Starting phenix.real_space_refine on Wed May 14 16:25:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xr9_38599/05_2025/8xr9_38599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xr9_38599/05_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_38599/05_2025/8xr9_38599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xr9_38599/05_2025/8xr9_38599.map" model { file = "/net/cci-nas-00/data/ceres_data/8xr9_38599/05_2025/8xr9_38599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xr9_38599/05_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-5687/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: 3.38 Conformation dependent library (CDL) restraints added in 1.7 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: 1.74 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: 4.42 Time building geometry restraints manager: 3.95 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: 2.130 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.340 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.330 ------------------------------------------------------------------------------- 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 : 1.428 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: 1.1592 time to fit residues: 486.0865 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 : 1.387 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.121482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108980 restraints weight = 16203.808| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.93 r_work: 0.3356 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12286 Z= 0.224 Angle : 0.614 8.063 16671 Z= 0.315 Chirality : 0.045 0.176 1848 Planarity : 0.005 0.055 2120 Dihedral : 10.502 94.854 2174 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.64 % Allowed : 27.64 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.21), residues: 1457 helix: 2.17 (0.27), residues: 377 sheet: -0.05 (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 0.009 0.001 HIS C 356 PHE 0.015 0.002 PHE B 100 TYR 0.018 0.002 TYR B 424 ARG 0.010 0.001 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 11) link_NAG-ASN : angle 1.55702 ( 33) link_BETA1-4 : bond 0.00591 ( 3) link_BETA1-4 : angle 2.68456 ( 9) hydrogen bonds : bond 0.05882 ( 464) hydrogen bonds : angle 4.98573 ( 1392) SS BOND : bond 0.00243 ( 18) SS BOND : angle 0.77808 ( 36) glycosidic custom : bond 0.00427 ( 3) glycosidic custom : angle 1.42257 ( 9) link_BETA1-3 : bond 0.00335 ( 3) link_BETA1-3 : angle 3.00664 ( 9) covalent geometry : bond 0.00532 (12248) covalent geometry : angle 0.60269 (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 434 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 361 time to evaluate : 1.380 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: 0.7621 (OUTLIER) cc_final: 0.7325 (pm20) REVERT: C 136 SER cc_start: 0.8454 (p) cc_final: 0.7871 (t) REVERT: C 157 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8652 (tttm) REVERT: C 269 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8166 (ttm) REVERT: C 493 GLU cc_start: 0.7003 (tp30) cc_final: 0.6652 (tp30) REVERT: C 494 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: C 495 GLU cc_start: 0.7441 (tp30) cc_final: 0.7167 (tp30) REVERT: A 48 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8025 (mttp) REVERT: A 388 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8499 (mmtm) REVERT: A 497 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8053 (ttpp) REVERT: B 151 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.7730 (mmt) REVERT: B 157 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8726 (tttp) REVERT: B 336 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7488 (mt) REVERT: B 354 TYR cc_start: 0.8408 (m-80) cc_final: 0.8110 (m-80) REVERT: B 405 ARG cc_start: 0.7982 (mmt180) cc_final: 0.7765 (mmm160) REVERT: B 431 LEU cc_start: 0.8692 (mp) cc_final: 0.8469 (mt) REVERT: B 433 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 476 ASP cc_start: 0.7753 (m-30) cc_final: 0.7432 (m-30) outliers start: 73 outliers final: 37 residues processed: 398 average time/residue: 1.2626 time to fit residues: 541.8576 Evaluate side-chains 394 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 348 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 269 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 428 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 20 THR 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 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 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: 2.