Starting phenix.real_space_refine on Sat Oct 11 05:14:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xg1_38311/10_2025/8xg1_38311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xg1_38311/10_2025/8xg1_38311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xg1_38311/10_2025/8xg1_38311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xg1_38311/10_2025/8xg1_38311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xg1_38311/10_2025/8xg1_38311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xg1_38311/10_2025/8xg1_38311.map" } resolution = 2.53 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 75 5.16 5 C 7495 2.51 5 N 2009 2.21 5 O 2362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11941 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.95, per 1000 atoms: 0.25 Number of scatterers: 11941 At special positions: 0 Unit cell: (87.55, 87.55, 149.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2362 8.00 N 2009 7.00 C 7495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " GAL D 1 " - " NAG D 2 " " GAL E 1 " - " NAG E 2 " " GAL F 1 " - " NAG F 2 " BETA1-4 " NAG D 2 " - " GAL D 3 " " NAG E 2 " - " GAL E 3 " " NAG F 2 " - " GAL F 3 " BETA2-6 " GAL D 3 " - " SIA D 4 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL E 3 " - " SIA E 4 " " GAL F 3 " - " SIA F 4 " NAG-ASN " NAG A 601 " - " ASN A 16 " " NAG A 602 " - " ASN A 28 " " NAG A 603 " - " ASN A 169 " " NAG B 601 " - " ASN B 16 " " NAG B 602 " - " ASN B 28 " " NAG B 603 " - " ASN B 169 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 169 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 432.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 32 sheets defined 27.1% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.915A pdb=" N ASP A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 387 Processing helix chain 'A' and resid 404 through 457 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.806A pdb=" N ASN A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.723A pdb=" N LEU B 75 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 76 " --> pdb=" O ASP B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 76' Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.688A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 368 through 387 Processing helix chain 'B' and resid 405 through 457 removed outlier: 3.586A pdb=" N GLU B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.718A pdb=" N SER B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 187 through 196 removed outlier: 3.546A pdb=" N LEU C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 389 removed outlier: 3.910A pdb=" N MET C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.780A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 445 " --> pdb=" O HIS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 488 through 502 removed outlier: 3.862A pdb=" N TYR C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU C 494 " --> pdb=" O PRO C 490 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 366 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.483A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.414A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS A 115 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG A 263 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 113 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.945A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.551A pdb=" N ALA A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N LYS A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.527A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.651A pdb=" N GLY B 361 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.404A pdb=" N GLU B 19 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB5, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 49 removed outlier: 7.763A pdb=" N LEU B 46 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR B 280 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS B 48 " --> pdb=" O THR B 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.658A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.607A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N HIS B 115 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG B 263 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 113 