 " pdb=" O8 SIA F 4 " model vdw 2.232 3.040 ... (remaining 94789 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 502 or resid 601 through 602)) selection = (chain 'B' and (resid 6 through 502 or resid 601 through 602)) selection = chain 'C' } 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.860 Find NCS groups from input model: 0.560 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: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12208 Z= 0.243 Angle : 0.820 30.310 16514 Z= 0.369 Chirality : 0.056 1.068 1819 Planarity : 0.004 0.046 2111 Dihedral : 19.938 112.008 4881 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.51 % Allowed : 31.24 % Favored : 64.26 % 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: -0.38 (0.22), residues: 1452 helix: 2.03 (0.28), residues: 366 sheet: 0.45 (0.29), residues: 303 loop : -1.77 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 422 HIS 0.013 0.001 HIS A 13 PHE 0.021 0.001 PHE C 440 TYR 0.012 0.001 TYR A 12 ARG 0.011 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 376 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.7301 (tmm) cc_final: 0.6881 (tmm) REVERT: A 457 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7986 (mtm180) REVERT: B 151 MET cc_start: 0.8995 (mmp) cc_final: 0.7946 (mmt) outliers start: 58 outliers final: 47 residues processed: 419 average time/residue: 1.3907 time to fit residues: 625.3341 Evaluate side-chains 396 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 349 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 488 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 196 GLN B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN C 13 HIS C 224 ASN C 360 GLN C 380 ASN C 409 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.124324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112373 restraints weight = 15661.682| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.75 r_work: 0.3436 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12208 Z= 0.349 Angle : 0.601 8.135 16514 Z= 0.312 Chirality : 0.045 0.167 1819 Planarity : 0.005 0.044 2111 Dihedral : 9.769 90.894 2096 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.66 % Allowed : 27.66 % Favored : 67.68 % 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: -0.40 (0.21), residues: 1452 helix: 1.96 (0.27), residues: 375 sheet: 0.43 (0.29), residues: 303 loop : -1.80 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.012 0.001 HIS A 13 PHE 0.031 0.002 PHE C 440 TYR 0.018 0.002 TYR A 12 ARG 0.010 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 382 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8244 (tmm-80) cc_final: 0.7925 (ttp80) REVERT: A 272 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 389 MET cc_start: 0.7360 (mmm) cc_final: 0.7034 (tmm) REVERT: A 458 ASP cc_start: 0.7766 (t0) cc_final: 0.7248 (t0) REVERT: A 491 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8314 (ttmm) REVERT: A 500 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7824 (ttm170) REVERT: B 91 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7947 (ttp80) REVERT: B 376 ASP cc_start: 0.8087 (m-30) cc_final: 0.7864 (m-30) REVERT: B 494 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: C 216 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: C 409 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8448 (t0) REVERT: C 457 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7259 (ttp80) outliers start: 60 outliers final: 35 residues processed: 411 average time/residue: 1.4250 time to fit residues: 627.5353 Evaluate side-chains 399 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 359 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 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 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 356 HIS B 380 ASN C 224 ASN C 360 GLN C 409 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112401 restraints weight = 15904.730| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.76 r_work: 0.3435 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12208 Z= 0.327 Angle : 0.577 6.216 16514 Z= 0.303 Chirality : 0.044 0.165 1819 Planarity : 0.004 0.044 2111 Dihedral : 8.784 92.540 2047 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.05 % Allowed : 27.27 % Favored : 67.68 % 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: -0.37 (0.21), residues: 1452 helix: 2.03 (0.27), residues: 375 sheet: 0.41 (0.29), residues: 303 loop : -1.78 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.012 0.001 HIS A 13 PHE 0.030 0.002 PHE C 440 TYR 0.017 0.002 TYR A 12 ARG 0.007 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 372 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8202 (tmm-80) cc_final: 0.7949 (ttp80) REVERT: A 272 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: A 389 MET cc_start: 