Starting phenix.real_space_refine on Sat May 17 22:59:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7b_29805/05_2025/8g7b_29805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7b_29805/05_2025/8g7b_29805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7b_29805/05_2025/8g7b_29805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7b_29805/05_2025/8g7b_29805.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7b_29805/05_2025/8g7b_29805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7b_29805/05_2025/8g7b_29805.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 916 atoms to isotropic. 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 64 5.16 5 C 9866 2.51 5 N 2568 2.21 5 O 2908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15406 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4518 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 31, 'TRANS': 534} Chain breaks: 2 Chain: "B" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4518 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 31, 'TRANS': 534} Chain breaks: 2 Chain: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "D" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4518 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 31, 'TRANS': 534} Chain breaks: 2 Chain: "A" 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 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: "D" 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: 10.45, per 1000 atoms: 0.68 Number of scatterers: 15406 At special positions: 0 Unit cell: (163.52, 148.19, 130.67, 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 64 16.00 O 2908 8.00 N 2568 7.00 C 9866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.01 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.02 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 NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 165 " " NAG D1301 " - " ASN D 331 " " NAG D1302 " - " ASN D 343 " Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 35 sheets defined 7.9% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.963A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.618A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.807A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.781A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.114A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.114A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA E 97 " --> pdb=" O TYR E 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 59 through 60 removed outlier: 7.674A pdb=" N TYR E 59 " --> pdb=" O GLU A 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.435A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.680A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.917A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.718A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.594A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.872A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.981A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.638A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.263A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.837A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.693A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.721A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.905A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.839A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.620A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AC9, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.565A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 104 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.262A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 47 through 55 removed outlier: 7.637A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.653A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.545A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.680A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AD7, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AD8, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.623A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4911 1.34 - 1.47: 4200 1.47 - 1.59: 6617 1.59 - 1.72: 1 1.72 - 1.85: 76 Bond restraints: 15805 Sorted by residual: bond pdb=" CB PRO A 217 " pdb=" CG PRO A 217 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.71e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.366 0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C SER E 30 " pdb=" N PRO E 31 " ideal model delta sigma weight residual 1.331 1.352 -0.022 1.31e-02 5.83e+03 2.73e+00 bond pdb=" CA SER E 30 " pdb=" C SER E 30 " ideal model delta sigma weight residual 1.524 1.544 -0.021 1.26e-02 6.30e+03 2.66e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 15800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 21238 2.88 - 5.76: 241 5.76 - 8.64: 14 8.64 - 11.52: 1 11.52 - 14.39: 1 Bond angle restraints: 21495 Sorted by residual: angle pdb=" CA PRO A 217 " pdb=" N PRO A 217 " pdb=" CD PRO A 217 " ideal model delta sigma