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.607A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.333A pdb=" N ALA B 138 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N LYS B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 364 removed outlier: 3.584A pdb=" N GLY C 361 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AC6, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC7, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AC8, first strand: chain 'C' and resid 48 through 49 removed outlier: 5.903A pdb=" N LYS C 48 " --> pdb=" O THR C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.763A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.752A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS C 115 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG C 263 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 113 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.752A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.386A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 287 through 288 499 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3873 1.35 - 1.47: 2965 1.47 - 1.59: 5256 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 12208 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C6 GAL E 3 " pdb=" O6 GAL E 3 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 12203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.06: 16498 6.06 - 12.12: 6 12.12 - 18.19: 5 18.19 - 24.25: 4 24.25 - 30.31: 1 Bond angle restraints: 16514 Sorted by residual: angle pdb=" C2 GAL F 1 " pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 107.49 137.80 -30.31 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C5 GAL D 3 " pdb=" C6 GAL D 3 " pdb=" O6 GAL D 3 " ideal model delta sigma weight residual 109.08 133.08 -24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sigma weight residual 107.29 130.01 -22.72 3.00e+00 1.11e-01 5.74e+01 angle pdb=" C5 NAG E 2 " pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 111.70 89.43 22.27 3.00e+00 1.11e-01 5.51e+01 angle pdb=" C5 GAL F 3 " pdb=" C6 GAL F 3 " pdb=" O6 GAL F 3 " ideal model delta sigma weight residual 109.08 130.86 -21.78 3.00e+00 1.11e-01 5.27e+01 ... (remaining 16509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 6575 22.40 - 44.80: 806 44.80 - 67.21: 213 67.21 - 89.61: 27 89.61 - 112.01: 8 Dihedral angle restraints: 7629 sinusoidal: 3414 harmonic: 4215 Sorted by residual: dihedral pdb=" CB CYS A 47 " pdb=" SG CYS A 47 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual -86.00 -8.76 -77.24 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 72 " pdb=" CB CYS A 72 " ideal model delta sinusoidal sigma weight residual -86.00 -137.37 51.37 1 1.00e+01 1.00e-02 3.61e+01 dihedral pdb=" CB CYS C 60 " pdb=" SG CYS C 60 " pdb=" SG CYS C 72 " pdb=" CB CYS C 72 " ideal model delta sinusoidal sigma weight residual 93.00 134.38 -41.38 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 7626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 1815 0.214 - 0.427: 1 0.427 - 0.641: 1 0.641 - 0.855: 1 0.855 - 1.068: 1 Chirality restraints: 1819 Sorted by residual: chirality pdb=" C2 SIA E 4 " pdb=" O6 GAL E 3 " pdb=" C1 SIA E 4 " pdb=" O6 SIA E 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.70 0.20 2.00e-02 2.50e+03 9.91e+01 chirality pdb=" C2 SIA F 4 " pdb=" O6 GAL F 3 " pdb=" C1 SIA F 4 " pdb=" O6 SIA F 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.65 0.15 2.00e-02 2.50e+03 5.91e+01 chirality pdb=" C2 SIA D 4 " pdb=" O6 GAL D 3 " pdb=" C1 SIA D 4 " pdb=" O6 SIA D 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.65 0.15 2.00e-02 2.50e+03 5.58e+01 ... (remaining 1816 not shown) Planarity restraints: 2119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 458 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C ASP A 458 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP A 458 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A 459 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 306 " 0.028 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 307 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 489 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 490 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " -0.022 5.00e-02 4.00e+02 ... (remaining 2116 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1047 