0.7372 (mmm) cc_final: 0.7107 (tmm) REVERT: A 458 ASP cc_start: 0.7912 (t0) cc_final: 0.7380 (t0) REVERT: A 500 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7919 (ttm170) REVERT: B 91 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7908 (ttp80) REVERT: C 20 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7977 (mmtt) REVERT: C 457 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7271 (ttp80) outliers start: 65 outliers final: 42 residues processed: 402 average time/residue: 1.4557 time to fit residues: 625.8589 Evaluate side-chains 404 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 360 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 131 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN A 299 HIS B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN C 224 ASN C 360 GLN C 455 GLN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112856 restraints weight = 15645.112| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.73 r_work: 0.3444 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12208 Z= 0.268 Angle : 0.557 5.682 16514 Z= 0.292 Chirality : 0.043 0.148 1819 Planarity : 0.004 0.043 2111 Dihedral : 8.313 93.256 2038 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.51 % Allowed : 28.05 % Favored : 67.44 % 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: -0.30 (0.21), residues: 1452 helix: 2.12 (0.27), residues: 375 sheet: 0.42 (0.29), residues: 303 loop : -1.75 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 81 HIS 0.012 0.001 HIS A 13 PHE 0.027 0.002 PHE C 440 TYR 0.015 0.001 TYR A 12 ARG 0.006 0.001 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 369 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: A 387 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: A 389 MET cc_start: 0.7329 (mmm) cc_final: 0.7113 (tmm) REVERT: A 458 ASP cc_start: 0.7965 (t0) cc_final: 0.7200 (t0) REVERT: A 500 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7740 (ttm170) REVERT: B 376 ASP cc_start: 0.8100 (m-30) cc_final: 0.7852 (m-30) REVERT: C 20 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7971 (mmtt) REVERT: C 409 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8346 (t0) outliers start: 58 outliers final: 36 residues processed: 396 average time/residue: 1.4084 time to fit residues: 597.8166 Evaluate side-chains 390 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 351 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 94 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 356 HIS B 380 ASN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110573 restraints weight = 15759.874| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.72 r_work: 0.3412 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 12208 Z= 0.566 Angle : 0.665 6.430 16514 Z= 0.349 Chirality : 0.050 0.243 1819 Planarity : 0.005 0.048 2111 Dihedral : 8.268 92.946 2033 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.21 % Allowed : 27.43 % Favored : 67.37 % 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: -0.51 (0.21), residues: 1452 helix: 1.87 (0.27), residues: 375 sheet: 0.35 (0.29), residues: 303 loop : -1.86 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 65 HIS 0.012 0.002 HIS A 13 PHE 0.040 0.003 PHE C 440 TYR 0.025 0.002 TYR A 12 ARG 0.010 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 364 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8250 (tmm-80) cc_final: 0.7982 (ttp80) REVERT: A 272 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: A 387 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: A 389 MET cc_start: 0.7431 (mmm) cc_final: 0.7212 (tmm) REVERT: A 424 TYR cc_start: 0.8172 (t80) cc_final: 0.7956 (t80) REVERT: A 458 ASP cc_start: 0.8011 (t0) cc_final: 0.7317 (t0) REVERT: A 500 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7752 (ttm170) REVERT: C 20 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7948 (mmtt) REVERT: C 457 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7272 (ttp80) REVERT: C 497 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7523 (mtpt) outliers start: 67 outliers final: 46 residues processed: 393 average time/residue: 1.4122 time to fit residues: 595.7852 Evaluate side-chains 409 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112115 restraints weight = 16055.960| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.77 r_work: 0.3436 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12208 Z= 0.237 Angle : 0.561 5.970 16514 Z= 0.296 Chirality : 0.043 0.224 1819 Planarity : 0.004 0.044 2111 Dihedral : 7.910 92.652 2033 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.89 % Allowed : 29.22 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1452 helix: 2.12 (0.27), residues: 375 sheet: 0.41 (0.29), residues: 303 loop : -1.76 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 81 HIS 