Starting phenix.real_space_refine on Wed May 14 15:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xg1_38311/05_2025/8xg1_38311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xg1_38311/05_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_38311/05_2025/8xg1_38311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xg1_38311/05_2025/8xg1_38311.map" model { file = "/net/cci-nas-00/data/ceres_data/8xg1_38311/05_2025/8xg1_38311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xg1_38311/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.95, per 1000 atoms: 0.58 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: 3.33 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: 2.40 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: 5.06 Time building geometry restraints manager: 3.67 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.800 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:16.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.430 ------------------------------------------------------------------------------- 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 0.062 12243 Z= 0.187 Angle : 0.953 41.725 16601 Z= 0.404 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01090 ( 8) link_NAG-ASN : angle 2.51117 ( 24) link_BETA1-4 : bond 0.03966 ( 3) link_BETA1-4 : angle 8.30519 ( 9) hydrogen bonds : bond 0.12444 ( 467) hydrogen bonds : angle 6.13701 ( 1392) SS BOND : bond 0.00326 ( 18) SS BOND : angle 1.81554 ( 36) glycosidic custom : bond 0.06086 ( 3) glycosidic custom : angle 7.78764 ( 9) link_BETA1-3 : bond 0.04901 ( 3) link_BETA1-3 : angle 16.77731 ( 9) covalent geometry : bond 0.00377 (12208) covalent geometry : angle 0.81984 (16514) *********************** 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 : 1.373 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: 1.2645 time to fit residues: 569.7216 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 : 1.332 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.8980 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: 1.0982 ------------------------------------------------------------------------------- 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 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112818 restraints weight = 15659.816| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.75 r_work: 0.3443 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12243 Z= 0.193 Angle : 0.601 9.969 16601 Z= 0.307 Chirality : 0.044 0.159 1819 Planarity : 0.004 0.044 2111 Dihedral : 9.743 90.646 2096 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.51 % Allowed : 27.66 % Favored : 67.83 % 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: -0.35 (0.21), residues: 1452 helix: 2.02 (0.27), residues: 375 sheet: 0.45 (0.29), residues: 303 loop : -1.77 (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 0.029 0.002 PHE C 440 TYR 0.016 0.002 TYR A 12 ARG 0.010 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 8) link_NAG-ASN : angle 3.02390 ( 24) link_BETA1-4 : bond 0.00433 ( 3) link_BETA1-4 : angle 2.55002 ( 9) hydrogen bonds : bond 0.05527 ( 467) hydrogen bonds : angle 4.95367 ( 1392) SS BOND : bond 0.00336 ( 18) SS BOND : angle 1.19051 ( 36) glycosidic custom : bond 0.00405 ( 3) glycosidic custom : angle 1.81450 ( 9) link_BETA1-3 : bond 0.00251 ( 3) link_BETA1-3 : angle 1.52103 ( 9) covalent geometry : bond 0.00458 (12208) covalent geometry : angle 0.58339 (16514) *********************** 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 440 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 382 time to evaluate : 1.389 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: 0.8232 (tmm-80) cc_final: 0.7912 (ttp80) REVERT: A 190 GLU cc_start: 0.7970 (pt0) cc_final: 0.7768 (pt0) REVERT: A 272 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: A 389 MET cc_start: 0.7345 (mmm) cc_final: 0.7019 (tmm) REVERT: A 458 ASP cc_start: 0.7762 (t0) cc_final: 0.7221 (t0) REVERT: A 491 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8328 (ttmm) REVERT: A 500 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7810 (ttm170) REVERT: B 91 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7935 (ttp80) REVERT: B 376 ASP cc_start: 0.8075 (m-30) cc_final: 0.7828 (m-30) REVERT: B 494 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6976 (mm-30) REVERT: C 216 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: C 272 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8056 (mm-30) outliers start: 58 outliers final: 34 residues processed: 409 average time/residue: 1.3405 time to fit residues: 588.2102 Evaluate side-chains 396 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 358 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG 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 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 272 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 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: 0.7980 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 chunk 49 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 356 HIS B 380 ASN C 224 ASN C 360 GLN ** 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 = 0.3725 r_free = 0.3725 target = 