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 465 ASN A 13 HIS A 175 GLN A 296 HIS A 455 GLN A 472 HIS B 299 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 = 0.3663 r_free = 0.3663 target = 0.122252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109740 restraints weight = 16465.665| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.95 r_work: 0.3356 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0809 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= 0.158 Angle : 0.553 7.931 16671 Z= 0.286 Chirality : 0.043 0.179 1848 Planarity : 0.004 0.055 2120 Dihedral : 9.181 98.743 2128 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.48 % Allowed : 29.50 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1457 helix: 2.29 (0.27), residues: 378 sheet: 0.06 (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 0.010 0.001 HIS C 356 PHE 0.010 0.001 PHE B 148 TYR 0.014 0.001 TYR C 492 ARG 0.010 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 11) link_NAG-ASN : angle 1.55203 ( 33) link_BETA1-4 : bond 0.00034 ( 3) link_BETA1-4 : angle 2.45731 ( 9) hydrogen bonds : bond 0.05286 ( 464) hydrogen bonds : angle 4.68422 ( 1392) SS BOND : bond 0.00262 ( 18) SS BOND : angle 0.64048 ( 36) glycosidic custom : bond 0.00288 ( 3) glycosidic custom : angle 0.82843 ( 9) link_BETA1-3 : bond 0.00123 ( 3) link_BETA1-3 : angle 2.43577 ( 9) covalent geometry : bond 0.00367 (12248) covalent geometry : angle 0.54312 (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 420 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 362 time to evaluate : 1.391 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: 0.7629 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: C 136 SER cc_start: 0.8434 (p) cc_final: 0.7909 (t) REVERT: C 137 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8085 (mtt90) REVERT: C 157 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8641 (tttm) REVERT: C 493 GLU cc_start: 0.7031 (tp30) cc_final: 0.6726 (tp30) REVERT: C 494 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: C 495 GLU cc_start: 0.7443 (tp30) cc_final: 0.7202 (tp30) REVERT: A 48 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8021 (mttp) REVERT: A 131 THR cc_start: 0.8931 (m) cc_final: 0.8571 (t) REVERT: A 388 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8437 (mmtm) REVERT: B 157 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8748 (tttp) REVERT: B 336 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7518 (mt) REVERT: B 354 TYR cc_start: 0.8382 (m-80) cc_final: 0.8075 (m-80) REVERT: B 431 LEU cc_start: 0.8571 (mp) cc_final: 0.8358 (mt) REVERT: B 433 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: B 476 ASP cc_start: 0.7702 (m-30) cc_final: 0.7339 (m-30) outliers start: 58 outliers final: 38 residues processed: 390 average time/residue: 1.2736 time to fit residues: 534.3611 Evaluate side-chains 399 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 353 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU 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 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR 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 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 494 GLU 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 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 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 292 THR Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 433 GLU 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: 0.6980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 296 HIS A 455 GLN A 472 HIS B 296 HIS B 299 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 = 0.3650 r_free = 0.3650 target = 0.121316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108830 restraints weight = 16163.145| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.93 r_work: 0.3355 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12286 Z= 0.223 Angle : 0.579 8.674 16671 Z= 0.299 Chirality : 0.045 0.197 1848 Planarity : 0.004 0.055 2120 Dihedral : 8.632 99.880 2117 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 6.02 % Allowed : 28.11 % 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: -0.17 (0.21), residues: 1457 helix: 2.28 (0.27), residues: 376 sheet: 0.11 (0.30), residues: 307 loop : -1.51 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 81 HIS 0.011 0.001 HIS C 356 PHE 0.015 0.002 PHE B 148 TYR 0.022 0.002 TYR B 424 ARG 0.010 0.001 ARG A 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 11) link_NAG-ASN : angle 1.68634 ( 33) link_BETA1-4 : bond 0.00178 ( 3) link_BETA1-4 : angle 2.31455 ( 9) hydrogen bonds : bond 0.05454 ( 464) hydrogen bonds : angle 4.61120 ( 1392) SS BOND : bond 0.00258 ( 18) SS BOND : angle 0.67755 ( 36) glycosidic custom : bond 0.00458 ( 3) glycosidic custom : angle 0.97822 ( 9) link_BETA1-3 : bond 0.00107 ( 3) link_BETA1-3 : angle 2.00270 ( 9) covalent geometry : bond 0.00532 (12248) covalent geometry : angle 0.56960 (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 431 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 353 time to evaluate : 1.334 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: 0.7583 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: C 136 SER cc_start: 0.8467 (p) cc_final: 0.7954 (t) REVERT: C 137 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8070 (mtt90) REVERT: C 157 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8651 (tttm) REVERT: C 190 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8073 (mt-10) REVERT: C 392 GLN cc_start: 0.5240 (OUTLIER) cc_final: 0.5023 (mt0) REVERT: C 495 GLU cc_start: 0.7467 (tp30) cc_final: 0.7223 (tp30) REVERT: A 48 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8015 (mttm) REVERT: A 388 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8516 (mmtm) REVERT: B 74 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8327 (ptt90) REVERT: B 151 