0.012 0.001 HIS A 13 PHE 0.024 0.001 PHE C 440 TYR 0.013 0.001 TYR A 12 ARG 0.010 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 378 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8213 (tmm-80) cc_final: 0.7937 (ttp80) REVERT: A 272 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: A 376 ASP cc_start: 0.7902 (m-30) cc_final: 0.7675 (m-30) REVERT: A 387 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: A 389 MET cc_start: 0.7399 (mmm) cc_final: 0.7196 (tmm) REVERT: A 424 TYR cc_start: 0.8101 (t80) cc_final: 0.7898 (t80) REVERT: A 458 ASP cc_start: 0.8026 (t0) cc_final: 0.7326 (t0) REVERT: A 486 THR cc_start: 0.8848 (p) cc_final: 0.8621 (p) REVERT: A 500 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7731 (ttm170) REVERT: B 77 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7196 (mtm-85) REVERT: C 20 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7943 (mmtt) REVERT: C 380 ASN cc_start: 0.7993 (t0) cc_final: 0.7626 (t160) REVERT: C 497 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7449 (mtpt) outliers start: 50 outliers final: 35 residues processed: 402 average time/residue: 1.4158 time to fit residues: 609.6301 Evaluate side-chains 387 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 349 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 356 HIS B 380 ASN C 191 GLN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112843 restraints weight = 15932.101| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.77 r_work: 0.3443 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12208 Z= 0.191 Angle : 0.545 7.088 16514 Z= 0.287 Chirality : 0.042 0.211 1819 Planarity : 0.004 0.045 2111 Dihedral : 7.623 92.308 2030 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.57 % Allowed : 29.84 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1452 helix: 2.25 (0.27), residues: 375 sheet: 0.45 (0.29), residues: 303 loop : -1.69 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 81 HIS 0.013 0.001 HIS A 13 PHE 0.019 0.001 PHE C 440 TYR 0.011 0.001 TYR B 92 ARG 0.013 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 357 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8196 (tmm-80) cc_final: 0.7913 (ttp80) REVERT: A 272 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: A 387 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: A 458 ASP cc_start: 0.8013 (t0) cc_final: 0.7284 (t0) REVERT: A 486 THR cc_start: 0.8838 (p) cc_final: 0.8619 (p) REVERT: A 500 ARG cc_start: 0.8283 (ttm170) cc_final: 0.7706 (ttm170) REVERT: B 71 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 92 TYR cc_start: 0.7165 (m-80) cc_final: 0.6960 (m-10) REVERT: C 380 ASN cc_start: 0.7991 (t0) cc_final: 0.7622 (t160) REVERT: C 497 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7420 (mtpt) outliers start: 46 outliers final: 30 residues processed: 379 average time/residue: 1.4366 time to fit residues: 582.5306 Evaluate side-chains 375 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 112 optimal weight: 3.9990 chunk 126 optimal weight: 0.0060 chunk 136 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN B 447 ASN C 191 GLN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN C 459 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113985 restraints weight = 16035.451| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.76 r_work: 0.3460 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12208 Z= 0.162 Angle : 0.538 8.800 16514 Z= 0.282 Chirality : 0.042 0.194 1819 Planarity : 0.004 0.038 2111 Dihedral : 7.352 92.548 2028 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.20 % Allowed : 29.06 % Favored : 66.74 % 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: -0.07 (0.22), residues: 1452 helix: 2.33 (0.27), residues: 375 sheet: 0.51 (0.30), residues: 288 loop : -1.55 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.013 0.001 HIS A 13 PHE 0.017 0.001 PHE C 440 TYR 0.015 0.001 TYR B 92 ARG 0.007 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 347 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8186 (tmm-80) cc_final: 0.7927 (ttp80) REVERT: A 387 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: A 458 ASP cc_start: 0.7995 (t0) cc_final: 0.7199 (t0) REVERT: A 486 THR cc_start: 0.8807 (p) cc_final: 0.8580 (p) REVERT: A 500 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7690 (ttm170) REVERT: B 71 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7610 (mt-10) REVERT: B 92 TYR cc_start: 0.7094 (m-80) cc_final: 0.6772 (m-10) REVERT: C 380 ASN cc_start: 0.7992 (t0) cc_final: 0.7605 (t160) REVERT: C 469 GLU cc_start: 0.7659 (tt0) cc_final: 0.7400 (tp30) REVERT: C 497 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7413 (mtpt) outliers start: 54 outliers final: 33 residues processed: 374 average time/residue: 1.5310 time to fit residues: 616.0868 Evaluate side-chains 