Starting phenix.real_space_refine on Wed Sep 17 22:53:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xr9_38599/09_2025/8xr9_38599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xr9_38599/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xr9_38599/09_2025/8xr9_38599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xr9_38599/09_2025/8xr9_38599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xr9_38599/09_2025/8xr9_38599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xr9_38599/09_2025/8xr9_38599.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.65, per 1000 atoms: 0.22 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: 0.97 Conformation dependent library (CDL) restraints added in 599.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.33 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: 2.09 Time building geometry restraints manager: 1.31 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 603) selection = (chain 'B' and (resid 6 through 327 or resid 336 through 603)) selection = (chain 'C' and (resid 6 through 327 or resid 336 through 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: 2.660 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG A 27 TYR 0.018 0.001 TYR C 492 PHE 0.009 0.001 PHE B 148 TRP 0.007 0.001 TRP A 422 HIS 0.008 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00390 (12248) covalent geometry : angle 0.89899 (16575) SS BOND : bond 0.00212 ( 18) SS BOND : angle 0.99030 ( 36) hydrogen bonds : bond 0.18749 ( 464) hydrogen bonds : angle 6.70596 ( 1392) 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) link_BETA1-4 : bond 0.03926 ( 3) link_BETA1-4 : angle 7.60257 ( 9) link_NAG-ASN : bond 0.00182 ( 11) link_NAG-ASN : angle 1.45970 ( 33) *********************** 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 : 0.479 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: 0.5681 time to fit residues: 238.1003 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 : 0.473 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 210 ASN C 356 HIS C 409 ASN C 465 ASN A 13 HIS A 175 GLN A 186 ASN A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 299 HIS B 345 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109325 restraints weight = 16268.485| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.94 r_work: 0.3350 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12286 Z= 0.199 Angle : 0.600 8.960 16671 Z= 0.308 Chirality : 0.045 0.178 1848 Planarity : 0.004 0.054 2120 Dihedral : 10.367 94.870 2174 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.41 % Allowed : 27.95 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.21), residues: 1457 helix: 2.21 (0.27), residues: 377 sheet: 0.08 (0.31), residues: 292 loop : -1.50 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.019 0.002 TYR B 424 PHE 0.015 0.002 PHE B 100 TRP 0.009 0.001 TRP B 81 HIS 0.009 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00468 (12248) covalent geometry : angle 0.59009 (16575) SS BOND : bond 0.00228 ( 18) SS BOND : angle 0.76234 ( 36) hydrogen bonds : bond 0.05595 ( 464) hydrogen bonds : angle 4.93452 ( 1392) glycosidic custom : bond 0.00297 ( 3) glycosidic custom : angle 1.28570 ( 9) link_BETA1-3 : bond 0.00363 ( 3) link_BETA1-3 : angle 2.57606 ( 9) link_BETA1-4 : bond 0.00714 ( 3) link_BETA1-4 : angle 2.68142 ( 9) link_NAG-ASN : bond 0.00283 ( 11) link_NAG-ASN : angle 1.51875 ( 33) *********************** 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 432 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 362 time to evaluate : 0.466 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: 0.7612 (OUTLIER) cc_final: 0.7332 (pm20) REVERT: C 136 SER cc_start: 0.8432 (p) cc_final: 0.7856 (t) REVERT: C 157 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8648 (tttm) REVERT: C 493 GLU cc_start: 0.7000 (tp30) cc_final: 0.6637 (tp30) REVERT: C 494 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: C 495 GLU cc_start: 0.7433 (tp30) cc_final: 0.7205 (tp30) REVERT: A 48 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8025 (mttp) REVERT: A 388 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8484 (mmtm) REVERT: B 157 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8718 (tttp) REVERT: B 336 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7460 (mt) REVERT: B 354 TYR cc_start: 0.8389 (m-80) cc_final: 0.8113 (m-80) REVERT: B 431 LEU cc_start: 0.8665 (mp) cc_final: 0.8439 (mt) REVERT: B 433 