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.7732 (mmt) REVERT: B 157 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8705 (tttp) REVERT: B 336 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7582 (mt) REVERT: B 354 TYR cc_start: 0.8431 (m-80) cc_final: 0.8112 (m-80) REVERT: B 360 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6646 (mp10) REVERT: B 403 LEU cc_start: 0.8524 (mp) cc_final: 0.8310 (mm) REVERT: B 431 LEU cc_start: 0.8588 (mp) cc_final: 0.8361 (mt) REVERT: B 433 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 476 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7383 (m-30) outliers start: 78 outliers final: 44 residues processed: 392 average time/residue: 1.2404 time to fit residues: 524.7278 Evaluate side-chains 413 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 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 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 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 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 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 274 THR 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 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 360 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 369 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 19 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 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 B 455 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 = 0.3664 r_free = 0.3664 target = 0.122323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109768 restraints weight = 16311.681| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.95 r_work: 0.3367 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12286 Z= 0.149 Angle : 0.542 8.910 16671 Z= 0.280 Chirality : 0.042 0.202 1848 Planarity : 0.004 0.054 2120 Dihedral : 8.008 100.094 2112 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.48 % Allowed : 28.73 % 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: -0.07 (0.21), residues: 1457 helix: 2.35 (0.27), residues: 378 sheet: 0.23 (0.30), residues: 305 loop : -1.47 (0.20), residues: 774 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 0.009 0.001 PHE B 148 TYR 0.016 0.001 TYR C 492 ARG 0.008 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 11) link_NAG-ASN : angle 1.66158 ( 33) link_BETA1-4 : bond 0.00131 ( 3) link_BETA1-4 : angle 2.08736 ( 9) hydrogen bonds : bond 0.04980 ( 464) hydrogen bonds : angle 4.46912 ( 1392) SS BOND : bond 0.00182 ( 18) SS BOND : angle 0.75793 ( 36) glycosidic custom : bond 0.00203 ( 3) glycosidic custom : angle 0.84288 ( 9) link_BETA1-3 : bond 0.00068 ( 3) link_BETA1-3 : angle 1.53112 ( 9) covalent geometry : bond 0.00348 (12248) covalent geometry : angle 0.53381 (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 433 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 362 time to evaluate : 1.318 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: 0.7568 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: C 136 SER cc_start: 0.8462 (p) cc_final: 0.7950 (t) REVERT: C 137 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8046 (mtt90) REVERT: C 157 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8645 (tttm) REVERT: C 190 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8066 (mt-10) REVERT: C 321 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8725 (mt) REVERT: C 392 GLN cc_start: 0.5197 (OUTLIER) cc_final: 0.4977 (mt0) REVERT: C 435 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: C 493 GLU cc_start: 0.7072 (tp30) cc_final: 0.6842 (tp30) REVERT: C 495 GLU cc_start: 0.7422 (tp30) cc_final: 0.7205 (tp30) REVERT: A 48 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7997 (mttp) REVERT: A 131 THR cc_start: 0.8921 (m) cc_final: 0.8559 (t) REVERT: A 419 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7425 (tp) REVERT: B 74 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8298 (ptt90) REVERT: B 157 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8692 (tttp) REVERT: B 336 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7592 (mt) REVERT: B 354 TYR cc_start: 0.8386 (m-80) cc_final: 0.7927 (m-80) REVERT: B 360 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6632 (mp10) REVERT: B 381 LYS cc_start: 0.8781 (tttp) cc_final: 0.8516 (tttm) REVERT: B 389 MET cc_start: 0.7986 (tpp) cc_final: 0.7604 (mmm) REVERT: B 428 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 431 LEU cc_start: 0.8523 (mp) cc_final: 0.8287 (mt) REVERT: B 476 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7290 (m-30) outliers start: 71 outliers final: 44 residues processed: 400 average time/residue: 1.3076 time to fit residues: 562.0382 Evaluate side-chains 412 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 354 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 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 228 SER 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 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 349 ASP Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 435 GLU 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 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 419 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 