Starting phenix.real_space_refine on Wed Jul 30 04:30:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xr9_38599/07_2025/8xr9_38599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xr9_38599/07_2025/8xr9_38599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xr9_38599/07_2025/8xr9_38599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xr9_38599/07_2025/8xr9_38599.map" model { file = "/net/cci-nas-00/data/ceres_data/8xr9_38599/07_2025/8xr9_38599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xr9_38599/07_2025/8xr9_38599.cif" } resolution = 2.6 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 72 5.16 5 C 7497 2.51 5 N 2023 2.21 5 O 2397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11989 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3905 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "A" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3877 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 19, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3882 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} 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: "C" 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 Time building chain proxies: 7.08, per 1000 atoms: 0.59 Number of scatterers: 11989 At special positions: 0 Unit cell: (88.4, 88.4, 149.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2397 8.00 N 2023 7.00 C 7497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 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 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 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 169 " " NAG A 602 " - " ASN A 484 " " NAG A 603 " - " ASN A 290 " " NAG A 604 " - " ASN A 16 " " NAG A 605 " - " ASN A 28 " " NAG B 601 " - " ASN B 169 " " NAG B 602 " - " ASN B 484 " " NAG B 603 " - " ASN B 28 " " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 28 " " NAG C 603 " - " ASN C 290 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 27.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 69 through 76 removed outlier: 4.166A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 367 through 388 Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.591A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.755A pdb=" N ASN C 501 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.572A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 368 through 388 Processing helix chain 'A' and resid 404 through 457 removed outlier: 3.747A pdb=" N ASP A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 488 through 501 removed outlier: 3.942A pdb=" N TYR A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.931A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 76 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 387 Processing helix chain 'B' and resid 404 through 457 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 493 through 501 removed outlier: 3.808A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 362 through 364 removed outlier: 3.516A pdb=" N GLY C 11 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN C 7 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 49 removed outlier: 5.885A pdb=" N LEU C 46 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.712A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.540A pdb=" N PHE C 232 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS C 115 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG C 263 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C 113 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.540A pdb=" N PHE C 232 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.578A pdb=" N ALA C 138 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N GLU C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 362 through 364 removed outlier: 3.515A pdb=" N GLY A 363 " --> pdb=" O HIS A 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.184A pdb=" N GLU A 19 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AB5, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.725A pdb=" N LEU A 46 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.586A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.478A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.924A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.645A pdb=" N ALA A 138 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 10.063A pdb=" N GLU A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.197A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 362 through 364 removed outlier: 4.354A pdb=" N GLN B 7 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AC6, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AC7, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AC8, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.351A pdb=" N LEU B 46 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N CYS B 278 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.513A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.403A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS B 115 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG B 263 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 