weight residual 112.00 97.61 14.39 1.40e+00 5.10e-01 1.06e+02 angle pdb=" N GLY C 108 " pdb=" CA GLY C 108 " pdb=" C GLY C 108 " ideal model delta sigma weight residual 111.95 116.99 -5.04 9.50e-01 1.11e+00 2.81e+01 angle pdb=" N VAL B 350 " pdb=" CA VAL B 350 " pdb=" C VAL B 350 " ideal model delta sigma weight residual 112.29 108.07 4.22 9.40e-01 1.13e+00 2.01e+01 angle pdb=" C SER E 30 " pdb=" CA SER E 30 " pdb=" CB SER E 30 " ideal model delta sigma weight residual 110.17 118.33 -8.16 1.97e+00 2.58e-01 1.72e+01 angle pdb=" N PRO A 217 " pdb=" CD PRO A 217 " pdb=" CG PRO A 217 " ideal model delta sigma weight residual 103.20 97.15 6.05 1.50e+00 4.44e-01 1.63e+01 ... (remaining 21490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 8220 16.47 - 32.95: 896 32.95 - 49.42: 230 49.42 - 65.90: 40 65.90 - 82.37: 22 Dihedral angle restraints: 9408 sinusoidal: 3789 harmonic: 5619 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -12.20 -73.80 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual 93.00 40.03 52.97 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS D 538 " pdb=" SG CYS D 538 " pdb=" SG CYS D 590 " pdb=" CB CYS D 590 " ideal model delta sinusoidal sigma weight residual -86.00 -132.44 46.44 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 9405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2044 0.070 - 0.140: 314 0.140 - 0.211: 18 0.211 - 0.281: 0 0.281 - 0.351: 2 Chirality restraints: 2378 Sorted by residual: chirality pdb=" C1 NAG D1301 " pdb=" ND2 ASN D 331 " pdb=" C2 NAG D1301 " pdb=" O5 NAG D1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 2375 not shown) Planarity restraints: 2783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " -0.118 5.00e-02 4.00e+02 1.66e-01 4.41e+01 pdb=" N PRO A 217 " 0.287 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 560 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO D 561 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 561 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 561 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 140 " -0.014 2.00e-02 2.50e+03 1.83e-02 5.89e+00 pdb=" CG PHE A 140 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 140 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 140 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 140 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 140 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 140 " 0.001 2.00e-02 2.50e+03 ... (remaining 2780 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 151 2.60 - 3.18: 12900 3.18 - 3.75: 22340 3.75 - 4.33: 32475 4.33 - 4.90: 53275 Nonbonded interactions: 121141 Sorted by model distance: nonbonded pdb=" OD1 ASN E 32 " pdb=" OG SER E 53 " model vdw 2.030 3.040 nonbonded pdb=" OG SER B 359 " pdb=" OD1 ASN B 394 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR E 96 " pdb=" OH TYR A 351 " model vdw 2.132 3.040 nonbonded pdb=" NH2 ARG D 454 " pdb=" O SER D 469 " model vdw 2.155 3.120 nonbonded pdb=" OG1 THR B 553 " pdb=" OD1 ASP B 586 " model vdw 2.156 3.040 ... (remaining 121136 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' selection = (chain 'B' and (resid 14 through 592 or resid 1301 through 1302)) selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } 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: 0.010 Normalize map: mean=0, sd=1: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.410 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 0.130 15833 Z= 0.171 Angle : 0.739 14.394 21558 Z= 0.401 Chirality : 0.050 0.351 2378 Planarity : 0.006 0.166 2776 Dihedral : 14.799 82.369 5743 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 0.35 % Allowed : 15.04 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 1906 helix: -2.14 (0.43), residues: 130 sheet: 0.04 (0.21), residues: 584 loop : -1.44 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.009 0.001 HIS A 69 PHE 0.038 0.002 PHE A 140 TYR 0.027 0.002 TYR A 495 ARG 0.009 0.001 ARG E 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 7) link_NAG-ASN : angle 3.30555 ( 21) hydrogen bonds : bond 0.13382 ( 469) hydrogen bonds : angle 8.01886 ( 1221) SS BOND : bond 0.00614 ( 21) SS BOND : angle 0.96303 ( 42) covalent geometry : bond 0.00386 (15805) covalent geometry : angle 0.73134 (21495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: E 25 SER cc_start: 0.6480 (m) cc_final: 0.6253 (p) REVERT: A 190 ARG cc_start: 0.6854 (mtt180) cc_final: 0.6356 (mtm180) REVERT: A 467 ASP cc_start: 0.7054 (t70) cc_final: 0.6275 (t70) outliers start: 6 outliers final: 2 residues processed: 141 average time/residue: 0.2566 time to fit residues: 55.9945 Evaluate side-chains 119 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 582 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0070 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.239055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.168853 restraints weight = 21502.961| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 4.09 r_work: 0.3778 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15833 Z= 0.197 Angle : 0.670 