0.125361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113267 restraints weight = 15878.999| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.78 r_work: 0.3449 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12243 Z= 0.145 Angle : 0.558 9.475 16601 Z= 0.287 Chirality : 0.042 0.140 1819 Planarity : 0.004 0.040 2111 Dihedral : 8.371 92.264 2046 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.27 % Allowed : 28.36 % 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: -0.24 (0.21), residues: 1452 helix: 2.19 (0.27), residues: 375 sheet: 0.44 (0.29), residues: 303 loop : -1.71 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.007 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00925 ( 8) link_NAG-ASN : angle 2.85590 ( 24) link_BETA1-4 : bond 0.00043 ( 3) link_BETA1-4 : angle 2.47731 ( 9) hydrogen bonds : bond 0.05135 ( 467) hydrogen bonds : angle 4.79099 ( 1392) SS BOND : bond 0.00277 ( 18) SS BOND : angle 1.22446 ( 36) glycosidic custom : bond 0.00211 ( 3) glycosidic custom : angle 0.67000 ( 9) link_BETA1-3 : bond 0.00271 ( 3) link_BETA1-3 : angle 1.20309 ( 9) covalent geometry : bond 0.00338 (12208) covalent geometry : angle 0.54140 (16514) *********************** 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 423 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 368 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8221 (tmm-80) cc_final: 0.7900 (ttp80) REVERT: A 190 GLU cc_start: 0.7971 (pt0) cc_final: 0.7764 (pt0) REVERT: A 272 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 389 MET cc_start: 0.7318 (mmm) cc_final: 0.7061 (tmm) REVERT: A 458 ASP cc_start: 0.7888 (t0) cc_final: 0.7317 (t0) REVERT: A 500 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7865 (ttm170) REVERT: B 91 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7912 (ttp80) REVERT: B 360 GLN cc_start: 0.8517 (pt0) cc_final: 0.8246 (pt0) REVERT: C 20 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7974 (mmtt) REVERT: C 26 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7678 (mt-10) REVERT: C 91 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7676 (ttt180) outliers start: 55 outliers final: 31 residues processed: 396 average time/residue: 1.3580 time to fit residues: 576.0526 Evaluate side-chains 389 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 357 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 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 209 LEU Chi-restraints excluded: chain B residue 211 LYS 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 478 CYS 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 209 LEU Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 131 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- 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 C 224 ASN C 360 GLN ** 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 = 0.3714 r_free = 0.3714 target = 0.124646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112781 restraints weight = 15645.767| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.73 r_work: 0.3439 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12243 Z= 0.196 Angle : 0.579 9.178 16601 Z= 0.299 Chirality : 0.044 0.153 1819 Planarity : 0.004 0.042 2111 Dihedral : 7.885 92.799 2037 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.58 % Allowed : 28.13 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1452 helix: 2.16 (0.27), residues: 375 sheet: 0.43 (0.29), residues: 303 loop : -1.73 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 65 HIS 0.012 0.001 HIS A 13 PHE 0.029 0.002 PHE C 440 TYR 0.017 0.002 TYR A 12 ARG 0.007 0.001 ARG B 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00940 ( 8) link_NAG-ASN : angle 2.84229 ( 24) link_BETA1-4 : bond 0.00231 ( 3) link_BETA1-4 : angle 2.38814 ( 9) hydrogen bonds : bond 0.05390 ( 467) hydrogen bonds : angle 4.78478 ( 1392) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.36204 ( 36) glycosidic custom : bond 0.00250 ( 3) glycosidic custom : angle 0.61662 ( 9) link_BETA1-3 : bond 0.00175 ( 3) link_BETA1-3 : angle 1.08689 ( 9) covalent geometry : bond 0.00467 (12208) covalent geometry : angle 0.56313 (16514) *********************** 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 437 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 378 time to evaluate : 1.429 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: 0.8203 (tmm-80) cc_final: 0.7951 (ttp80) REVERT: A 190 GLU cc_start: 0.7988 (pt0) cc_final: 0.7778 (pt0) REVERT: A 272 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: A 387 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: A 389 MET cc_start: 0.7310 (mmm) cc_final: 0.7098 (tmm) REVERT: A 458 ASP cc_start: 0.7966 (t0) cc_final: 0.7375 (t0) REVERT: A 500 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7811 (ttm170) REVERT: C 20 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7985 (mmtt) REVERT: C 26 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 91 ARG cc_start: 0.7975 (ttt180) cc_final: 0.7636 (ttt180) outliers start: 59 outliers final: 40 residues processed: 405 average time/residue: 1.3777 time to fit residues: 597.3848 Evaluate side-chains 416 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 