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7423 (mm-30) REVERT: B 476 ASP cc_start: 0.7726 (m-30) cc_final: 0.7404 (m-30) outliers start: 70 outliers final: 38 residues processed: 397 average time/residue: 0.6287 time to fit residues: 268.6311 Evaluate side-chains 391 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain 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 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 70 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 C 499 ASN A 13 HIS A 175 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 = 0.3656 r_free = 0.3656 target = 0.121736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109210 restraints weight = 16461.877| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3358 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12286 Z= 0.195 Angle : 0.568 7.978 16671 Z= 0.294 Chirality : 0.044 0.184 1848 Planarity : 0.004 0.055 2120 Dihedral : 9.067 99.331 2124 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.25 % Allowed : 28.42 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.21), residues: 1457 helix: 2.27 (0.27), residues: 376 sheet: 0.06 (0.30), residues: 307 loop : -1.49 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.015 0.002 TYR C 492 PHE 0.012 0.002 PHE B 148 TRP 0.009 0.001 TRP B 81 HIS 0.010 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00462 (12248) covalent geometry : angle 0.55847 (16575) SS BOND : bond 0.00253 ( 18) SS BOND : angle 0.68343 ( 36) hydrogen bonds : bond 0.05451 ( 464) hydrogen bonds : angle 4.67753 ( 1392) glycosidic custom : bond 0.00384 ( 3) glycosidic custom : angle 0.91557 ( 9) link_BETA1-3 : bond 0.00132 ( 3) link_BETA1-3 : angle 2.40792 ( 9) link_BETA1-4 : bond 0.00101 ( 3) link_BETA1-4 : angle 2.46003 ( 9) link_NAG-ASN : bond 0.00220 ( 11) link_NAG-ASN : angle 1.62503 ( 33) *********************** 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 425 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 357 time to evaluate : 0.487 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: 0.7625 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: C 136 SER cc_start: 0.8444 (p) cc_final: 0.7956 (t) REVERT: C 137 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8058 (mtt90) REVERT: C 157 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8649 (tttm) REVERT: C 190 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8085 (mt-10) REVERT: C 269 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8203 (ttm) REVERT: C 493 GLU cc_start: 0.7034 (tp30) cc_final: 0.6811 (tp30) REVERT: C 494 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: C 495 GLU cc_start: 0.7445 (tp30) cc_final: 0.7180 (tp30) REVERT: A 48 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8010 (mttm) REVERT: A 388 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8447 (mmtm) REVERT: B 151 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.7787 (mmt) REVERT: B 157 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8747 (tttp) REVERT: B 336 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7557 (mt) REVERT: B 354 TYR cc_start: 0.8394 (m-80) cc_final: 0.8116 (m-80) REVERT: B 431 LEU cc_start: 0.8604 (mp) cc_final: 0.8381 (mt) REVERT: B 433 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 476 ASP cc_start: 0.7740 (m-30) cc_final: 0.7366 (m-30) outliers start: 68 outliers final: 45 residues processed: 391 average time/residue: 0.6157 time to fit residues: 259.4372 Evaluate side-chains 402 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 348 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 465 ASN 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 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 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 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 117 GLU 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 316 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 465 ASN C 480 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109746 restraints weight = 16395.871| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.95 r_work: 0.3365 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12286 Z= 0.146 Angle : 0.535 8.622 16671 Z= 0.277 Chirality : 0.042 0.191 1848 Planarity : 0.004 0.054 2120 Dihedral : 8.524 99.996 2118 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.56 % Allowed : 28.