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 336 ILE Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 428 LEU 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: 1.9990 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 81 optimal weight: 0.0370 chunk 92 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 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 = 0.3668 r_free = 0.3668 target = 0.122757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110297 restraints weight = 16461.576| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.95 r_work: 0.3363 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12286 Z= 0.131 Angle : 0.528 9.492 16671 Z= 0.272 Chirality : 0.042 0.205 1848 Planarity : 0.004 0.054 2120 Dihedral : 7.730 99.997 2112 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.41 % Allowed : 29.19 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1457 helix: 2.44 (0.27), residues: 378 sheet: 0.25 (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 0.009 0.001 PHE B 148 TYR 0.024 0.001 TYR B 424 ARG 0.010 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 11) link_NAG-ASN : angle 1.63391 ( 33) link_BETA1-4 : bond 0.00148 ( 3) link_BETA1-4 : angle 1.94256 ( 9) hydrogen bonds : bond 0.04774 ( 464) hydrogen bonds : angle 4.35156 ( 1392) SS BOND : bond 0.00201 ( 18) SS BOND : angle 0.87917 ( 36) glycosidic custom : bond 0.00121 ( 3) glycosidic custom : angle 0.79078 ( 9) link_BETA1-3 : bond 0.00085 ( 3) link_BETA1-3 : angle 1.26603 ( 9) covalent geometry : bond 0.00304 (12248) covalent geometry : angle 0.52023 (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 431 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 361 time to evaluate : 1.280 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: 0.7567 (OUTLIER) cc_final: 0.7338 (pm20) REVERT: C 137 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8094 (mtt90) REVERT: C 157 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8645 (tttm) REVERT: C 190 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8080 (mt-10) REVERT: C 321 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8739 (mt) REVERT: C 435 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: C 495 GLU cc_start: 0.7440 (tp30) cc_final: 0.7210 (tp30) REVERT: A 7 GLN cc_start: 0.8238 (mt0) cc_final: 0.7976 (mt0) REVERT: A 27 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7114 (mtm-85) REVERT: A 48 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7993 (mttp) REVERT: A 131 THR cc_start: 0.8931 (m) cc_final: 0.8563 (t) REVERT: A 384 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 74 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8355 (ptt90) REVERT: B 157 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8693 (tttp) REVERT: B 354 TYR cc_start: 0.8349 (m-80) cc_final: 0.7946 (m-80) REVERT: B 360 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6612 (mp10) REVERT: B 389 MET cc_start: 0.7887 (tpp) cc_final: 0.7511 (mmm) REVERT: B 405 ARG cc_start: 0.7961 (mmt180) cc_final: 0.7698 (mmm160) REVERT: B 431 LEU cc_start: 0.8521 (mp) cc_final: 0.8302 (mt) REVERT: B 433 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: B 476 ASP cc_start: 0.7655 (m-30) cc_final: 0.7259 (m-30) outliers start: 70 outliers final: 36 residues processed: 395 average time/residue: 1.2945 time to fit residues: 552.1409 Evaluate side-chains 406 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 358 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS 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 435 GLU 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 27 ARG 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 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 313 GLU Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 433 GLU 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: 4.9990 chunk 114 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 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: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS C 380 ASN C 392 GLN 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 345 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108609 restraints weight = 16423.460| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.95 r_work: 0.3353 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12286 Z= 0.234 Angle : 0.601 9.487 16671 Z= 0.310 Chirality : 0.045 0.230 1848 Planarity : 0.005 0.055 2120 Dihedral : 7.772 99.935 2110 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.94 % Allowed : 29.88 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1457 helix: 2.25 (0.27), residues: 378 sheet: 0.19 (0.30), residues: 309 loop : -1.49 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 65 HIS 0.013 0.002 HIS C 356 PHE 0.015 0.002 PHE A 148 TYR 0.016 0.002 TYR C 492 ARG 0.016 0.001 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 11) link_NAG-ASN : angle 1.77041 ( 33) link_BETA1-4 : bond 0.00228 ( 3) link_BETA1-4 : angle 2.11470 ( 9) hydrogen bonds : bond 0.05380 ( 464) hydrogen bonds : angle 4.49229 ( 1392) SS BOND : bond 0.00254 ( 18) SS BOND : angle 0.84760 ( 36) glycosidic custom : bond 0.00463 ( 3) glycosidic custom : angle 1.00176 ( 9) link_BETA1-3 : bond 0.00062 ( 3) link_BETA1-3 : angle 1.50834 ( 9) covalent geometry : bond 0.00563 (12248) covalent geometry : angle 0.59304 (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 423 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 359 time to evaluate : 1.307 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: 0.7589 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: C 74 ARG cc_start: 0.8412 (ttp-110) cc_final: 0.8210 (ptt90) REVERT: C 137 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8408 (mtt90) REVERT: C 157 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8659 (tttm) REVERT: C 190 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8031 (mt-10) REVERT: C 269 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8149 (ttm) REVERT: C 435 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: C 493 GLU cc_start: 0.7118 (tp30) cc_final: 0.6889 (tp30) REVERT: C 495 GLU cc_start: 0.7463 (tp30) cc_final: 0.7236 (tp30) REVERT: A 27 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6960 (mtm-85) REVERT: A 48 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7995 (mttm) REVERT: B 74 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8420 (ptt90) REVERT: B 157 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8712 (tttp) REVERT: B 347 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7509 (ttm) REVERT: B 354 TYR cc_start: 0.8411 (m-80) cc_final: 0.8121 (m-80) REVERT: B 360 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6585 (mp-120) REVERT: B 373 LYS cc_start: 0.8562 (mptt) cc_final: 0.8350 (mptt) REVERT: B 389 MET cc_start: 0.7857 (tpp) cc_final: 0.7615 (mmm) REVERT: B 431 LEU cc_start: 0.8565 (mp) cc_final: 0.8342 (mt) REVERT: B 433 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: B 476 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7185 (m-30) outliers start: 64 outliers final: 42 residues processed: 392 average time/residue: 1.3135 time to fit residues: 553.2986 Evaluate side-chains 410 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 355 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 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 269 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 22 ASP Chi-restraints excluded: chain A residue 27 ARG 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 414 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 40 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 27 optimal weight: 0.8980 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: 0.0020 chunk 87 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- 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 380 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109379 restraints weight = 16390.007| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.96 r_work: 0.3361 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12286 Z= 0.185 Angle : 0.573 9.966 16671 Z= 0.296 Chirality : 0.044 0.231 1848 Planarity : 0.005 0.056 2120 Dihedral : 7.627 99.790 2110 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.63 % Allowed : 30.50 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1457 helix: 2.25 (0.27), residues: 378 sheet: 0.23 (0.30), residues: 309 loop : -1.47 (0.20), residues: 770 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 0.012 0.002 PHE B 148 TYR 0.024 0.002 TYR B 424 ARG 0.013 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 11) link_NAG-ASN : angle 1.71357 ( 33) link_BETA1-4 : bond 0.00136 ( 3) link_BETA1-4 : angle 2.02173 ( 9) hydrogen bonds : bond 0.05113 ( 464) hydrogen bonds : angle 4.43835 ( 1392) SS BOND : bond 0.00232 ( 18) SS BOND : angle 0.89301 ( 36) glycosidic custom : bond 0.00257 ( 3) glycosidic custom : angle 0.87720 ( 9) link_BETA1-3 : bond 0.00064 ( 3) link_BETA1-3 : angle 1.30218 ( 9) covalent geometry : bond 0.00440 (12248) covalent geometry : angle 0.56486 (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 419 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 359 time to evaluate : 1.475 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: 0.7589 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: C 74 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.8199 (ptt90) REVERT: C 137 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8390 (mtt90) REVERT: C 157 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8646 (tttm) REVERT: C 190 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8104 (mt-10) REVERT: C 269 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8136 (ttm) REVERT: C 435 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: C 465 ASN cc_start: 0.8562 (p0) cc_final: 0.8337 (p0) REVERT: C 495 GLU cc_start: 0.7449 (tp30) cc_final: 0.7234 (tp30) REVERT: A 7 GLN cc_start: 0.8255 (mt0) cc_final: 0.7991 (mt0) REVERT: A 27 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6962 (mtm-85) REVERT: A 48 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7993 (mttp) REVERT: A 131 THR cc_start: 0.8934 (m) cc_final: 0.8562 (t) REVERT: B 74 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8429 (ptt90) REVERT: B 157 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8685 (tttp) REVERT: B 347 MET cc_start: 0.7819 (ttm) cc_final: 0.7498 (ttm) REVERT: B 354 TYR cc_start: 0.8392 (m-80) cc_final: 0.7989 (m-80) REVERT: B 360 