2.74 - 3.28: 10559 3.28 - 3.82: 19229 3.82 - 4.36: 23223 4.36 - 4.90: 40736 Nonbonded interactions: 94794 Sorted by model distance: nonbonded pdb=" O SER B 443 " pdb=" ND2 ASN B 447 " model vdw 2.199 3.120 nonbonded pdb=" OE1 GLU C 39 " pdb=" OG1 THR C 291 " model vdw 2.208 3.040 nonbonded pdb=" O SER C 142 " pdb=" OG SER C 142 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASN A 484 " pdb=" OG1 THR A 486 " model vdw 2.231 3.040 nonbonded pdb=" O6 SIA F 4 " pdb=" O8 SIA F 4 " model vdw 2.232 3.040 ... (remaining 94789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 602) selection = (chain 'B' and resid 6 through 602) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12243 Z= 0.187 Angle : 0.953 41.725 16601 Z= 0.404 Chirality : 0.056 1.068 1819 Planarity : 0.004 0.046 2111 Dihedral : 19.938 112.008 4881 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.51 % Allowed : 31.24 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1452 helix: 2.03 (0.28), residues: 366 sheet: 0.45 (0.29), residues: 303 loop : -1.77 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 91 TYR 0.012 0.001 TYR A 12 PHE 0.021 0.001 PHE C 440 TRP 0.008 0.001 TRP B 422 HIS 0.013 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00377 (12208) covalent geometry : angle 0.81984 (16514) SS BOND : bond 0.00326 ( 18) SS BOND : angle 1.81554 ( 36) hydrogen bonds : bond 0.12444 ( 467) hydrogen bonds : angle 6.13701 ( 1392) glycosidic custom : bond 0.06086 ( 3) glycosidic custom : angle 7.78764 ( 9) link_BETA1-3 : bond 0.04901 ( 3) link_BETA1-3 : angle 16.77731 ( 9) link_BETA1-4 : bond 0.03966 ( 3) link_BETA1-4 : angle 8.30519 ( 9) link_NAG-ASN : bond 0.01090 ( 8) link_NAG-ASN : angle 2.51117 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 376 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.7301 (tmm) cc_final: 0.6881 (tmm) REVERT: A 457 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7986 (mtm180) REVERT: B 151 MET cc_start: 0.8995 (mmp) cc_final: 0.7946 (mmt) outliers start: 58 outliers final: 47 residues processed: 419 average time/residue: 0.5962 time to fit residues: 267.7364 Evaluate side-chains 396 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 349 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 488 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 196 GLN B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN C 13 HIS C 224 ASN C 360 GLN C 380 ASN C 409 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.124251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112301 restraints weight = 15779.579| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.75 r_work: 0.3436 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12243 Z= 0.224 Angle : 0.620 10.170 16601 Z= 0.316 Chirality : 0.045 0.165 1819 Planarity : 0.005 0.044 2111 Dihedral : 9.775 90.680 2096 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.58 % Allowed : 27.74 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.40 (0.21), residues: 1452 helix: 1.97 (0.27), residues: 375 sheet: 0.43 (0.29), residues: 303 loop : -1.80 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 91 TYR 0.018 0.002 TYR A 12 PHE 0.031 0.002 PHE C 440 TRP 0.010 0.001 TRP C 81 HIS 0.012 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00534 (12208) covalent geometry : angle 0.60171 (16514) SS BOND : bond 0.00366 ( 18) SS BOND : angle 1.22316 ( 36) hydrogen bonds : bond 0.05696 ( 467) hydrogen bonds : angle 4.98180 ( 1392) glycosidic custom : bond 0.00480 ( 3) glycosidic custom : angle 1.94195 ( 9) link_BETA1-3 : bond 0.00336 ( 3) link_BETA1-3 : angle 1.63729 ( 9) link_BETA1-4 : bond 0.00398 ( 3) link_BETA1-4 : angle 2.61024 ( 9) link_NAG-ASN : bond 0.00692 ( 8) link_NAG-ASN : angle 3.03703 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 382 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8233 (tmm-80) cc_final: 0.7913 (ttp80) REVERT: A 272 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: A 389 MET cc_start: 0.7349 (mmm) cc_final: 0.7020 (tmm) REVERT: A 458 ASP cc_start: 0.7771 (t0) cc_final: 0.7245 (t0) REVERT: A 491 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8311 (ttmm) REVERT: A 500 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7820 (ttm170) REVERT: B 91 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7962 (ttp80) REVERT: B 376 ASP