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.21), residues: 1457 helix: 2.39 (0.27), residues: 378 sheet: 0.24 (0.31), residues: 300 loop : -1.47 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.021 0.002 TYR B 424 PHE 0.009 0.001 PHE A 148 TRP 0.008 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00338 (12248) covalent geometry : angle 0.52672 (16575) SS BOND : bond 0.00180 ( 18) SS BOND : angle 0.52566 ( 36) hydrogen bonds : bond 0.05008 ( 464) hydrogen bonds : angle 4.50613 ( 1392) glycosidic custom : bond 0.00237 ( 3) glycosidic custom : angle 0.80616 ( 9) link_BETA1-3 : bond 0.00078 ( 3) link_BETA1-3 : angle 1.74577 ( 9) link_BETA1-4 : bond 0.00153 ( 3) link_BETA1-4 : angle 2.14070 ( 9) link_NAG-ASN : bond 0.00208 ( 11) link_NAG-ASN : angle 1.59459 ( 33) *********************** 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 426 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 354 time to evaluate : 0.438 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: 0.7567 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: C 136 SER cc_start: 0.8436 (p) cc_final: 0.7918 (t) REVERT: C 137 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8060 (mtt90) REVERT: C 157 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8646 (tttm) REVERT: C 190 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8050 (mt-10) REVERT: C 392 GLN cc_start: 0.5209 (OUTLIER) cc_final: 0.4980 (mt0) REVERT: C 493 GLU cc_start: 0.7063 (tp30) cc_final: 0.6843 (tp30) REVERT: C 495 GLU cc_start: 0.7434 (tp30) cc_final: 0.7196 (tp30) REVERT: A 47 CYS cc_start: 0.7021 (m) cc_final: 0.6761 (m) REVERT: A 48 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7995 (mttp) REVERT: A 131 THR cc_start: 0.8932 (m) cc_final: 0.8584 (t) REVERT: A 388 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8483 (mmtm) REVERT: A 403 LEU cc_start: 0.8773 (mm) cc_final: 0.8571 (mp) REVERT: B 74 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8321 (ptt90) REVERT: B 157 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8729 (tttp) REVERT: B 336 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7563 (mt) REVERT: B 354 TYR cc_start: 0.8381 (m-80) cc_final: 0.8093 (m-80) REVERT: B 431 LEU cc_start: 0.8547 (mp) cc_final: 0.8323 (mt) REVERT: B 433 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7242 (mm-30) REVERT: B 436 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7570 (mtm-85) REVERT: B 476 ASP cc_start: 0.7725 (m-30) cc_final: 0.7416 (m-30) outliers start: 72 outliers final: 43 residues processed: 392 average time/residue: 0.6200 time to fit residues: 261.9848 Evaluate side-chains 398 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 347 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU 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 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 391 THR Chi-restraints excluded: chain C residue 392 GLN 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 C residue 501 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 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 384 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 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 369 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 142 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS C 480 ASN C 499 ASN A 13 HIS A 283 GLN A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 345 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110123 restraints weight = 16376.420| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.95 r_work: 0.3371 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12286 Z= 0.134 Angle : 0.529 9.406 16671 Z= 0.272 Chirality : 0.042 0.198 1848 Planarity : 0.004 0.054 2120 Dihedral : 7.931 100.164 2112 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.48 % Allowed : 28.65 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.22), residues: 1457 helix: 2.46 (0.27), residues: 378 sheet: 0.26 (0.31), residues: 302 loop : -1.45 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 27 TYR 0.016 0.001 TYR C 492 PHE 0.009 0.001 PHE B 148 TRP 0.008 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00311 (12248) covalent geometry : angle 0.51992 (16575) SS BOND : bond 0.00231 ( 18) SS BOND : angle 1.09547 ( 36) hydrogen bonds : bond 0.04825 ( 464) hydrogen bonds : angle 4.38228 ( 1392) glycosidic custom : bond 0.00146 ( 3) glycosidic custom : angle 0.81288 ( 9) link_BETA1-3 : bond 0.00082 ( 3) link_BETA1-3 : angle 1.40077 ( 9) link_BETA1-4 : bond 0.00146 ( 3) link_BETA1-4 : angle 1.98961 ( 9) link_NAG-ASN : bond 0.00209 ( 11) link_NAG-ASN : angle 1.59006 ( 33) *********************** 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 423 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 352 time to evaluate : 0.441 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: 0.7584 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: C 74 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8070 (ptt90) REVERT: C 136 SER cc_start: 0.8435 (p) cc_final: 0.7909 (t) REVERT: C 137 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8065 (mtt90) REVERT: C 157 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8655 (tttm) REVERT: C 190 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 321 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8730 (mt) REVERT: C 435 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: C 493 GLU cc_start: 0.7082 (tp30) cc_final: 0.6840 (tp30) REVERT: C 495 GLU cc_start: 0.7421 (tp30) cc_final: 0.7187 (tp30) REVERT: A 7 GLN cc_start: 0.8235 (mt0) cc_final: 0.7896 (mt0) REVERT: A 48 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8009 (mttp) REVERT: A 131 THR cc_start: 0.8935 (m) cc_final: 0.8578 (t) REVERT: A 384 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8656 (p) REVERT: A 403 LEU cc_start: 0.8740 (mm) cc_final: 0.8538 (mp) REVERT: A 419 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7426 (tp) REVERT: B 74 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8331 (ptt90) REVERT: B 157 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8688 (tttp) REVERT: B 336 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7582 (mt) REVERT: B 347 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7437 (ttm) REVERT: B 354 TYR cc_start: 0.8353 (m-80) cc_final: 0.7897 (m-80) REVERT: B 360 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6675 (mp10) REVERT: B 389 MET cc_start: 0.8011 (tpp) cc_final: 0.7704 (mmm) REVERT: B 431 LEU cc_start: 0.8538 (mp) cc_final: 0.8310 (mt) REVERT: B 433 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 476 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7302 (m-30) outliers start: 71 outliers final: 41 residues processed: 388 average time/residue: 0.6049 time to fit residues: 252.9131 Evaluate side-chains 406 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 350 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 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 391 THR 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 C residue 501 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 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 419 LEU Chi-restraints excluded: chain A residue 435 GLU 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 157 LYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 32 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 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 B 472 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110245 restraints weight = 16400.808| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.95 r_work: 0.3374 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12286 Z= 0.132 Angle : 0.527 9.666 16671 Z= 0.271 Chirality : 0.042 0.205 1848 Planarity : 0.004 0.054 2120 Dihedral : 7.646 100.056 2111 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1457 helix: 2.54 (0.27), residues: 378 sheet: 0.25 (0.30), residues: 307 loop : -1.44 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 91 TYR 0.024 0.001 TYR B 424 PHE 0.009 0.001 PHE B 148 TRP 0.008 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00306 (12248) covalent geometry : angle 0.51865 (16575) SS BOND : bond 0.00178 ( 18) SS BOND : angle 0.90863 ( 36) hydrogen bonds : bond 0.04732 ( 464) hydrogen bonds : angle 4.31176 ( 1392) glycosidic custom : bond 0.00134 ( 3) glycosidic custom : angle 0.77359 ( 9) link_BETA1-3 : bond 0.00085 ( 3) link_BETA1-3 : angle 1.23055 ( 9) link_BETA1-4 : bond 0.00150 ( 3) link_BETA1-4 : angle 1.90303 ( 9) link_NAG-ASN : bond 0.00201 ( 11) link_NAG-ASN : angle 1.59102 ( 33) *********************** 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 421 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 350 time to evaluate : 0.477 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: 0.7553 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: C 137 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8107 (mtt90) REVERT: C 157 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8650 (tttm) REVERT: C 321 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8727 (mt) REVERT: C 435 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: C 493 GLU cc_start: 0.7106 (tp30) cc_final: 0.6864 (tp30) REVERT: C 495 GLU cc_start: 0.7435 (tp30) cc_final: 0.7201 (tp30) REVERT: A 7 GLN cc_start: 0.8228 (mt0) cc_final: 0.7923 (mt0) REVERT: A 48 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7954 (mttp) REVERT: A 131 THR cc_start: 0.8924 (m) cc_final: 0.8568 (t) REVERT: A 384 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8648 (p) REVERT: A 403 LEU cc_start: 0.8728 (mm) cc_final: 0.8528 (mp) REVERT: B 74 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8368 (ptt90) REVERT: B 157 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8688 (tttp) REVERT: B 336 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7591 (mt) REVERT: B 347 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7429 (ttm) REVERT: B 354 TYR cc_start: 0.8331 (m-80) cc_final: 0.7939 (m-80) REVERT: B 360 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: B 389 MET cc_start: 0.7885 (tpp) cc_final: 0.7528 (mmm) REVERT: B 431 LEU cc_start: 0.8531 (mp) cc_final: 0.8295 (mt) REVERT: B 433 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: B 436 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7641 (mtp180) REVERT: B 476 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7313 (m-30) outliers start: 71 outliers final: 46 residues processed: 384 average time/residue: 0.6138 time to fit residues: 254.4234 Evaluate side-chains 406 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 346 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 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 208 THR 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 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 446 LYS 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 301 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 380 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 54 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.0010 chunk 131 optimal weight: 1.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109206 restraints weight = 16362.544| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3361 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12286 Z= 0.194 Angle : 0.567 10.174 16671 Z= 0.291 Chirality : 0.044 0.223 1848 Planarity : 0.004 0.054 2120 Dihedral : 7.723 103.161 2111 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.41 % Allowed : 29.03 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1457 helix: 2.45 (0.27), residues: 378 sheet: 0.20 (0.30), residues: 309 loop : -1.45 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 74 TYR 0.016 0.002 TYR C 492 PHE 0.013 0.002 PHE B 148 TRP 0.009 0.001 TRP B 127 HIS 0.012 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00465 (12248) covalent geometry : angle 0.55953 (16575) SS BOND : bond 0.00234 ( 18) SS BOND : angle 0.82661 ( 36) hydrogen bonds : bond 0.05092 ( 464) hydrogen bonds : angle 4.38176 ( 1392) glycosidic custom : bond 0.00341 ( 3) glycosidic custom : angle 0.91286 ( 9) link_BETA1-3 : bond 0.00055 ( 3) link_BETA1-3 : angle 1.34250 ( 9) link_BETA1-4 : bond 0.00174 ( 3) link_BETA1-4 : angle 1.98326 ( 9) link_NAG-ASN : bond 0.00218 ( 11) link_NAG-ASN : angle 1.68245 ( 33) *********************** 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: 70 poor density : 353 time to evaluate : 0.456 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: 0.7578 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: C 74 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.8203 (ptt90) REVERT: C 137 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8399 (mtt90) REVERT: C 157 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8642 (tttm) REVERT: C 435 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: C 493 GLU cc_start: 0.7127 (tp30) cc_final: 0.6888 (tp30) REVERT: C 495 GLU cc_start: 0.7449 (tp30) cc_final: 0.7222 (tp30) REVERT: A 7 GLN cc_start: 0.8250 (mt0) cc_final: 0.7910 (mt0) REVERT: A 48 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7983 (mttp) REVERT: A 384 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8651 (p) REVERT: A 403 LEU cc_start: 0.8747 (mm) cc_final: 0.8546 (mp) REVERT: B 74 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8383 (ptt90) REVERT: B 157 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8692 (tttp) REVERT: B 336 