382 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 347 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 356 HIS B 380 ASN B 447 ASN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.124124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112287 restraints weight = 16049.681| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.75 r_work: 0.3439 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12208 Z= 0.298 Angle : 0.596 16.386 16514 Z= 0.310 Chirality : 0.044 0.167 1819 Planarity : 0.004 0.038 2111 Dihedral : 7.423 92.661 2028 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.89 % Allowed : 29.99 % Favored : 66.12 % 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: -0.21 (0.22), residues: 1452 helix: 2.23 (0.27), residues: 375 sheet: 0.41 (0.30), residues: 288 loop : -1.64 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.014 0.001 HIS A 13 PHE 0.025 0.002 PHE C 440 TYR 0.016 0.002 TYR A 12 ARG 0.009 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8181 (tmm-80) cc_final: 0.7921 (ttp80) REVERT: A 272 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: A 387 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: A 458 ASP cc_start: 0.8027 (t0) cc_final: 0.7235 (t0) REVERT: A 486 THR cc_start: 0.8823 (p) cc_final: 0.8610 (p) REVERT: A 500 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7739 (ttm170) REVERT: B 77 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7238 (mtm-85) REVERT: C 91 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7777 (ttt180) REVERT: C 380 ASN cc_start: 0.8017 (t0) cc_final: 0.7635 (t160) REVERT: C 389 MET cc_start: 0.7327 (mmt) cc_final: 0.6950 (mmp) REVERT: C 469 GLU cc_start: 0.7661 (tt0) cc_final: 0.7409 (tp30) REVERT: C 497 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7435 (mtpt) outliers start: 50 outliers final: 38 residues processed: 381 average time/residue: 1.4427 time to fit residues: 588.7189 Evaluate side-chains 396 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 355 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN A 299 HIS B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN B 447 ASN C 191 GLN C 224 ASN C 360 GLN C 459 ASN C 476 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113256 restraints weight = 15780.991| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.76 r_work: 0.3448 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12208 Z= 0.207 Angle : 0.582 17.920 16514 Z= 0.301 Chirality : 0.042 0.153 1819 Planarity : 0.004 0.040 2111 Dihedral : 7.384 92.815 2028 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.65 % Allowed : 30.61 % Favored : 65.73 % 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: -0.16 (0.22), residues: 1452 helix: 2.26 (0.27), residues: 375 sheet: 0.44 (0.30), residues: 288 loop : -1.59 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 422 HIS 0.014 0.001 HIS A 13 PHE 0.020 0.001 PHE C 440 TYR 0.015 0.001 TYR B 92 ARG 0.009 0.001 ARG B 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 359 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7898 (ttp80) REVERT: A 387 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: A 458 ASP cc_start: 0.7986 (t0) cc_final: 0.7235 (t0) REVERT: A 486 THR cc_start: 0.8809 (p) cc_final: 0.8588 (p) REVERT: A 500 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7725 (ttm170) REVERT: C 91 ARG cc_start: 0.8100 (ttt180) cc_final: 0.7805 (ttt180) REVERT: C 389 MET cc_start: 0.7267 (mmt) cc_final: 0.6866 (mmp) REVERT: C 469 GLU cc_start: 0.7664 (tt0) cc_final: 0.7404 (tp30) REVERT: C 497 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7410 (mtpt) outliers start: 47 outliers final: 36 residues processed: 385 average time/residue: 1.3866 time to fit residues: 572.7256 Evaluate side-chains 383 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 356 HIS B 380 ASN B 447 ASN C 191 GLN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN C 455 GLN C 459 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111043 restraints weight = 16014.943| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.74 r_work: 0.3422 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12208 Z= 0.426 Angle : 0.667 18.740 16514 Z= 0.346 Chirality : 0.047 0.185 1819 Planarity : 0.005 0.046 2111 Dihedral : 7.616 92.997 2028 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.65 % Allowed : 30.85 % Favored : 65.50 % 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: -0.32 (0.21), residues: 1452 helix: 2.01 (0.27), residues: 375 sheet: 0.43 (0.29), residues: 303 loop : -1.71 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 65 HIS 0.014 0.002 HIS A 13 PHE 0.033 0.002 PHE C 440 TYR 0.019 0.002 TYR A 12 ARG 0.011 0.001 ARG B 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11542.61 seconds wall clock time: 204 minutes 5.81 seconds (12245.81 seconds total)