374 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 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 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 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 336 ILE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 94 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 13 HIS 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 409 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111124 restraints weight = 15933.201| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.75 r_work: 0.3420 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12243 Z= 0.254 Angle : 0.618 9.529 16601 Z= 0.320 Chirality : 0.046 0.175 1819 Planarity : 0.005 0.051 2111 Dihedral : 7.730 92.132 2033 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.74 % Allowed : 28.44 % Favored : 66.82 % 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: -0.35 (0.21), residues: 1452 helix: 2.06 (0.27), residues: 375 sheet: 0.40 (0.29), residues: 303 loop : -1.78 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 65 HIS 0.012 0.002 HIS A 13 PHE 0.034 0.002 PHE C 440 TYR 0.020 0.002 TYR A 12 ARG 0.011 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 8) link_NAG-ASN : angle 3.05864 ( 24) link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 2.50046 ( 9) hydrogen bonds : bond 0.05768 ( 467) hydrogen bonds : angle 4.84555 ( 1392) SS BOND : bond 0.00412 ( 18) SS BOND : angle 1.72269 ( 36) glycosidic custom : bond 0.00404 ( 3) glycosidic custom : angle 0.77426 ( 9) link_BETA1-3 : bond 0.00130 ( 3) link_BETA1-3 : angle 1.09474 ( 9) covalent geometry : bond 0.00610 (12208) covalent geometry : angle 0.59936 (16514) *********************** 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 438 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 377 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: A 372 GLN cc_start: 0.7613 (tp40) cc_final: 0.7168 (tp-100) REVERT: A 376 ASP cc_start: 0.7927 (m-30) cc_final: 0.7711 (m-30) REVERT: A 387 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: A 389 MET cc_start: 0.7410 (mmm) cc_final: 0.7203 (tmm) REVERT: A 457 ARG cc_start: 0.8272 (ttm170) cc_final: 0.8068 (mtm180) REVERT: A 458 ASP cc_start: 0.8059 (t0) cc_final: 0.7311 (t0) REVERT: A 500 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7748 (ttm170) REVERT: C 20 LYS cc_start: 0.8291 (mmtt) cc_final: 0.7938 (mmtt) REVERT: C 26 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7753 (mt-10) REVERT: C 216 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: C 313 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: C 409 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8477 (t0) REVERT: C 476 ASN cc_start: 0.7952 (m-40) cc_final: 0.7751 (m110) REVERT: C 497 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7454 (mtpt) outliers start: 61 outliers final: 38 residues processed: 404 average time/residue: 1.3772 time to fit residues: 595.9054 Evaluate side-chains 406 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 362 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN 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 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 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 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 389 MET 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 216 GLU Chi-restraints excluded: chain C residue 313 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 409 ASN Chi-restraints excluded: chain C residue 478 CYS 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: 0.9990 chunk 94 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 13 HIS B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN C 224 ASN C 360 GLN C 380 ASN C 409 ASN C 455 GLN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111915 restraints weight = 16167.602| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.76 r_work: 0.3433 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 0.037 12243 Z= 0.171 Angle : 0.581 5.768 16601 Z= 0.303 Chirality : 0.044 0.271 1819 Planarity : 0.004 0.059 2111 Dihedral : 7.673 92.348 2033 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.90 % Allowed : 28.52 % 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: -0.32 (0.22), residues: 1452 helix: 2.12 (0.27), residues: 375 sheet: 0.36 (0.30), residues: 288 loop : -1.71 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 81 HIS 0.013 0.001 HIS A 13 PHE 0.027 0.002 PHE C 440 TYR 0.015 0.001 TYR A 12 ARG 0.011 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 8) link_NAG-ASN : angle 1.88686 ( 24) link_BETA1-4 : bond 0.00158 ( 3) link_BETA1-4 : angle 2.30399 ( 9) hydrogen bonds : bond 0.05347 ( 467) hydrogen bonds : angle 4.76355 ( 1392) SS BOND : bond 0.00328 ( 18) SS BOND : angle 1.48117 ( 36) glycosidic custom : bond 0.00358 ( 3) glycosidic custom : angle 0.58573 ( 9) link_BETA1-3 : bond 0.00190 ( 3) link_BETA1-3 : angle 0.88798 ( 9) covalent geometry : bond 0.00405 (12208) covalent geometry : angle 0.57136 (16514) *********************** 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 432 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 369 time to evaluate : 1.372 