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7650 (mt) REVERT: B 347 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7458 (ttm) REVERT: B 354 TYR cc_start: 0.8354 (m-80) cc_final: 0.7953 (m-80) REVERT: B 360 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.6634 (mp10) REVERT: B 389 MET cc_start: 0.7877 (tpp) cc_final: 0.7582 (mmm) REVERT: B 431 LEU cc_start: 0.8543 (mp) cc_final: 0.8316 (mt) REVERT: B 433 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: B 476 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7293 (m-30) outliers start: 70 outliers final: 45 residues processed: 388 average time/residue: 0.6285 time to fit residues: 262.9202 Evaluate side-chains 407 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 349 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 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 228 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 435 GLU 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 301 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 380 ASN 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 44 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109739 restraints weight = 16294.381| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.94 r_work: 0.3369 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12286 Z= 0.161 Angle : 0.562 10.269 16671 Z= 0.291 Chirality : 0.043 0.228 1848 Planarity : 0.004 0.057 2120 Dihedral : 7.652 102.959 2110 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.10 % Allowed : 29.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.22), residues: 1457 helix: 2.45 (0.27), residues: 378 sheet: 0.22 (0.30), residues: 309 loop : -1.43 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 91 TYR 0.023 0.002 TYR B 424 PHE 0.010 0.001 PHE B 148 TRP 0.008 0.001 TRP B 127 HIS 0.012 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00379 (12248) covalent geometry : angle 0.55360 (16575) SS BOND : bond 0.00212 ( 18) SS BOND : angle 1.06571 ( 36) hydrogen bonds : bond 0.04931 ( 464) hydrogen bonds : angle 4.36355 ( 1392) glycosidic custom : bond 0.00204 ( 3) glycosidic custom : angle 0.83783 ( 9) link_BETA1-3 : bond 0.00077 ( 3) link_BETA1-3 : angle 1.19799 ( 9) link_BETA1-4 : bond 0.00131 ( 3) link_BETA1-4 : angle 1.92013 ( 9) link_NAG-ASN : bond 0.00214 ( 11) link_NAG-ASN : angle 1.64410 ( 33) *********************** 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 412 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 346 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: C 137 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8402 (mtt90) REVERT: C 157 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8652 (tttm) REVERT: C 321 LEU cc_start: 0.8930 (mp) cc_final: 0.8725 (mt) REVERT: C 435 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: C 493 GLU cc_start: 0.7124 (tp30) cc_final: 0.6882 (tp30) REVERT: C 495 GLU cc_start: 0.7420 (tp30) cc_final: 0.7203 (tp30) REVERT: A 7 GLN cc_start: 0.8241 (mt0) cc_final: 0.7920 (mt0) REVERT: A 48 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7964 (mttp) REVERT: A 131 THR cc_start: 0.8922 (m) cc_final: 0.8577 (t) REVERT: A 384 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 403 LEU cc_start: 0.8739 (mm) cc_final: 0.8537 (mp) REVERT: B 74 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8419 (ptt90) REVERT: B 139 CYS cc_start: 0.7544 (m) cc_final: 0.7031 (m) REVERT: B 157 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8682 (tttp) REVERT: B 336 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7641 (mt) REVERT: B 347 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7417 (ttm) REVERT: B 354 TYR cc_start: 0.8341 (m-80) cc_final: 0.7957 (m-80) REVERT: B 360 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6604 (mp10) REVERT: B 389 MET cc_start: 0.7843 (tpp) cc_final: 0.7590 (mmm) REVERT: B 431 LEU cc_start: 0.8523 (mp) cc_final: 0.8289 (mt) REVERT: B 433 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: B 476 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7236 (m-30) outliers start: 66 outliers final: 43 residues processed: 380 average time/residue: 0.6207 time to fit residues: 254.1677 Evaluate side-chains 404 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 348 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 157 LYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 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 228 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 