113 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 98 through 100 removed outlier: 7.816A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.705A pdb=" N ALA B 138 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N GLU B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'B' and resid 282 through 283 removed outlier: 4.358A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3910 1.34 - 1.46: 2622 1.46 - 1.58: 5605 1.58 - 1.69: 3 1.69 - 1.81: 108 Bond restraints: 12248 Sorted by residual: 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 3.06e+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 3.05e+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 3.04e+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 2.71e+00 bond pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 1.406 1.373 0.033 2.00e-02 2.50e+03 2.66e+00 ... (remaining 12243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.17: 16562 8.17 - 16.34: 4 16.34 - 24.51: 5 24.51 - 32.68: 2 32.68 - 40.86: 2 Bond angle restraints: 16575 Sorted by residual: angle pdb=" C2 GAL E 1 " pdb=" C3 GAL E 1 " pdb=" O3 GAL E 1 " ideal model delta sigma weight residual 107.49 148.35 -40.86 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C2 GAL F 1 " pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 107.49 142.22 -34.73 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C4 GAL E 1 " pdb=" C3 GAL E 1 " pdb=" O3 GAL E 1 " ideal model delta sigma weight residual 113.26 81.43 31.83 3.00e+00 1.11e-01 1.13e+02 angle pdb=" C5 GAL D 3 " pdb=" C6 GAL D 3 " pdb=" O6 GAL D 3 " ideal model delta sigma weight residual 109.08 136.66 -27.58 3.00e+00 1.11e-01 8.45e+01 angle pdb=" C4 GAL F 1 " pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 113.26 90.19 23.07 3.00e+00 1.11e-01 5.92e+01 ... (remaining 16570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 6540 21.69 - 43.39: 884 43.39 - 65.08: 215 65.08 - 86.77: 29 86.77 - 108.46: 5 Dihedral angle restraints: 7673 sinusoidal: 3463 harmonic: 4210 Sorted by residual: 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 -86.00 -119.89 33.89 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" CA THR A 291 " pdb=" C THR A 291 " pdb=" N THR A 292 " pdb=" CA THR A 292 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS C 282 " pdb=" SG CYS C 282 " pdb=" SG CYS C 306 " pdb=" CB CYS C 306 " ideal model delta sinusoidal sigma weight residual 93.00 125.50 -32.50 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 7670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 1841 0.178 - 0.355: 5 0.355 - 0.533: 0 0.533 - 0.710: 0 0.710 - 0.888: 2 Chirality restraints: 1848 Sorted by residual: 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 -2.70 0.20 2.00e-02 2.50e+03 1.01e+02 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 -2.66 0.16 2.00e-02 2.50e+03 6.77e+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 -2.64 0.14 2.00e-02 2.50e+03 4.82e+01 ... (remaining 1845 not shown) Planarity restraints: 2131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 420 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" CG ASP A 420 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP A 420 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 420 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 293 " -0.035 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 294 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 294 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 294 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 69 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A 70 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.029 5.00e-02 4.00e+02 ... (remaining 2128 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 311 2.69 - 3.24: 10398 3.24 - 3.80: 18070 3.80 - 4.35: 24085 4.35 - 4.90: 40962 Nonbonded interactions: 93826 Sorted by model distance: nonbonded pdb=" OD1 ASP C 475 " pdb=" N ASP C 476 " model vdw 2.141 3.120 nonbonded pdb=" OD1 ASP C 450 " pdb=" NH1 ARG C 453 " model vdw 2.224 3.120 nonbonded pdb=" N GLU B 477 " pdb=" OE1 GLU B 477 " model vdw 2.241 3.120 nonbonded pdb=" N GLN A 360 " pdb=" OE1 GLN A 360 " model vdw 2.296 3.120 nonbonded pdb=" NH2 ARG A 27 " pdb=" OG SER B 384 " model vdw 2.299 3.120 ... (remaining 93821 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 501 or resid 601 through 603)) selection = (chain 'B' and (resid 6 through 327 or resid 336 through 501 or resid 601 throug \ h 603)) selection = (chain 'C' and (resid 6 through 327 or resid 336 through 501 or resid 601 throug \ h 603)) } 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: 1.370 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.550 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 0.063 12286 Z= 0.190 Angle : 1.041 42.197 16671 Z= 0.414 Chirality : 0.053 0.888 1848 Planarity : 0.004 0.054 2120 Dihedral : 19.541 108.464 4929 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.02 % Allowed : 31.58 % Favored : 64.40 % 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: 1457 helix: 2.15 (0.27), residues: 364 sheet: -0.36 (0.32), residues: 305 loop : -1.42 