cc_start: 0.8087 (m-30) cc_final: 0.7847 (m-30) REVERT: B 494 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: C 216 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: C 409 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8446 (t0) outliers start: 59 outliers final: 34 residues processed: 411 average time/residue: 0.5942 time to fit residues: 261.5320 Evaluate side-chains 398 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 360 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 356 HIS B 380 ASN C 224 ASN C 360 GLN C 409 ASN C 459 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113375 restraints weight = 15848.735| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.75 r_work: 0.3446 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12243 Z= 0.150 Angle : 0.565 9.002 16601 Z= 0.291 Chirality : 0.042 0.145 1819 Planarity : 0.004 0.041 2111 Dihedral : 8.674 92.401 2047 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.35 % Allowed : 28.05 % Favored : 67.60 % 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: -0.29 (0.21), residues: 1452 helix: 2.13 (0.27), residues: 375 sheet: 0.43 (0.29), residues: 303 loop : -1.73 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 91 TYR 0.013 0.001 TYR A 12 PHE 0.025 0.001 PHE C 440 TRP 0.008 0.001 TRP C 81 HIS 0.012 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00349 (12208) covalent geometry : angle 0.54802 (16514) SS BOND : bond 0.00306 ( 18) SS BOND : angle 1.29554 ( 36) hydrogen bonds : bond 0.05223 ( 467) hydrogen bonds : angle 4.82159 ( 1392) glycosidic custom : bond 0.00299 ( 3) glycosidic custom : angle 0.78608 ( 9) link_BETA1-3 : bond 0.00224 ( 3) link_BETA1-3 : angle 1.24633 ( 9) link_BETA1-4 : bond 0.00048 ( 3) link_BETA1-4 : angle 2.49047 ( 9) link_NAG-ASN : bond 0.01005 ( 8) link_NAG-ASN : angle 2.86148 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 370 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8202 (tmm-80) cc_final: 0.7906 (ttp80) REVERT: A 272 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: A 389 MET cc_start: 0.7313 (mmm) cc_final: 0.7053 (tmm) REVERT: A 458 ASP cc_start: 0.7879 (t0) cc_final: 0.7326 (t0) REVERT: A 500 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7866 (ttm170) REVERT: B 91 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7899 (ttp80) outliers start: 56 outliers final: 35 residues processed: 397 average time/residue: 0.6054 time to fit residues: 256.7722 Evaluate side-chains 403 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 367 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN A 299 HIS B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN C 224 ASN C 360 GLN C 392 GLN C 459 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114307 restraints weight = 15833.955| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.76 r_work: 0.3466 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12243 Z= 0.110 Angle : 0.528 10.772 16601 Z= 0.271 Chirality : 0.041 0.131 1819 Planarity : 0.004 0.037 2111 Dihedral : 7.954 92.345 2037 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.81 % Allowed : 29.29 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.09 (0.22), residues: 1452 helix: 2.35 (0.27), residues: 375 sheet: 0.51 (0.30), residues: 288 loop : -1.58 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 74 TYR 0.010 0.001 TYR B 92 PHE 0.018 0.001 PHE C 440 TRP 0.007 0.001 TRP C 81 HIS 0.013 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00243 (12208) covalent geometry : angle 0.51180 (16514) SS BOND : bond 0.00253 ( 18) SS BOND : angle 1.15140 ( 36) hydrogen bonds : bond 0.04698 ( 467) hydrogen bonds : angle 4.63430 ( 1392) glycosidic custom : bond 0.00063 ( 3) glycosidic custom : angle 0.48537 ( 9) link_BETA1-3 : bond 0.00254 ( 3) link_BETA1-3 : angle 0.85848 ( 9) link_BETA1-4 : bond 0.00083 ( 3) link_BETA1-4 : angle 2.11767 ( 9) link_NAG-ASN : bond 0.00669 ( 8) link_NAG-ASN : angle 2.92900 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 379 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8220 (tmm-80) cc_final: 0.7962 (ttp80) REVERT: A 308 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7353 (mmtt) REVERT: A 389 MET cc_start: 0.7306 (mmm) cc_final: 0.7102 (tmm) REVERT: A 424 TYR cc_start: 0.8012 (t80) cc_final: 0.7792 (t80) REVERT: A 458 ASP cc_start: 0.7928 (t0) cc_final: 0.7202 (t0) REVERT: A 500 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7629 (ttm170) REVERT: B 376 ASP cc_start: 0.8106 (m-30) cc_final: 0.7851 (m-30) REVERT: C 73 ASP cc_start: 0.8315 (m-30) cc_final: 0.8114 (m-30) REVERT: C 91 ARG cc_start: 0.8014 (ttt180) cc_final: 0.7673 (ttt180) REVERT: C 409 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8336 (t0) outliers start: 49 outliers final: 28 residues processed: 403 average time/residue: 0.6287 time to fit residues: 270.6293 Evaluate side-chains 386 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 357 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 13 HIS B 165 GLN B 191 GLN B 356 HIS B 380 ASN C 196 GLN C 224 ASN C 360 GLN C 380 ASN C 459 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.124395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112555 restraints weight = 16088.228| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.76 r_work: 0.3446 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12243 Z= 0.162 Angle : 0.556 9.967 16601 Z= 0.286 Chirality : 0.043 0.147 1819 Planarity : 0.004 0.047 2111 Dihedral : 7.771 91.557 2032 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.27 % Allowed : 29.14 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1452 helix: 2.32 (0.27), residues: 375 sheet: 0.52 (0.29), residues: 303 loop : -1.65 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 91 TYR 0.015 0.001 TYR A 12 PHE 0.025 0.001 PHE C 440 TRP 0.008 0.001 TRP C 65 HIS 0.013 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00383 (12208) covalent geometry : angle 0.53991 (16514) SS BOND : bond 0.00303 ( 18) SS BOND : angle 1.11927 ( 36) hydrogen bonds : bond 0.05003 ( 467) hydrogen bonds : angle 4.62770 ( 1392) glycosidic custom : bond 0.00135 ( 3) glycosidic custom : angle 0.59870 ( 9) link_BETA1-3 : bond 0.00209 ( 3) link_BETA1-3 : angle 0.88173 ( 9) link_BETA1-4 : bond 0.00138 ( 3) link_BETA1-4 : angle 2.17914 ( 9) link_NAG-ASN : bond 0.00688 ( 8) link_NAG-ASN : angle 2.99255 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 365 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8213 (tmm-80) cc_final: 0.7958 (ttp80) REVERT: A 272 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: A 308 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7374 (mmtt) REVERT: A 376 ASP cc_start: 0.7938 (m-30) cc_final: 0.7722 (m-30) REVERT: A 387 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: A 458 ASP cc_start: 0.7994 (t0) cc_final: 0.7248 (t0) REVERT: A 500 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7708 (ttm170) REVERT: C 20 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7980 (mmtt) REVERT: C 73 ASP cc_start: 0.8319 (m-30) cc_final: 0.8106 (m-30) REVERT: C 91 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7761 (ttt180) REVERT: C 409 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8339 (t0) outliers start: 55 outliers final: 37 residues processed: 390 average time/residue: 0.6092 time to fit residues: 254.2912 Evaluate side-chains 398 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 140 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN C 196 GLN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN C 459 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112343 restraints weight = 16087.107| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.76 r_work: 0.3437 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12243 Z= 0.173 Angle : 0.563 7.026 16601 Z= 0.292 Chirality : 0.043 0.260 1819 Planarity : 0.004 0.041 2111 Dihedral : 7.706 91.303 2031 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.43 % Allowed : 29.14 % Favored : 66.43 % 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: 1452 helix: 2.28 (0.27), residues: 375 sheet: 0.50 (0.29), residues: 303 loop : -1.64 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 91 TYR 0.015 0.001 TYR A 12 PHE 0.027 0.002 PHE C 440 TRP 0.008 0.001 TRP C 65 HIS 0.014 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00409 (12208) covalent geometry : angle 0.55468 (16514) SS BOND : bond 0.00337 ( 18) SS BOND : angle 1.31711 ( 36) hydrogen bonds : bond 0.05131 ( 467) hydrogen bonds : angle 4.65596 ( 1392) glycosidic custom : bond 0.00174 ( 3) glycosidic custom : angle 0.62214 ( 9) link_BETA1-3 : bond 0.00140 ( 3) link_BETA1-3 : angle 0.83157 ( 