446 LYS 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 301 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS C 358 ASN C 480 ASN C 499 ASN A 13 HIS A 283 GLN A 296 HIS ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS B 296 HIS B 345 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110802 restraints weight = 16245.919| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.95 r_work: 0.3385 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1276 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= 0.113 Angle : 0.527 11.043 16671 Z= 0.273 Chirality : 0.042 0.212 1848 Planarity : 0.004 0.057 2120 Dihedral : 7.426 102.726 2110 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.71 % Allowed : 29.81 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.22), residues: 1457 helix: 2.54 (0.27), residues: 378 sheet: 0.30 (0.30), residues: 309 loop : -1.36 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 91 TYR 0.016 0.001 TYR C 492 PHE 0.008 0.001 PHE B 148 TRP 0.008 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00254 (12248) covalent geometry : angle 0.52075 (16575) SS BOND : bond 0.00160 ( 18) SS BOND : angle 0.71680 ( 36) hydrogen bonds : bond 0.04535 ( 464) hydrogen bonds : angle 4.26714 ( 1392) glycosidic custom : bond 0.00127 ( 3) glycosidic custom : angle 0.71239 ( 9) link_BETA1-3 : bond 0.00143 ( 3) link_BETA1-3 : angle 0.93645 ( 9) link_BETA1-4 : bond 0.00153 ( 3) link_BETA1-4 : angle 1.76431 ( 9) link_NAG-ASN : bond 0.00208 ( 11) link_NAG-ASN : angle 1.53881 ( 33) *********************** 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 416 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 355 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: C 137 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8107 (mtt90) REVERT: C 321 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8726 (mt) REVERT: C 435 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: C 493 GLU cc_start: 0.7117 (tp30) cc_final: 0.6873 (tp30) REVERT: C 495 GLU cc_start: 0.7398 (tp30) cc_final: 0.7180 (tp30) REVERT: A 7 GLN cc_start: 0.8225 (mt0) cc_final: 0.7902 (mt0) REVERT: A 48 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7969 (mttp) REVERT: A 131 THR cc_start: 0.8918 (m) cc_final: 0.8568 (t) REVERT: A 276 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 354 TYR cc_start: 0.8543 (m-80) cc_final: 0.8303 (m-80) REVERT: A 384 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8667 (p) REVERT: A 388 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8367 (mmtm) REVERT: A 403 LEU cc_start: 0.8725 (mm) cc_final: 0.8521 (mp) REVERT: B 26 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: B 74 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8357 (ptt90) REVERT: B 139 CYS cc_start: 0.7536 (m) cc_final: 0.7011 (m) REVERT: B 347 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7316 (ttm) REVERT: B 354 TYR cc_start: 0.8272 (m-80) cc_final: 0.7957 (m-80) REVERT: B 360 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6574 (mp10) REVERT: B 389 MET cc_start: 0.7753 (tpp) cc_final: 0.7521 (mmm) REVERT: B 431 LEU cc_start: 0.8449 (mp) cc_final: 0.8227 (mt) REVERT: B 476 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7204 (m-30) outliers start: 61 outliers final: 36 residues processed: 384 average time/residue: 0.6479 time to fit residues: 267.0413 Evaluate side-chains 396 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 478 CYS Chi-restraints excluded: chain C residue 497 LYS 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 269 MET Chi-restraints excluded: chain A residue 276 GLU 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 435 GLU Chi-restraints excluded: chain A residue 446 LYS 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 26 GLU 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 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 23 optimal weight: 0.3980 chunk 124 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- 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 380 ASN C 499 ASN A 13 HIS A 160 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110425 restraints weight = 16490.407| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.97 r_work: 0.3381 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12286 Z= 0.125 Angle : 0.538 11.219 16671 Z= 0.279 Chirality : 0.042 0.225 1848 Planarity : 0.004 0.055 2120 Dihedral : 7.288 102.909 2110 