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 422 HIS 0.008 0.001 HIS C 356 PHE 0.009 0.001 PHE B 148 TYR 0.018 0.001 TYR C 492 ARG 0.011 0.001 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 11) link_NAG-ASN : angle 1.45970 ( 33) link_BETA1-4 : bond 0.03926 ( 3) link_BETA1-4 : angle 7.60257 ( 9) hydrogen bonds : bond 0.18749 ( 464) hydrogen bonds : angle 6.70596 ( 1392) SS BOND : bond 0.00212 ( 18) SS BOND : angle 0.99030 ( 36) glycosidic custom : bond 0.06200 ( 3) glycosidic custom : angle 7.34672 ( 9) link_BETA1-3 : bond 0.04878 ( 3) link_BETA1-3 : angle 19.83767 ( 9) covalent geometry : bond 0.00390 (12248) covalent geometry : angle 0.89899 (16575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 345 time to evaluate : 1.335 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: B 302 THR cc_start: 0.8142 (p) cc_final: 0.7929 (t) REVERT: B 431 LEU cc_start: 0.8677 (mp) cc_final: 0.8432 (mt) outliers start: 52 outliers final: 49 residues processed: 387 average time/residue: 1.1741 time to fit residues: 492.9435 Evaluate side-chains 387 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 338 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 210 ASN C 356 HIS C 409 ASN C 465 ASN A 13 HIS A 175 GLN A 186 ASN A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 299 HIS B 345 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109347 restraints weight = 16205.773| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.94 r_work: 0.3353 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12286 Z= 0.198 Angle : 0.601 7.896 16671 Z= 0.308 Chirality : 0.044 0.172 1848 Planarity : 0.004 0.054 2120 Dihedral : 10.565 94.248 2174 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.48 % Allowed : 28.03 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1457 helix: 2.23 (0.27), residues: 377 sheet: 0.03 (0.31), residues: 297 loop : -1.48 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 81 HIS 0.008 0.001 HIS C 356 PHE 0.013 0.002 PHE B 100 TYR 0.019 0.002 TYR B 424 ARG 0.009 0.001 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 11) link_NAG-ASN : angle 1.50450 ( 33) link_BETA1-4 : bond 0.00676 ( 3) link_BETA1-4 : angle 2.76731 ( 9) hydrogen bonds : bond 0.05675 ( 464) hydrogen bonds : angle 4.95835 ( 1392) SS BOND : bond 0.00215 ( 18) SS BOND : angle 0.73873 ( 36) glycosidic custom : bond 0.00092 ( 3) glycosidic custom : angle 1.43200 ( 9) link_BETA1-3 : bond 0.00026 ( 3) link_BETA1-3 : angle 3.19600 ( 9) covalent geometry : bond 0.00464 (12248) covalent geometry : angle 0.58914 (16575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 362 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: C 157 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8641 (tttm) REVERT: C 493 GLU cc_start: 0.6994 (tp30) cc_final: 0.6649 (tp30) REVERT: C 494 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: C 495 GLU cc_start: 0.7437 (tp30) cc_final: 0.7173 (tp30) REVERT: A 48 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8027 (mttp) REVERT: A 388 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8489 (mmtm) REVERT: A 497 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: B 157 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8724 (tttp) REVERT: B 174 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: B 336 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7459 (mt) REVERT: B 354 TYR cc_start: 0.8375 (m-80) cc_final: 0.8092 (m-80) REVERT: B 431 LEU cc_start: 0.8667 (mp) cc_final: 0.8444 (mt) REVERT: B 476 ASP cc_start: 0.7717 (m-30) cc_final: 0.7382 (m-30) outliers start: 71 outliers final: 40 residues processed: 399 average time/residue: 1.3215 time to fit residues: 568.6423 Evaluate side-chains 394 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 346 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 12 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 ASN C 356 HIS C 499 ASN A 13 HIS A 175 GLN A 210 ASN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 299 HIS B 345 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109956 restraints weight = 16485.718| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.95 r_work: 0.3370 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12286 Z= 0.145 Angle : 0.535 8.127 16671 Z= 0.277 Chirality : 0.042 0.174 1848 Planarity : 0.004 0.054 2120 Dihedral : 9.035 99.332 2132 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.48 % Allowed : 29.03 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1457 helix: 2.37 (0.27), residues: 378 sheet: 0.21 (0.31), residues: 300 loop : -1.46 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 PHE 0.009 0.001 PHE A 148 TYR 0.015 0.001 TYR C 492 ARG 0.009 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 11) link_NAG-ASN : angle 1.53445 ( 33) link_BETA1-4 : bond 0.00151 ( 3) link_BETA1-4 : angle 2.35444 ( 9) hydrogen bonds : bond 0.05092 ( 464) hydrogen bonds : angle 4.59939 ( 1392) SS BOND : bond 0.00203 ( 18) SS BOND : angle 0.56672 ( 36) glycosidic custom : bond 0.00223 ( 3) glycosidic custom : angle 0.81316 ( 9) link_BETA1-3 : bond 0.00171 ( 3) link_BETA1-3 : angle 2.13675 ( 9) covalent geometry : bond 0.00334 (12248) covalent geometry : angle 0.52579 (16575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 348 time to evaluate : 1.358 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: C 26 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: C 74 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8243 (ptp90) REVERT: C 136 SER cc_start: 0.8411 (p) cc_final: 0.7932 (t) REVERT: C 137 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8059 (mtt90) REVERT: C 157 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8655 (tttm) REVERT: C 190 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8062 (mt-10) REVERT: C 493 GLU cc_start: 0.7010 (tp30) cc_final: 0.6712 (tp30) REVERT: C 495 GLU cc_start: 0.7421 (tp30) cc_final: 0.7181 (tp30) REVERT: A 48 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8001 (mttp) REVERT: A 131 THR cc_start: 0.8930 (m) cc_final: 0.8584 (t) REVERT: A 388 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8443 (mmtm) REVERT: A 403 LEU cc_start: 0.8760 (mm) cc_final: 0.8554 (mp) REVERT: B 157 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8729 (tttp) REVERT: B 336 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7507 (mt) REVERT: B 354 TYR cc_start: 0.8363 (m-80) cc_final: 0.8062 (m-80) REVERT: B 431 LEU cc_start: 0.8591 (mp) cc_final: 0.8385 (mt) REVERT: B 476 ASP cc_start: 0.7722 (m-30) cc_final: 0.7360 (m-30) outliers start: 58 outliers final: 39 residues processed: 378 average time/residue: 1.2793 time to fit residues: 521.1492 Evaluate side-chains 391 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 345 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 210 ASN C 356 HIS C 480 ASN A 13 HIS A 210 ASN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 299 HIS B 345 GLN B 455 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109557 restraints weight = 16124.198| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.93 r_work: 0.3364 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12286 Z= 0.171 Angle : 0.544 8.951 16671 Z= 0.281 Chirality : 0.043 0.191 1848 Planarity : 0.004 0.054 2120 Dihedral : 8.307 100.015 2114 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.48 % Allowed : 28.65 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.21), residues: 1457 helix: 2.40 (0.27), residues: 378 sheet: 0.17 (0.30), residues: 307 loop : -1.45 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 PHE 0.011 0.002 PHE B 148 TYR 0.021 0.002 TYR B 424 ARG 0.010 0.001 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 11) link_NAG-ASN : angle 1.61445 ( 33) link_BETA1-4 : bond 0.00126 ( 3) link_BETA1-4 : angle 2.13672 ( 9) hydrogen bonds : bond 0.05106 ( 464) hydrogen bonds : angle 4.49211 ( 1392) SS BOND : bond 0.00258 ( 18) SS BOND : angle 0.58598 ( 36) glycosidic custom : bond 0.00324 ( 3) glycosidic custom : angle 0.84480 ( 9) link_BETA1-3 : bond 0.00080 ( 3) link_BETA1-3 : angle 1.73688 ( 9) covalent geometry : bond 0.00403 (12248) covalent geometry : angle 0.53541 (16575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 349 time to evaluate : 1.347 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: C 26 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: C 136 SER cc_start: 0.8442 (p) cc_final: 0.7942 (t) REVERT: C 137 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8043 (mtt90) REVERT: C 157 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8649 (tttm) REVERT: C 190 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8056 (mt-10) REVERT: C 392 GLN cc_start: 0.5213 (OUTLIER) cc_final: 0.4985 (mt0) REVERT: C 493 GLU cc_start: 0.7065 (tp30) cc_final: 0.6842 (tp30) REVERT: C 495 GLU cc_start: 0.7433 (tp30) cc_final: 0.7202 (tp30) REVERT: A 48 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8012 (mttp) REVERT: A 388 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8499 (mmtm) REVERT: A 403 LEU cc_start: 0.8744 (mm) cc_final: 0.8540 (mp) REVERT: B 74 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8321 (ptt90) REVERT: B 151 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.7762 (mmt) REVERT: B 157 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8695 (tttp) REVERT: B 336 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7549 (mt) REVERT: B 354 TYR cc_start: 0.8382 (m-80) cc_final: 0.8095 (m-80) REVERT: B 431 LEU cc_start: 0.8596 (mp) cc_final: 0.8375 (mt) REVERT: B 476 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7415 (m-30) outliers start: 71 outliers final: 45 residues processed: 386 average time/residue: 1.2618 time to fit residues: 526.3402 Evaluate side-chains 402 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 347 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 20 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 ASN C 356 HIS C 480 ASN C 499 ASN A 13 HIS A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 299 HIS B 345 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.121998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109432 restraints weight = 16282.405| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.94 r_work: 0.3354 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12286 Z= 0.175 Angle : 0.550 