9) link_BETA1-4 : bond 0.00169 ( 3) link_BETA1-4 : angle 2.20185 ( 9) link_NAG-ASN : bond 0.00399 ( 8) link_NAG-ASN : angle 1.57193 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 373 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: A 308 LYS cc_start: 0.7636 (mmtt) cc_final: 0.7381 (mmtt) REVERT: A 387 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 458 ASP cc_start: 0.8049 (t0) cc_final: 0.7278 (t0) REVERT: A 500 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7694 (ttm170) REVERT: B 91 ARG cc_start: 0.8247 (ttp80) cc_final: 0.8020 (ttp80) REVERT: C 20 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7978 (mmtt) REVERT: C 91 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7793 (ttt180) REVERT: C 216 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7206 (pt0) REVERT: C 272 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8170 (mm-30) outliers start: 57 outliers final: 37 residues processed: 398 average time/residue: 0.6145 time to fit residues: 261.7453 Evaluate side-chains 405 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 364 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 356 HIS B 380 ASN C 196 GLN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111991 restraints weight = 16040.242| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.74 r_work: 0.3435 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12243 Z= 0.194 Angle : 0.590 10.953 16601 Z= 0.306 Chirality : 0.044 0.226 1819 Planarity : 0.004 0.042 2111 Dihedral : 7.601 92.062 2028 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.13 % Allowed : 29.06 % Favored : 65.81 % 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: -0.19 (0.22), residues: 1452 helix: 2.22 (0.27), residues: 375 sheet: 0.47 (0.29), residues: 303 loop : -1.67 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 91 TYR 0.017 0.001 TYR A 12 PHE 0.029 0.002 PHE C 440 TRP 0.009 0.001 TRP C 65 HIS 0.013 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00463 (12208) covalent geometry : angle 0.57959 (16514) SS BOND : bond 0.00377 ( 18) SS BOND : angle 1.72414 ( 36) hydrogen bonds : bond 0.05281 ( 467) hydrogen bonds : angle 4.68416 ( 1392) glycosidic custom : bond 0.00211 ( 3) glycosidic custom : angle 0.64651 ( 9) link_BETA1-3 : bond 0.00161 ( 3) link_BETA1-3 : angle 0.84917 ( 9) link_BETA1-4 : bond 0.00233 ( 3) link_BETA1-4 : angle 2.25724 ( 9) link_NAG-ASN : bond 0.00194 ( 8) link_NAG-ASN : angle 1.70432 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 368 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8217 (tmm-80) cc_final: 0.7942 (ttp80) REVERT: A 272 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 376 ASP cc_start: 0.7924 (m-30) cc_final: 0.7686 (m-30) REVERT: A 387 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: A 458 ASP cc_start: 0.8050 (t0) cc_final: 0.7278 (t0) REVERT: A 486 THR cc_start: 0.8840 (p) cc_final: 0.8623 (p) REVERT: A 500 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7719 (ttm170) REVERT: C 20 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7969 (mmtt) REVERT: C 91 ARG cc_start: 0.8073 (ttt180) cc_final: 0.7781 (ttt180) REVERT: C 272 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: C 497 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7429 (mtpt) outliers start: 66 outliers final: 44 residues processed: 396 average time/residue: 0.6187 time to fit residues: 261.7527 Evaluate side-chains 411 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 363 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 128 optimal weight: 0.0040 chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.0030 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN C 196 GLN C 224 ASN C 360 GLN C 380 ASN C 459 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113532 restraints weight = 15901.522| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.76 r_work: 0.3456 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12243 Z= 0.116 Angle : 0.548 11.670 16601 Z= 0.284 Chirality : 0.042 0.209 1819 Planarity : 0.004 0.037 2111 Dihedral : 7.348 92.400 2028 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.89 % Allowed : 30.61 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1452 helix: 2.41 (0.27), residues: 375 sheet: 0.51 (0.30), residues: 288 loop : -1.53 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 