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.02 % Allowed : 31.04 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1457 helix: 2.48 (0.27), residues: 378 sheet: 0.38 (0.30), residues: 309 loop : -1.35 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 91 TYR 0.022 0.001 TYR B 424 PHE 0.008 0.001 PHE B 148 TRP 0.008 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00287 (12248) covalent geometry : angle 0.53161 (16575) SS BOND : bond 0.00174 ( 18) SS BOND : angle 0.71359 ( 36) hydrogen bonds : bond 0.04571 ( 464) hydrogen bonds : angle 4.25702 ( 1392) glycosidic custom : bond 0.00132 ( 3) glycosidic custom : angle 0.77927 ( 9) link_BETA1-3 : bond 0.00138 ( 3) link_BETA1-3 : angle 0.91672 ( 9) link_BETA1-4 : bond 0.00145 ( 3) link_BETA1-4 : angle 1.73322 ( 9) link_NAG-ASN : bond 0.00207 ( 11) link_NAG-ASN : angle 1.54196 ( 33) ********************** 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 401 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8373 (mtt90) REVERT: C 321 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8722 (mt) REVERT: C 435 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: C 493 GLU cc_start: 0.7129 (tp30) cc_final: 0.6770 (tp30) REVERT: C 495 GLU cc_start: 0.7408 (tp30) cc_final: 0.7191 (tp30) REVERT: A 7 GLN cc_start: 0.8225 (mt0) cc_final: 0.7873 (mt0) REVERT: A 48 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7963 (mttp) REVERT: A 276 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: A 354 TYR cc_start: 0.8522 (m-80) cc_final: 0.8287 (m-80) REVERT: A 388 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8372 (mmtm) REVERT: A 403 LEU cc_start: 0.8721 (mm) cc_final: 0.8517 (mp) REVERT: B 74 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8413 (ptt90) REVERT: B 139 CYS cc_start: 0.7557 (m) cc_final: 0.7032 (m) REVERT: B 157 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8671 (tttp) REVERT: B 347 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7339 (ttm) REVERT: B 354 TYR cc_start: 0.8308 (m-80) cc_final: 0.7996 (m-80) REVERT: B 360 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.6545 (mp10) REVERT: B 389 MET cc_start: 0.7732 (tpp) cc_final: 0.7501 (mmm) REVERT: B 431 LEU cc_start: 0.8478 (mp) cc_final: 0.8231 (mt) REVERT: B 476 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7297 (m-30) outliers start: 52 outliers final: 36 residues processed: 377 average time/residue: 0.6044 time to fit residues: 245.6298 Evaluate side-chains 390 residues out of total 1295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 478 CYS 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 228 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 435 GLU 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 301 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 123 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.0270 chunk 50 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 106 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS C 358 ASN C 499 ASN A 13 HIS A 160 ASN A 210 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS A 455 GLN A 472 HIS B 296 HIS B 345 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110752 restraints weight = 16371.774| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.95 r_work: 0.3385 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12286 Z= 0.123 Angle : 0.538 11.310 16671 Z= 0.280 Chirality : 0.042 0.218 1848 Planarity : 0.004 0.058 2120 Dihedral : 7.078 102.975 2103 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.17 % Allowed : 30.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.22), residues: 1457 helix: 2.43 (0.27), residues: 378 sheet: 0.41 (0.30), residues: 309 loop : -1.32 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 91 TYR 0.021 0.001 TYR C 449 PHE 0.008 0.001 PHE B 148 TRP 0.009 0.001 TRP B 127 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00284 (12248) covalent geometry : angle 0.53260 (16575) SS BOND : bond 0.00171 ( 18) SS BOND : angle 0.69599 ( 36) hydrogen bonds : bond 0.04531 ( 464) hydrogen bonds : angle 4.30389 ( 1392) glycosidic custom : bond 0.00077 ( 3) glycosidic custom : angle 0.76616 ( 9) link_BETA1-3 : bond 0.00145 ( 3) link_BETA1-3 : angle 0.86647 ( 9) link_BETA1-4 : bond 0.00142 ( 3) link_BETA1-4 : angle 1.69545 ( 9) link_NAG-ASN : bond 0.00204 ( 11) link_NAG-ASN : angle 1.52698 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5725.14 seconds wall clock time: 97 minutes 59.93 seconds (5879.93 seconds total)