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 20 LYS cc_start: 0.8147 (mttt) cc_final: 0.7920 (tttt) REVERT: A 91 ARG cc_start: 0.8230 (tmm-80) cc_final: 0.7948 (ttp80) REVERT: A 272 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: A 387 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: A 457 ARG cc_start: 0.8254 (ttm170) cc_final: 0.8049 (mtm180) REVERT: A 458 ASP cc_start: 0.8056 (t0) cc_final: 0.7311 (t0) REVERT: A 500 ARG cc_start: 0.8282 (ttm170) cc_final: 0.7730 (ttm170) REVERT: B 314 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8603 (ttmt) REVERT: C 26 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 91 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7766 (ttt180) outliers start: 63 outliers final: 41 residues processed: 398 average time/residue: 1.3391 time to fit residues: 571.5660 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 : 1.230 ------------------------------------------------------------------------------- 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 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 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 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 389 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 436 ARG 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 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 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 403 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER 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: 1.9990 chunk 33 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 380 ASN C 409 ASN 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 = 0.3709 r_free = 0.3709 target = 0.124032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112252 restraints weight = 15988.635| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.75 r_work: 0.3440 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12243 Z= 0.161 Angle : 0.577 8.099 16601 Z= 0.301 Chirality : 0.043 0.223 1819 Planarity : 0.004 0.051 2111 Dihedral : 7.546 92.341 2032 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.27 % Allowed : 29.60 % 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: -0.30 (0.22), residues: 1452 helix: 2.14 (0.27), residues: 375 sheet: 0.36 (0.30), residues: 288 loop : -1.69 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.013 0.001 HIS A 13 PHE 0.025 0.002 PHE C 440 TYR 0.014 0.001 TYR A 12 ARG 0.011 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 8) link_NAG-ASN : angle 1.64924 ( 24) link_BETA1-4 : bond 0.00130 ( 3) link_BETA1-4 : angle 2.22906 ( 9) hydrogen bonds : bond 0.05207 ( 467) hydrogen bonds : angle 4.72022 ( 1392) SS BOND : bond 0.00333 ( 18) SS BOND : angle 1.47304 ( 36) glycosidic custom : bond 0.00138 ( 3) glycosidic custom : angle 0.63216 ( 9) link_BETA1-3 : bond 0.00190 ( 3) link_BETA1-3 : angle 0.80542 ( 9) covalent geometry : bond 0.00378 (12208) covalent geometry : angle 0.56853 (16514) *********************** 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 423 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 368 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: A 20 LYS cc_start: 0.8140 (mttt) cc_final: 0.7884 (mttt) REVERT: A 91 ARG cc_start: 0.8205 (tmm-80) cc_final: 0.7931 (ttp80) REVERT: A 272 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: A 376 ASP cc_start: 0.7925 (m-30) cc_final: 0.7693 (m-30) REVERT: A 387 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6874 (mt-10) REVERT: A 457 ARG cc_start: 0.8242 (ttm170) cc_final: 0.8041 (mtm180) REVERT: A 458 ASP cc_start: 0.8036 (t0) cc_final: 0.7261 (t0) REVERT: A 486 THR cc_start: 0.8844 (p) cc_final: 0.8633 (p) REVERT: A 500 ARG cc_start: 0.8281 (ttm170) cc_final: 0.7705 (ttm170) REVERT: C 20 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7977 (mmtt) REVERT: C 26 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7693 (mt-10) REVERT: C 91 ARG cc_start: 0.8084 (ttt180) cc_final: 0.7782 (ttt180) REVERT: C 313 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: C 497 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7440 (mtpt) outliers start: 55 outliers final: 40 residues processed: 393 average time/residue: 1.3515 time to fit residues: 569.9016 Evaluate side-chains 409 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 365 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 MET 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 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 313 GLU 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 403 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 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: 2.