91 TYR 0.010 0.001 TYR A 12 PHE 0.018 0.001 PHE C 440 TRP 0.007 0.001 TRP A 422 HIS 0.012 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00261 (12208) covalent geometry : angle 0.54114 (16514) SS BOND : bond 0.00274 ( 18) SS BOND : angle 1.43471 ( 36) hydrogen bonds : bond 0.04666 ( 467) hydrogen bonds : angle 4.55974 ( 1392) glycosidic custom : bond 0.00111 ( 3) glycosidic custom : angle 0.58600 ( 9) link_BETA1-3 : bond 0.00257 ( 3) link_BETA1-3 : angle 0.63797 ( 9) link_BETA1-4 : bond 0.00059 ( 3) link_BETA1-4 : angle 1.98547 ( 9) link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 1.29472 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 361 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7708 (mmt-90) REVERT: A 91 ARG cc_start: 0.8173 (tmm-80) cc_final: 0.7909 (ttp80) REVERT: A 387 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: A 458 ASP cc_start: 0.8027 (t0) cc_final: 0.7200 (t0) REVERT: A 486 THR cc_start: 0.8821 (p) cc_final: 0.8592 (p) REVERT: A 500 ARG cc_start: 0.8256 (ttm170) cc_final: 0.7690 (ttm170) REVERT: C 73 ASP cc_start: 0.8313 (m-30) cc_final: 0.8107 (m-30) REVERT: C 91 ARG cc_start: 0.8074 (ttt180) cc_final: 0.7785 (ttt180) REVERT: C 375 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: C 389 MET cc_start: 0.7280 (mmt) cc_final: 0.6974 (mmp) REVERT: C 497 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7418 (mtpt) outliers start: 50 outliers final: 34 residues processed: 386 average time/residue: 0.6339 time to fit residues: 261.2785 Evaluate side-chains 400 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 363 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 138 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 356 HIS B 380 ASN B 447 ASN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN C 459 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112876 restraints weight = 15887.451| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.75 r_work: 0.3445 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12243 Z= 0.164 Angle : 0.588 14.936 16601 Z= 0.304 Chirality : 0.043 0.194 1819 Planarity : 0.004 0.039 2111 Dihedral : 7.351 92.859 2028 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.42 % Allowed : 31.55 % Favored : 65.03 % 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: 1452 helix: 2.28 (0.27), residues: 375 sheet: 0.52 (0.29), residues: 303 loop : -1.63 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 126 TYR 0.014 0.001 TYR A 12 PHE 0.025 0.002 PHE C 440 TRP 0.008 0.001 TRP C 65 HIS 0.014 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00389 (12208) covalent geometry : angle 0.58012 (16514) SS BOND : bond 0.00334 ( 18) SS BOND : angle 1.49800 ( 36) hydrogen bonds : bond 0.05022 ( 467) hydrogen bonds : angle 4.60423 ( 1392) glycosidic custom : bond 0.00097 ( 3) glycosidic custom : angle 0.64581 ( 9) link_BETA1-3 : bond 0.00171 ( 3) link_BETA1-3 : angle 0.72328 ( 9) link_BETA1-4 : bond 0.00152 ( 3) link_BETA1-4 : angle 2.08625 ( 9) link_NAG-ASN : bond 0.00193 ( 8) link_NAG-ASN : angle 1.40406 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 376 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7925 (ttp80) REVERT: A 308 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7388 (mmtt) REVERT: A 387 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: A 458 ASP cc_start: 0.8057 (t0) cc_final: 0.7251 (t0) REVERT: A 486 THR cc_start: 0.8818 (p) cc_final: 0.8603 (p) REVERT: A 500 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7740 (ttm170) REVERT: C 20 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7969 (mmtt) REVERT: C 91 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7785 (ttt180) REVERT: C 212 ARG cc_start: 0.8682 (ttt-90) cc_final: 0.8455 (ttt-90) REVERT: C 347 MET cc_start: 0.8227 (ttp) cc_final: 0.8014 (ttp) REVERT: C 375 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: C 389 MET cc_start: 0.7322 (mmt) cc_final: 0.6962 (mmp) REVERT: C 497 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7408 (mtpt) outliers start: 44 outliers final: 36 residues processed: 396 average time/residue: 0.6442 time to fit residues: 272.1515 Evaluate side-chains 400 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 361 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN B 165 GLN B 191 GLN B 196 GLN B 356 HIS B 380 ASN