9.400 16671 Z= 0.284 Chirality : 0.043 0.205 1848 Planarity : 0.004 0.054 2120 Dihedral : 7.977 100.039 2114 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.33 % Allowed : 28.96 % Favored : 65.71 % 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: -0.05 (0.21), residues: 1457 helix: 2.37 (0.27), residues: 378 sheet: 0.21 (0.30), residues: 307 loop : -1.46 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 127 HIS 0.012 0.001 HIS C 356 PHE 0.012 0.002 PHE B 148 TYR 0.016 0.002 TYR C 492 ARG 0.010 0.000 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 11) link_NAG-ASN : angle 1.65433 ( 33) link_BETA1-4 : bond 0.00149 ( 3) link_BETA1-4 : angle 2.08176 ( 9) hydrogen bonds : bond 0.05091 ( 464) hydrogen bonds : angle 4.44941 ( 1392) SS BOND : bond 0.00206 ( 18) SS BOND : angle 0.88497 ( 36) glycosidic custom : bond 0.00352 ( 3) glycosidic custom : angle 0.89105 ( 9) link_BETA1-3 : bond 0.00014 ( 3) link_BETA1-3 : angle 1.50793 ( 9) covalent geometry : bond 0.00415 (12248) covalent geometry : angle 0.54143 (16575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 355 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: C 137 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8377 (mtt90) REVERT: C 157 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8630 (tttm) REVERT: C 190 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8085 (mt-10) REVERT: C 392 GLN cc_start: 0.5155 (OUTLIER) cc_final: 0.4934 (mt0) REVERT: C 402 ASN cc_start: 0.8480 (p0) cc_final: 0.8214 (p0) REVERT: C 435 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: C 493 GLU cc_start: 0.7083 (tp30) cc_final: 0.6860 (tp30) REVERT: C 495 GLU cc_start: 0.7402 (tp30) cc_final: 0.7184 (tp30) REVERT: A 7 GLN cc_start: 0.8250 (mt0) cc_final: 0.7944 (mt0) REVERT: A 48 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8006 (mttp) REVERT: A 131 THR cc_start: 0.8932 (m) cc_final: 0.8594 (t) REVERT: A 403 LEU cc_start: 0.8751 (mm) cc_final: 0.8549 (mp) REVERT: B 74 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8357 (ptt90) REVERT: B 157 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8690 (tttp) REVERT: B 336 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7599 (mt) REVERT: B 354 TYR cc_start: 0.8385 (m-80) cc_final: 0.8044 (m-80) REVERT: B 360 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.6678 (mp10) REVERT: B 389 MET cc_start: 0.7948 (tpp) cc_final: 0.7612 (mmm) REVERT: B 431 LEU cc_start: 0.8594 (mp) cc_final: 0.8382 (mt) REVERT: B 476 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7310 (m-30) outliers start: 69 outliers final: 42 residues processed: 391 average time/residue: 1.2870 time to fit residues: 542.9917 Evaluate side-chains 402 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 349 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 104 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 356 HIS C 480 ASN C 499 ASN A 13 HIS A 210 ASN A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 299 HIS B 345 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.122447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109941 restraints weight = 16417.366| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.95 r_work: 0.3369 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12286 Z= 0.150 Angle : 0.543 9.530 16671 Z= 0.280 Chirality : 0.043 0.211 1848 Planarity : 0.004 0.054 2120 Dihedral : 7.711 99.935 2110 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.79 % Allowed : 29.03 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.22), residues: 1457 helix: 2.45 (0.27), residues: 378 sheet: 0.27 (0.30), residues: 307 loop : -1.45 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 127 HIS 0.012 0.001 HIS C 356 PHE 0.010 0.001 PHE B 148 TYR 0.024 0.002 TYR B 424 ARG 0.010 0.000 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 11) link_NAG-ASN : angle 1.63376 ( 33) link_BETA1-4 : bond 0.00137 ( 3) link_BETA1-4 : angle 1.97479 ( 9) hydrogen bonds : bond 0.04903 ( 464) hydrogen bonds : angle 4.38244 ( 1392) SS BOND : bond 0.00201 ( 18) SS BOND : angle 0.94471 ( 36) glycosidic custom : bond 0.00184 ( 3) glycosidic custom : angle 0.84330 ( 9) link_BETA1-3 : bond 0.00075 ( 3) link_BETA1-3 : angle 1.30581 ( 9) covalent geometry : bond 0.00353 (12248) covalent geometry : angle 0.53422 (16575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 347 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: C 137 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8144 (mtt90) REVERT: C 157 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (tttm) REVERT: C 190 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8050 (mt-10) REVERT: C 321 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8729 (mt) REVERT: C 392 GLN cc_start: 0.5169 (OUTLIER) cc_final: 0.4952 (mt0) REVERT: C 435 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: C 465 ASN cc_start: 0.8556 (p0) cc_final: 0.8350 (p0) REVERT: C 495 GLU cc_start: 0.7400 (tp30) cc_final: 0.7174 (tp30) REVERT: A 7 GLN cc_start: 0.8253 (mt0) cc_final: 0.7982 (mt0) REVERT: A 48 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7997 (mttp) REVERT: A 384 