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.6562 (mp-120) REVERT: B 389 MET cc_start: 0.7820 (tpp) cc_final: 0.7559 (mmm) REVERT: B 431 LEU cc_start: 0.8529 (mp) cc_final: 0.8299 (mt) REVERT: B 476 ASP cc_start: 0.7723 (m-30) cc_final: 0.7209 (m-30) outliers start: 60 outliers final: 41 residues processed: 393 average time/residue: 1.3133 time to fit residues: 554.7743 Evaluate side-chains 399 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 348 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 269 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 316 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 435 GLU 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 22 ASP Chi-restraints excluded: chain A residue 27 ARG 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 414 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 40 LYS 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 292 THR Chi-restraints excluded: chain B residue 316 VAL 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: 2.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 0.0570 chunk 128 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.109165 restraints weight = 16366.329| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.94 r_work: 0.3359 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12286 Z= 0.200 Angle : 0.596 10.024 16671 Z= 0.310 Chirality : 0.045 0.233 1848 Planarity : 0.005 0.060 2120 Dihedral : 7.665 99.753 2110 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.79 % Allowed : 30.73 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1457 helix: 2.19 (0.27), residues: 378 sheet: 0.23 (0.30), residues: 309 loop : -1.47 (0.20), residues: 770 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 0.013 0.002 PHE B 148 TYR 0.017 0.002 TYR C 492 ARG 0.014 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 11) link_NAG-ASN : angle 1.72413 ( 33) link_BETA1-4 : bond 0.00161 ( 3) link_BETA1-4 : angle 2.04026 ( 9) hydrogen bonds : bond 0.05201 ( 464) hydrogen bonds : angle 4.46502 ( 1392) SS BOND : bond 0.00244 ( 18) SS BOND : angle 0.86914 ( 36) glycosidic custom : bond 0.00321 ( 3) glycosidic custom : angle 0.90592 ( 9) link_BETA1-3 : bond 0.00051 ( 3) link_BETA1-3 : angle 1.29694 ( 9) covalent geometry : bond 0.00477 (12248) covalent geometry : angle 0.58874 (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 415 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 353 time to evaluate : 1.271 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: 0.7574 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: C 74 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.8159 (ptt90) REVERT: C 137 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8398 (mtt90) REVERT: C 157 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8641 (tttm) REVERT: C 190 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8063 (mt-10) REVERT: C 269 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8139 (ttm) REVERT: C 435 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: C 465 ASN cc_start: 0.8552 (p0) cc_final: 0.8321 (p0) REVERT: C 495 GLU cc_start: 0.7460 (tp30) cc_final: 0.7239 (tp30) REVERT: A 7 GLN cc_start: 0.8260 (mt0) cc_final: 0.7965 (mt0) REVERT: A 27 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7218 (mtm-85) REVERT: A 48 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7993 (mttp) REVERT: A 131 THR cc_start: 0.8931 (m) cc_final: 0.8573 (t) REVERT: A 388 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8433 (mmtm) REVERT: B 74 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8420 (ptt90) REVERT: B 157 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8694 (tttp) REVERT: B 347 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7477 (ttm) REVERT: B 354 TYR cc_start: 0.8387 (m-80) cc_final: 0.8050 (m-80) REVERT: B 360 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6563 (mp10) REVERT: B 369 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7323 (tm-30) REVERT: B 389 MET cc_start: 0.7789 (tpp) cc_final: 0.7562 (mmm) REVERT: B 431 LEU cc_start: 0.8539 (mp) cc_final: 0.8312 (mt) REVERT: B 433 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7262 (mm-30) REVERT: B 476 ASP cc_start: 0.7690 (m-30) cc_final: 0.7221 (m-30) outliers start: 62 outliers final: 43 residues processed: 383 average time/residue: 1.3437 time to fit residues: 552.0925 Evaluate side-chains 408 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 354 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 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 269 MET 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 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 478 CYS Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG 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 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 40 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 61 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 134 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110622 restraints weight = 16278.169| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.95 r_work: 0.3380 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1258 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= 0.126 Angle : 0.553 10.453 16671 