B 447 ASN C 196 GLN C 224 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN C 459 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.124700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112901 restraints weight = 15983.343| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.76 r_work: 0.3445 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12243 Z= 0.165 Angle : 0.615 18.505 16601 Z= 0.317 Chirality : 0.044 0.190 1819 Planarity : 0.004 0.043 2111 Dihedral : 7.371 92.978 2028 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.50 % Allowed : 31.55 % Favored : 64.96 % 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: 1452 helix: 2.26 (0.27), residues: 375 sheet: 0.52 (0.29), residues: 303 loop : -1.63 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 74 TYR 0.015 0.001 TYR A 12 PHE 0.025 0.001 PHE C 440 TRP 0.008 0.001 TRP C 81 HIS 0.013 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00393 (12208) covalent geometry : angle 0.60703 (16514) SS BOND : bond 0.00328 ( 18) SS BOND : angle 1.55401 ( 36) hydrogen bonds : bond 0.05050 ( 467) hydrogen bonds : angle 4.63996 ( 1392) glycosidic custom : bond 0.00128 ( 3) glycosidic custom : angle 0.63342 ( 9) link_BETA1-3 : bond 0.00197 ( 3) link_BETA1-3 : angle 0.71452 ( 9) link_BETA1-4 : bond 0.00137 ( 3) link_BETA1-4 : angle 2.09903 ( 9) link_NAG-ASN : bond 0.00222 ( 8) link_NAG-ASN : angle 1.52326 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 355 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8176 (tmm-80) cc_final: 0.7912 (ttp80) REVERT: A 308 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7405 (mmtt) REVERT: A 347 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7149 (tmm) REVERT: A 387 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: A 458 ASP cc_start: 0.8045 (t0) cc_final: 0.7238 (t0) REVERT: A 486 THR cc_start: 0.8821 (p) cc_final: 0.8596 (p) REVERT: A 500 ARG cc_start: 0.8301 (ttm170) cc_final: 0.7740 (ttm170) REVERT: B 77 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7213 (mtm-85) REVERT: C 20 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7978 (mmtt) REVERT: C 91 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7759 (ttt180) REVERT: C 212 ARG cc_start: 0.8686 (ttt-90) cc_final: 0.8453 (ttt-90) REVERT: C 389 MET cc_start: 0.7327 (mmt) cc_final: 0.6976 (mmp) REVERT: C 497 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7399 (mtpt) outliers start: 45 outliers final: 37 residues processed: 379 average time/residue: 0.6034 time to fit residues: 244.6178 Evaluate side-chains 390 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 350 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.0670 chunk 58 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 175 GLN A 196 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 191 GLN B 356 HIS B 380 ASN B 447 ASN C 224 ASN C 355 HIS ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN C 459 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113476 restraints weight = 16025.565| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.75 r_work: 0.3457 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12243 Z= 0.130 Angle : 0.594 17.569 16601 Z= 0.305 Chirality : 0.042 0.177 1819 Planarity : 0.004 0.041 2111 Dihedral : 7.311 92.960 2028 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.26 % Allowed : 31.86 % Favored : 64.88 % 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: -0.12 (0.22), residues: 1452 helix: 2.30 (0.27), residues: 375 sheet: 0.39 (0.29), residues: 309 loop : -1.59 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 91 TYR 0.011 0.001 TYR A 12 PHE 0.021 0.001 PHE C 440 TRP 0.007 0.001 TRP C 81 HIS 0.013 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00300 (12208) covalent geometry : angle 0.58658 (16514) SS BOND : bond 0.00283 ( 18) SS BOND : angle 1.45290 ( 36) hydrogen bonds : bond 0.04821 ( 467) hydrogen bonds : angle 4.59860 ( 1392) glycosidic custom : bond 0.00056 ( 3) glycosidic custom : angle 0.63084 ( 9) link_BETA1-3 : bond 0.00212 ( 3) link_BETA1-3 : angle 0.63852 ( 9) link_BETA1-4 : bond 0.00059 ( 3) link_BETA1-4 : angle 1.97996 ( 9) link_NAG-ASN : bond 0.00445 ( 8) link_NAG-ASN : angle 1.41568 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5487.94 seconds wall clock time: 93 minutes 54.72 seconds (5634.72 seconds total)