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8652 (p) REVERT: A 403 LEU cc_start: 0.8731 (mm) cc_final: 0.8525 (mp) REVERT: B 74 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8368 (ptt90) REVERT: B 157 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8695 (tttp) REVERT: B 354 TYR cc_start: 0.8375 (m-80) cc_final: 0.8079 (m-80) REVERT: B 360 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6658 (mp10) REVERT: B 389 MET cc_start: 0.7886 (tpp) cc_final: 0.7580 (mmm) REVERT: B 431 LEU cc_start: 0.8588 (mp) cc_final: 0.8369 (mt) REVERT: B 476 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7320 (m-30) outliers start: 62 outliers final: 39 residues processed: 379 average time/residue: 1.2626 time to fit residues: 517.2921 Evaluate side-chains 393 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 342 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS C 480 ASN C 499 ASN A 13 HIS A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 345 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.121196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108684 restraints weight = 16444.019| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.95 r_work: 0.3354 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12286 Z= 0.231 Angle : 0.591 9.808 16671 Z= 0.304 Chirality : 0.045 0.231 1848 Planarity : 0.004 0.054 2120 Dihedral : 7.756 99.723 2110 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.10 % Allowed : 28.73 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1457 helix: 2.34 (0.27), residues: 378 sheet: 0.25 (0.30), residues: 307 loop : -1.49 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 65 HIS 0.012 0.001 HIS C 356 PHE 0.015 0.002 PHE B 148 TYR 0.016 0.002 TYR C 492 ARG 0.011 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 11) link_NAG-ASN : angle 1.73155 ( 33) link_BETA1-4 : bond 0.00206 ( 3) link_BETA1-4 : angle 2.09908 ( 9) hydrogen bonds : bond 0.05345 ( 464) hydrogen bonds : angle 4.47789 ( 1392) SS BOND : bond 0.00257 ( 18) SS BOND : angle 0.89342 ( 36) glycosidic custom : bond 0.00427 ( 3) glycosidic custom : angle 0.97752 ( 9) link_BETA1-3 : bond 0.00056 ( 3) link_BETA1-3 : angle 1.47477 ( 9) covalent geometry : bond 0.00553 (12248) covalent geometry : angle 0.58267 (16575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 351 time to evaluate : 1.293 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: C 26 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: C 137 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8410 (mtt90) REVERT: C 157 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8655 (tttm) REVERT: C 190 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8073 (mt-10) REVERT: C 435 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: C 465 ASN cc_start: 0.8566 (p0) cc_final: 0.8318 (p0) REVERT: C 493 GLU cc_start: 0.7118 (tp30) cc_final: 0.6889 (tp30) REVERT: C 495 GLU cc_start: 0.7453 (tp30) cc_final: 0.7228 (tp30) REVERT: A 48 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8004 (mttm) REVERT: A 403 LEU cc_start: 0.8763 (mm) cc_final: 0.8560 (mp) REVERT: B 74 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8421 (ptt90) REVERT: B 157 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8708 (tttp) REVERT: B 347 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7510 (ttm) REVERT: B 354 TYR cc_start: 0.8405 (m-80) cc_final: 0.8047 (m-80) REVERT: B 360 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6642 (mp10) REVERT: B 389 MET cc_start: 0.7848 (tpp) cc_final: 0.7545 (mmm) REVERT: B 431 LEU cc_start: 0.8666 (mp) cc_final: 0.8455 (mt) REVERT: B 476 ASP cc_start: 0.7696 (m-30) cc_final: 0.7270 (m-30) outliers start: 66 outliers final: 44 residues processed: 386 average time/residue: 1.4093 time to fit residues: 585.8465 Evaluate side-chains 400 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 27 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 210 ASN C 356 HIS C 392 GLN C 480 ASN C 499 ASN A 13 HIS A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 345 GLN B 472 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109653 restraints weight = 16423.498| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.95 r_work: 0.3368 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12286 Z= 0.157 Angle : 0.556 10.871 16671 Z= 0.287 Chirality : 0.043 0.221 1848 Planarity : 0.004 0.054 2120 Dihedral : 7.595 99.603 2110 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.48 % Allowed : 29.58 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1457 helix: 2.41 (0.27), residues: 378 sheet: 0.26 (0.30), residues: 309 loop : -1.44 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 127 HIS 0.012 0.001 HIS C 356 PHE 0.010 0.001 PHE B 148 TYR 0.024 0.002 TYR B 424 ARG 0.013 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 11) link_NAG-ASN : angle 1.64236 ( 33) link_BETA1-4 : bond 0.00126 ( 3) link_BETA1-4 : angle 1.96626 ( 9) hydrogen bonds : bond 0.04967 ( 464) hydrogen bonds : angle 4.38240 ( 1392) SS BOND : bond 0.00192 ( 18) SS BOND : angle 0.69906 ( 36) glycosidic custom : bond 0.00173 ( 3) glycosidic custom : angle 0.82744 ( 9) link_BETA1-3 : bond 0.00080 ( 3) link_BETA1-3 : angle 1.19831 ( 9) covalent geometry : bond 0.00370 (12248) covalent geometry : angle 0.54853 (16575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 351 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: C 137 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8400 (mtt90) REVERT: C 157 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8647 (tttm) REVERT: C 190 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8047 (mt-10) REVERT: C 435 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: C 465 ASN cc_start: 0.8544 (p0) cc_final: 0.8276 (p0) REVERT: C 495 GLU cc_start: 0.7437 (tp30) cc_final: 0.7219 (tp30) REVERT: A 7 GLN cc_start: 0.8238 (mt0) cc_final: 0.7971 (mt0) REVERT: A 47 CYS cc_start: 0.7042 (m) cc_final: 0.6782 (m) REVERT: A 48 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8002 (mttp) REVERT: A 131 THR cc_start: 0.8925 (m) cc_final: 0.8577 (t) REVERT: A 384 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 403 LEU cc_start: 0.8746 (mm) cc_final: 0.8534 (mp) REVERT: B 74 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8411 (ptt90) REVERT: B 157 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8694 (tttp) REVERT: B 347 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7463 (ttm) REVERT: B 354 TYR cc_start: 0.8356 (m-80) cc_final: 0.8013 (m-80) REVERT: B 360 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: B 389 MET cc_start: 0.7840 (tpp) cc_final: 0.7581 (mmm) REVERT: B 431 LEU cc_start: 0.8588 (mp) cc_final: 0.8374 (mt) REVERT: B 476 ASP cc_start: 0.7646 (m-30) cc_final: 0.7252 (m-30) outliers start: 58 outliers final: 38 residues processed: 382 average time/residue: 1.3399 time to fit residues: 552.0651 Evaluate side-chains 397 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 349 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.0270 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS C 358 ASN C 499 ASN A 13 HIS A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 345 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109840 restraints weight = 16384.152| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.95 r_work: 0.3372 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12286 Z= 0.149 Angle : 0.559 10.772 16671 Z= 0.289 Chirality : 0.043 0.227 1848 Planarity : 0.004 0.060 2120 Dihedral : 7.531 99.318 2110 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.56 % Allowed : 29.65 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1457 helix: 2.45 (0.27), residues: 378 sheet: 0.27 (0.30), residues: 309 loop : -1.43 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 127 HIS 0.012 0.001 HIS C 356 PHE 0.010 0.001 PHE B 148 TYR 0.016 0.001 TYR C 492 ARG 0.014 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 11) link_NAG-ASN : angle 1.61977 ( 33) link_BETA1-4 : bond 0.00128 ( 3) link_BETA1-4 : angle 1.90175 ( 9) hydrogen bonds : bond 0.04888 ( 464) hydrogen bonds : angle 4.33637 ( 1392) SS BOND : bond 0.00200 ( 18) SS BOND : angle 1.04285 ( 36) glycosidic custom : bond 0.00191 ( 3) glycosidic custom : angle 0.81216 ( 9) link_BETA1-3 : bond 0.00088 ( 3) link_BETA1-3 : angle 1.09259 ( 9) covalent geometry : bond 0.00352 (12248) covalent geometry : angle 0.55088 (16575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 349 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: C 137 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8391 (mtt90) REVERT: C 157 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8652 (tttm) REVERT: C 190 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8021 (mt-10) REVERT: C 405 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7963 (mmp-170) REVERT: C 435 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: C 465 ASN cc_start: 0.8531 (p0) cc_final: 0.8244 (p0) REVERT: C 495 GLU cc_start: 0.7449 (tp30) cc_final: 0.7227 (tp30) REVERT: A 7 GLN cc_start: 0.8207 (mt0) cc_final: 0.7956 (mt0) REVERT: A 48 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8012 (mttp) REVERT: A 131 THR cc_start: 0.8923 (m) cc_final: 0.8579 (t) REVERT: A 354 TYR cc_start: 0.8568 (m-80) cc_final: 0.8259 (m-80) REVERT: A 384 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 388 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8416 (mmtm) REVERT: A 403 LEU cc_start: 0.8740 (mm) cc_final: 0.8532 (mp) REVERT: B 74 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8401 (ptt90) REVERT: B 139 CYS cc_start: 0.7545 (m) cc_final: 0.7024 (m) REVERT: B 157 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8685 (tttp) REVERT: B 347 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7448 (ttm) REVERT: B 354 TYR cc_start: 0.8336 (m-80) cc_final: 0.7996 (m-80) REVERT: B 360 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6608 (mp10) REVERT: B 389 MET cc_start: 0.7821 (tpp) cc_final: 0.7567 (mmm) REVERT: B 431 LEU cc_start: 0.8636 (mp) cc_final: 0.8425 (mt) REVERT: B 433 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: B 476 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7250 (m-30) outliers start: 59 outliers final: 38 residues processed: 377 average time/residue: 1.3336 time to fit residues: 