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 126 optimal weight: 0.0470 chunk 136 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- 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 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN 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 = 0.3699 r_free = 0.3699 target = 0.123419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111467 restraints weight = 16075.242| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.77 r_work: 0.3425 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12243 Z= 0.234 Angle : 0.631 12.038 16601 Z= 0.328 Chirality : 0.046 0.212 1819 Planarity : 0.004 0.053 2111 Dihedral : 7.514 92.573 2028 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.58 % Allowed : 29.45 % Favored : 65.97 % 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: -0.34 (0.22), residues: 1452 helix: 2.03 (0.27), residues: 375 sheet: 0.44 (0.29), residues: 303 loop : -1.75 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 81 HIS 0.013 0.001 HIS A 13 PHE 0.032 0.002 PHE C 440 TYR 0.019 0.002 TYR A 12 ARG 0.012 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 8) link_NAG-ASN : angle 1.66810 ( 24) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 2.38534 ( 9) hydrogen bonds : bond 0.05608 ( 467) hydrogen bonds : angle 4.79508 ( 1392) SS BOND : bond 0.00399 ( 18) SS BOND : angle 1.78953 ( 36) glycosidic custom : bond 0.00298 ( 3) glycosidic custom : angle 0.67841 ( 9) link_BETA1-3 : bond 0.00129 ( 3) link_BETA1-3 : angle 0.89977 ( 9) covalent geometry : bond 0.00562 (12208) covalent geometry : angle 0.62047 (16514) *********************** 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 431 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 372 time to evaluate : 1.249 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 20 LYS cc_start: 0.8191 (mttt) cc_final: 0.7920 (mttt) REVERT: A 91 ARG cc_start: 0.8196 (tmm-80) cc_final: 0.7921 (ttp80) REVERT: A 272 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: A 387 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: A 458 ASP cc_start: 0.8058 (t0) cc_final: 0.7223 (t0) REVERT: A 486 THR cc_start: 0.8843 (p) cc_final: 0.8630 (p) REVERT: A 500 ARG cc_start: 0.8316 (ttm170) cc_final: 0.7765 (ttm170) REVERT: B 77 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7228 (mtm-85) REVERT: C 20 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7962 (mmtt) REVERT: C 26 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7722 (mt-10) REVERT: C 91 ARG cc_start: 0.8087 (ttt180) cc_final: 0.7781 (ttt180) REVERT: C 497 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7477 (mtpt) outliers start: 59 outliers final: 40 residues processed: 395 average time/residue: 1.3661 time to fit residues: 576.9340 Evaluate side-chains 408 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 365 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 347 MET 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 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 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 316 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 MET 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 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 448 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 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: 0.8980 chunk 138 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.0040 chunk 141 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 380 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 = 0.3720 r_free = 0.3720 target = 0.124897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112932 restraints weight = 15949.729| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.78 r_work: 0.3448 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12243 Z= 0.130 Angle : 0.579 14.213 16601 Z= 0.300 Chirality : 0.042 0.199 1819 Planarity : 0.004 0.044 2111 Dihedral : 7.303 92.802 2028 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.73 % Allowed : 30.38 % Favored : 65.89 % 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: -0.23 (0.22), residues: 1452 helix: 2.17 (0.27), residues: 375 sheet: 0.40 (0.30), residues: 288 loop : -1.63 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.013 0.001 HIS A 13 PHE 0.020 0.001 PHE C 440 TYR 0.011 0.001 TYR A 12 ARG 0.008 0.001 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 1.39330 ( 24) link_BETA1-4 : bond 0.00061 ( 3) link_BETA1-4 : angle 2.10859 ( 9) hydrogen bonds : bond 0.04951 ( 467) hydrogen bonds : angle 4.67654 ( 1392) SS BOND : bond 0.00301 ( 18) SS BOND : angle 1.51262 ( 36) glycosidic custom : bond 0.00129 ( 3) glycosidic custom : angle 0.55309 ( 9) link_BETA1-3 : bond 0.00218 ( 3) link_BETA1-3 : angle 0.66541 ( 9) covalent geometry : bond 0.00296 (12208) covalent geometry : angle 0.57097 (16514) *********************** 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 406 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 358 time to evaluate : 1.371 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 20 LYS cc_start: 0.8161 (mttt) cc_final: 0.7875 (mttt) REVERT: A 91 ARG cc_start: 0.8193 (tmm-80) cc_final: 0.7917 (ttp80) REVERT: A 272 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: A 387 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: A 424 TYR cc_start: 0.7968 (t80) cc_final: 0.7767 (t80) REVERT: A 458 ASP cc_start: 0.7994 (t0) cc_final: 0.7242 (t0) REVERT: A 486 THR cc_start: 0.8825 (p) cc_final: 0.8600 (p) REVERT: A 500 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7697 (ttm170) REVERT: B 188 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 26 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 91 ARG cc_start: 0.8091 (ttt180) cc_final: 