Z= 0.287 Chirality : 0.043 0.222 1848 Planarity : 0.005 0.054 2120 Dihedral : 7.433 99.269 2110 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.17 % Allowed : 31.51 % Favored : 64.32 % 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: 2.32 (0.27), residues: 378 sheet: 0.35 (0.30), residues: 307 loop : -1.40 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 127 HIS 0.012 0.001 HIS C 356 PHE 0.010 0.001 PHE B 148 TYR 0.025 0.001 TYR B 424 ARG 0.014 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 11) link_NAG-ASN : angle 1.60017 ( 33) link_BETA1-4 : bond 0.00130 ( 3) link_BETA1-4 : angle 1.84625 ( 9) hydrogen bonds : bond 0.04678 ( 464) hydrogen bonds : angle 4.34019 ( 1392) SS BOND : bond 0.00189 ( 18) SS BOND : angle 0.74560 ( 36) glycosidic custom : bond 0.00054 ( 3) glycosidic custom : angle 0.74391 ( 9) link_BETA1-3 : bond 0.00137 ( 3) link_BETA1-3 : angle 0.94106 ( 9) covalent geometry : bond 0.00290 (12248) covalent geometry : angle 0.54699 (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 416 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 362 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: C 26 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7369 (pm20) REVERT: C 74 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.8157 (ptt90) REVERT: C 137 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8380 (mtt90) REVERT: C 190 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8050 (mt-10) REVERT: C 321 LEU cc_start: 0.8951 (mp) cc_final: 0.8741 (mt) REVERT: C 435 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: C 465 ASN cc_start: 0.8561 (p0) cc_final: 0.8312 (p0) REVERT: C 495 GLU cc_start: 0.7424 (tp30) cc_final: 0.7201 (tp30) REVERT: A 7 GLN cc_start: 0.8269 (mt0) cc_final: 0.7992 (mt0) REVERT: A 27 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6975 (mtm-85) REVERT: A 48 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7977 (mttp) REVERT: A 131 THR cc_start: 0.8931 (m) cc_final: 0.8561 (t) REVERT: A 354 TYR cc_start: 0.8547 (m-80) cc_final: 0.8218 (m-80) REVERT: A 384 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8667 (p) REVERT: A 388 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8400 (mmtm) REVERT: B 74 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8395 (ptt90) REVERT: B 139 CYS cc_start: 0.7543 (m) cc_final: 0.7030 (m) REVERT: B 157 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8682 (tttp) REVERT: B 347 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7372 (ttm) REVERT: B 354 TYR cc_start: 0.8308 (m-80) cc_final: 0.7997 (m-80) REVERT: B 360 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6506 (mp10) REVERT: B 381 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8283 (tttm) REVERT: B 389 MET cc_start: 0.7751 (tpp) cc_final: 0.7496 (mmm) REVERT: B 431 LEU cc_start: 0.8464 (mp) cc_final: 0.8236 (mt) REVERT: B 433 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7045 (mm-30) REVERT: B 476 ASP cc_start: 0.7657 (m-30) cc_final: 0.7161 (m-30) outliers start: 54 outliers final: 32 residues processed: 390 average time/residue: 1.3316 time to fit residues: 558.3543 Evaluate side-chains 408 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 365 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU 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 228 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 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 349 ASP 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 C residue 493 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 27 ARG 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 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 316 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 381 LYS 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: 0.7980 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 118 optimal weight: 0.0070 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS C 499 ASN A 13 HIS A 210 ASN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110656 restraints weight = 16295.161| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.94 r_work: 0.3382 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12286 Z= 0.128 Angle : 0.562 10.752 16671 Z= 0.290 Chirality : 0.043 0.225 1848 Planarity : 0.004 0.058 2120 Dihedral : 7.334 99.073 2110 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: 0.03 (0.22), residues: 1457 helix: 2.25 (0.27), residues: 378 sheet: 0.39 (0.31), residues: 304 loop : -1.35 (0.20), residues: 775 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 0.016 0.001 TYR C 492 ARG 0.013 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 11) link_NAG-ASN : angle 1.58326 ( 33) link_BETA1-4 : bond 0.00143 ( 3) link_BETA1-4 : angle 1.76785 ( 9) hydrogen bonds : bond 0.04618 ( 464) hydrogen bonds : angle 4.34570 ( 1392) SS BOND : bond 0.00179 ( 18) SS BOND : angle 0.74081 ( 36) glycosidic custom : bond 0.00118 ( 3) glycosidic custom : angle 0.77518 ( 9) link_BETA1-3 : bond 0.00126 ( 3) link_BETA1-3 : angle 0.91465 ( 9) covalent geometry : bond 0.00296 (12248) covalent geometry : angle 0.55563 (16575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11182.63 seconds wall clock time: 192 minutes 40.96 seconds (11560.96 seconds total)