541.8062 Evaluate side-chains 398 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 347 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 61 optimal weight: 0.0970 chunk 127 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.0270 chunk 134 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 356 HIS C 499 ASN A 13 HIS A 210 ASN A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 345 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.110446 restraints weight = 16341.205| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.95 r_work: 0.3379 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12286 Z= 0.130 Angle : 0.546 10.933 16671 Z= 0.283 Chirality : 0.043 0.232 1848 Planarity : 0.004 0.056 2120 Dihedral : 7.354 99.073 2110 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.17 % Allowed : 30.19 % Favored : 65.64 % 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: 0.06 (0.22), residues: 1457 helix: 2.45 (0.27), residues: 378 sheet: 0.37 (0.30), residues: 307 loop : -1.42 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 PHE 0.009 0.001 PHE B 148 TYR 0.024 0.001 TYR B 424 ARG 0.013 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 11) link_NAG-ASN : angle 1.56712 ( 33) link_BETA1-4 : bond 0.00136 ( 3) link_BETA1-4 : angle 1.82004 ( 9) hydrogen bonds : bond 0.04707 ( 464) hydrogen bonds : angle 4.29180 ( 1392) SS BOND : bond 0.00202 ( 18) SS BOND : angle 1.01087 ( 36) glycosidic custom : bond 0.00118 ( 3) glycosidic custom : angle 0.78406 ( 9) link_BETA1-3 : bond 0.00115 ( 3) link_BETA1-3 : angle 0.96187 ( 9) covalent geometry : bond 0.00301 (12248) covalent geometry : angle 0.53885 (16575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 352 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: C 137 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8379 (mtt90) REVERT: C 157 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8657 (tttm) REVERT: C 190 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8083 (mt-10) REVERT: C 432 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6795 (mtt) REVERT: C 435 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: C 465 ASN cc_start: 0.8532 (p0) cc_final: 0.8229 (p0) REVERT: C 495 GLU cc_start: 0.7449 (tp30) cc_final: 0.7226 (tp30) REVERT: A 7 GLN cc_start: 0.8163 (mt0) cc_final: 0.7901 (mt0) REVERT: A 48 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7968 (mttp) REVERT: A 131 THR cc_start: 0.8917 (m) cc_final: 0.8566 (t) REVERT: A 354 TYR cc_start: 0.8553 (m-80) cc_final: 0.8308 (m-80) REVERT: A 384 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8667 (p) REVERT: A 388 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8402 (mmtm) REVERT: A 403 LEU cc_start: 0.8717 (mm) cc_final: 0.8503 (mp) REVERT: B 74 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8406 (ptt90) REVERT: B 139 CYS cc_start: 0.7580 (m) cc_final: 0.7059 (m) REVERT: B 157 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8667 (tttp) REVERT: B 347 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7419 (ttm) REVERT: B 354 TYR cc_start: 0.8292 (m-80) cc_final: 0.8022 (m-80) REVERT: B 360 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6592 (mp10) REVERT: B 389 MET cc_start: 0.7809 (tpp) cc_final: 0.7567 (mmm) REVERT: B 431 LEU cc_start: 0.8562 (mp) cc_final: 0.8334 (mt) REVERT: B 433 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7321 (mm-30) REVERT: B 476 ASP cc_start: 0.7681 (m-30) cc_final: 0.7340 (m-30) outliers start: 54 outliers final: 38 residues processed: 381 average time/residue: 1.2939 time to fit residues: 531.7120 Evaluate side-chains 394 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS C 358 ASN C 480 ASN C 499 ASN A 13 HIS A 296 HIS A 455 GLN A 472 HIS A 480 ASN B 296 HIS B 345 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.110367 restraints weight = 16300.915| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.95 r_work: 0.3379 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12286 Z= 0.137 Angle : 0.550 11.228 16671 Z= 0.286 Chirality : 0.043 0.225 1848 Planarity : 0.004 0.057 2120 Dihedral : 7.212 98.849 2106 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.32 % Allowed : 30.35 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.22), residues: 1457 helix: 2.41 (0.27), residues: 378 sheet: 0.39 (0.30), residues: 307 loop : -1.41 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 127 HIS 0.012 0.001 HIS C 356 PHE 0.010 0.001 PHE B 148 TYR 0.017 0.001 TYR C 492 ARG 0.013 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 11) link_NAG-ASN : angle 1.55582 ( 33) link_BETA1-4 : bond 0.00134 ( 3) link_BETA1-4 : angle 1.79034 ( 9) hydrogen bonds : bond 0.04711 ( 464) hydrogen bonds : angle 4.29810 ( 1392) SS BOND : bond 0.00207 ( 18) SS BOND : angle 0.95357 ( 36) glycosidic custom : bond 0.00162 ( 3) glycosidic custom : angle 0.79679 ( 9) link_BETA1-3 : bond 0.00116 ( 3) link_BETA1-3 : angle 0.93516 ( 9) covalent geometry : bond 0.00319 (12248) covalent geometry : angle 0.54274 (16575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12611.30 seconds wall clock time: 220 minutes 37.47 seconds (13237.47 seconds total)