0.7782 (ttt180) REVERT: C 380 ASN cc_start: 0.8048 (t0) cc_final: 0.7653 (t160) REVERT: C 497 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7416 (mtpt) outliers start: 48 outliers final: 34 residues processed: 383 average time/residue: 1.3745 time to fit residues: 563.9883 Evaluate side-chains 383 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 346 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER 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 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 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 71 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 211 LYS 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 373 LYS Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 459 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113079 restraints weight = 15801.028| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.75 r_work: 0.3453 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12243 Z= 0.132 Angle : 0.594 18.126 16601 Z= 0.306 Chirality : 0.043 0.165 1819 Planarity : 0.004 0.043 2111 Dihedral : 7.255 92.803 2028 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.50 % Allowed : 30.61 % Favored : 65.89 % 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: 2.22 (0.27), residues: 375 sheet: 0.40 (0.30), residues: 288 loop : -1.62 (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 0.021 0.001 PHE C 440 TYR 0.011 0.001 TYR A 12 ARG 0.008 0.001 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 8) link_NAG-ASN : angle 1.29029 ( 24) link_BETA1-4 : bond 0.00054 ( 3) link_BETA1-4 : angle 2.05310 ( 9) hydrogen bonds : bond 0.04883 ( 467) hydrogen bonds : angle 4.65477 ( 1392) SS BOND : bond 0.00291 ( 18) SS BOND : angle 1.51714 ( 36) glycosidic custom : bond 0.00055 ( 3) glycosidic custom : angle 0.57123 ( 9) link_BETA1-3 : bond 0.00209 ( 3) link_BETA1-3 : angle 0.66107 ( 9) covalent geometry : bond 0.00303 (12208) covalent geometry : angle 0.58704 (16514) ********************** 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 398 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 353 time to evaluate : 1.355 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 20 LYS cc_start: 0.8172 (mttt) cc_final: 0.7904 (mttt) REVERT: A 91 ARG cc_start: 0.8181 (tmm-80) cc_final: 0.7916 (ttp80) REVERT: A 272 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: A 387 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: A 424 TYR cc_start: 0.8001 (t80) cc_final: 0.7652 (t80) REVERT: A 458 ASP cc_start: 0.7976 (t0) cc_final: 0.7218 (t0) REVERT: A 486 THR cc_start: 0.8816 (p) cc_final: 0.8588 (p) REVERT: A 500 ARG cc_start: 0.8288 (ttm170) cc_final: 0.7704 (ttm170) REVERT: C 26 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7697 (mt-10) REVERT: C 91 ARG cc_start: 0.8051 (ttt180) cc_final: 0.7757 (ttt180) REVERT: C 497 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7424 (mtpt) outliers start: 45 outliers final: 33 residues processed: 375 average time/residue: 1.3281 time to fit residues: 534.4979 Evaluate side-chains 382 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 346 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER 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 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 378 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 B residue 71 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 211 LYS 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 373 LYS Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS 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 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: 2.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 409 ASN C 455 GLN ** C 459 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 = 0.3670 r_free = 0.3670 target = 0.121251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109395 restraints weight = 16017.502| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.75 r_work: 0.3396 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.078 12243 Z= 0.417 Angle : 0.776 20.068 16601 Z= 0.398 Chirality : 0.053 0.214 1819 Planarity : 0.005 0.051 2111 Dihedral : 7.804 93.959 2028 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.73 % Allowed : 31.00 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1452 helix: 1.69 (0.27), residues: 375 sheet: 0.35 (0.29), residues: 303 loop : -1.84 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 81 HIS 0.014 0.002 HIS A 13 PHE 0.043 0.003 PHE C 440 TYR 0.028 0.003 TYR A 12 ARG 0.010 0.001 ARG B 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 8) link_NAG-ASN : angle 3.53445 ( 24) link_BETA1-4 : bond 0.00732 ( 3) link_BETA1-4 : angle 2.75662 ( 9) hydrogen bonds : bond 0.06617 ( 467) hydrogen bonds : angle 5.01540 ( 1392) SS BOND : bond 0.00585 ( 18) SS BOND : angle 2.09539 ( 36) glycosidic custom : bond 0.00686 ( 3) glycosidic custom : angle 0.90960 ( 9) link_BETA1-3 : bond 0.00058 ( 3) link_BETA1-3 : angle 1.16245 ( 9) covalent geometry : bond 0.01006 (12208) covalent geometry : angle 0.75608 (16514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11712.23 seconds wall clock time: 201 minutes 44.42 seconds (12104.42 seconds total)