9.698 21558 Z= 0.348 Chirality : 0.049 0.263 2378 Planarity : 0.005 0.084 2776 Dihedral : 6.097 54.888 2250 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.46 % Favored : 95.38 % Rotamer: Outliers : 3.53 % Allowed : 14.28 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 1906 helix: -2.21 (0.42), residues: 132 sheet: -0.10 (0.20), residues: 630 loop : -1.41 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.005 0.001 HIS A 207 PHE 0.023 0.002 PHE D 86 TYR 0.020 0.002 TYR D 265 ARG 0.007 0.001 ARG E 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 7) link_NAG-ASN : angle 3.18698 ( 21) hydrogen bonds : bond 0.03662 ( 469) hydrogen bonds : angle 6.82268 ( 1221) SS BOND : bond 0.00591 ( 21) SS BOND : angle 0.70283 ( 42) covalent geometry : bond 0.00474 (15805) covalent geometry : angle 0.66287 (21495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 1.837 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6491 (m-90) cc_final: 0.6202 (m-90) REVERT: A 118 LEU cc_start: 0.6578 (tt) cc_final: 0.6347 (tp) REVERT: A 190 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7596 (mtm180) REVERT: A 227 VAL cc_start: 0.7370 (p) cc_final: 0.7129 (p) REVERT: A 495 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.5982 (t80) REVERT: B 215 ASP cc_start: 0.6382 (p0) cc_final: 0.6149 (p0) REVERT: B 468 ILE cc_start: 0.4668 (OUTLIER) cc_final: 0.4439 (tt) REVERT: B 510 VAL cc_start: 0.5478 (OUTLIER) cc_final: 0.5183 (t) REVERT: D 63 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8055 (t) REVERT: D 328 ARG cc_start: 0.5885 (OUTLIER) cc_final: 0.5237 (mmt180) REVERT: D 580 GLN cc_start: 0.5102 (OUTLIER) cc_final: 0.4835 (mt0) outliers start: 60 outliers final: 25 residues processed: 181 average time/residue: 0.2693 time to fit residues: 74.1841 Evaluate side-chains 149 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 4.9990 chunk 88 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 114 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 422 ASN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.237918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.165152 restraints weight = 21398.463| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 4.60 r_work: 0.3708 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15833 Z= 0.123 Angle : 0.597 9.272 21558 Z= 0.307 Chirality : 0.046 0.228 2378 Planarity : 0.005 0.076 2776 Dihedral : 5.329 55.382 2246 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.09 % Favored : 95.70 % Rotamer: Outliers : 3.00 % Allowed : 14.98 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 1906 helix: -2.27 (0.39), residues: 145 sheet: 0.06 (0.21), residues: 569 loop : -1.40 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.008 0.001 HIS A 69 PHE 0.022 0.001 PHE D 338 TYR 0.014 0.001 TYR D 265 ARG 0.006 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 7) link_NAG-ASN : angle 2.67801 ( 21) hydrogen bonds : bond 0.03318 ( 469) hydrogen bonds : angle 6.45031 ( 1221) SS BOND : bond 0.00368 ( 21) SS BOND : angle 0.62930 ( 42) covalent geometry : bond 0.00285 (15805) covalent geometry : angle 0.59084 (21495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 1.825 Fit side-chains REVERT: E 29 PHE cc_start: 0.7659 (m-80) cc_final: 0.7318 (m-80) REVERT: E 100 LYS cc_start: 0.7280 (tttt) cc_final: 0.7060 (tttt) REVERT: A 118 LEU cc_start: 0.6459 (tt) cc_final: 0.6160 (tp) REVERT: A 190 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7615 (mtm180) REVERT: A 201 PHE cc_start: 0.4369 (t80) cc_final: 0.4088 (t80) REVERT: A 495 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.5955 (t80) REVERT: A 541 PHE cc_start: 0.8504 (p90) cc_final: 0.8294 (p90) REVERT: B 131 CYS cc_start: 0.5692 (OUTLIER) cc_final: 0.5253 (m) REVERT: B 468 ILE cc_start: 0.4647 (OUTLIER) cc_final: 0.4406 (tt) REVERT: B 558 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7713 (mmtt) REVERT: D 266 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8933 (m-80) REVERT: D 319 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.3250 (ppt90) REVERT: D 580 GLN cc_start: 0.4979 (OUTLIER) cc_final: 0.4662 (mt0) outliers start: 51 outliers final: 30 residues processed: 172 average time/residue: 0.2574 time to fit residues: 67.9180 Evaluate side-chains 150 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 121 optimal weight: 0.2980 chunk 170 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 388 ASN C 5 GLN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.233343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.161493 restraints weight = 21356.520| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 4.18 r_work: 0.3685 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15833 Z= 0.211 Angle : 0.649 9.674 21558 Z= 0.336 Chirality : 0.048 0.231 2378 Planarity : 0.005 0.073 2776 Dihedral : 5.250 53.036 2246 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.14 % Favored : 94.65 % Rotamer: Outliers : 4.17 % Allowed : 14.39 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.18), residues: 1906 helix: -2.30 (0.38), residues: 145 sheet: -0.12 (0.21), residues: 614 loop : -1.39 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.007 0.001 HIS A 69 PHE 0.026 0.002 PHE B 497 TYR 0.022 0.002 TYR D 265 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 7) link_NAG-ASN : angle 2.63670 ( 21) hydrogen bonds : bond 0.03584 ( 469) hydrogen bonds : angle 6.39123 ( 1221) SS BOND : bond 0.00435 ( 21) SS BOND : angle 0.78416 ( 42) covalent geometry : bond 0.00507 (15805) covalent geometry : angle 0.64394 (21495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 125 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7895 (mtm180) REVERT: A 205 SER cc_start: 0.8952 (p) cc_final: 0.8702 (t) REVERT: A 386 LYS cc_start: 0.3728 (mtmt) cc_final: 0.3427 (mtmt) REVERT: A 537 LYS cc_start: 0.7385 (mtpp) cc_final: 0.7117 (tttt) REVERT: B 131 CYS cc_start: 0.5833 (OUTLIER) cc_final: 0.5434 (m) REVERT: D 63 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8115 (t) REVERT: D 319 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.3597 (ppt90) REVERT: D 328 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.4843 (tpp-160) REVERT: D 580 GLN cc_start: 0.5025 (OUTLIER) cc_final: 0.4493 (mt0) outliers start: 71 outliers final: 46 residues processed: 182 average time/residue: 0.2472 time to fit residues: 68.8597 Evaluate side-chains 167 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 62 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 179 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.234725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.162080 restraints weight = 21591.887| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 4.38 r_work: 0.3780 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15833 Z= 0.123 Angle : 0.578 9.373 21558 Z= 0.298 Chirality : 0.046 0.222 2378 Planarity : 0.005 0.071 2776 Dihedral : 5.012 55.082 2246 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 3.47 % Allowed : 15.57 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.18), residues: 1906 helix: -2.26 (0.38), residues: 145 sheet: 0.00 (0.21), residues: 582 loop : -1.34 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.006 0.001 HIS A 69 PHE 0.023 0.001 PHE E 29 TYR 0.015 0.001 TYR D 265 ARG 0.006 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 7) link_NAG-ASN : angle 2.35009 ( 21) hydrogen bonds : bond 0.03119 ( 469) hydrogen bonds : angle 6.24411 ( 1221) SS BOND : bond 0.00295 ( 21) SS BOND : angle 0.68048 ( 42) covalent geometry : bond 0.00289 (15805) covalent geometry : angle 0.57388 (21495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 1.647 Fit side-chains REVERT: A 190 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7885 (mtm180) REVERT: A 226 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.5129 (mp) REVERT: A 386 LYS cc_start: 0.3566 (mtmt) cc_final: 0.3243 (mtmt) REVERT: A 437 ASN cc_start: 0.7882 (t0) cc_final: 0.7347 (t0) REVERT: A 508 TYR cc_start: 0.6567 (m-80) cc_final: 0.6091 (m-80) REVERT: B 131 CYS cc_start: 0.5615 (OUTLIER) cc_final: 0.5373 (m) REVERT: B 558 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7758 (mmtt) REVERT: C 80 LEU cc_start: -0.1203 (OUTLIER) cc_final: -0.1447 (tp) REVERT: D 319 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.3598 (ppt90) REVERT: D 328 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4850 (tpp-160) REVERT: D 571 ASP cc_start: 0.5463 (p0) cc_final: 0.5140 (p0) REVERT: D 580 GLN cc_start: 0.5045 (OUTLIER) cc_final: 0.4558 (mt0) outliers start: 59 outliers final: 42 residues processed: 166 average time/residue: 0.2550 time to fit residues: 65.1270 Evaluate side-chains 159 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 157 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 chunk 102 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 187 optimal weight: 0.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.232585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.160888 restraints weight = 21381.863| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 4.59 r_work: 0.3666 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15833 Z= 0.165 Angle : 0.599 9.688 21558 Z= 0.309 Chirality : 0.047 0.227 2378 Planarity : 0.005 0.068 2776 Dihedral : 4.907 53.555 2246 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.19 % Favored : 94.60 % Rotamer: Outliers : 3.76 % Allowed : 15.86 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1906 helix: -2.00 (0.41), residues: 138 sheet: -0.10 (0.21), residues: 613 loop : -1.34 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.018 0.002 PHE A 400 TYR 0.019 0.001 TYR D 265 ARG 0.011 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 7) link_NAG-ASN : angle 2.23022 ( 21) hydrogen bonds : bond 0.03256 ( 469) hydrogen bonds : angle 6.12787 ( 1221) SS BOND : bond 0.00327 ( 21) SS BOND : angle 0.89925 ( 42) covalent geometry : bond 0.00392 (15805) covalent geometry : angle 0.59408 (21495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 118 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8016 (p0) cc_final: 0.7804 (p0) REVERT: A 190 ARG cc_start: 0.8345 (mtt180) cc_final: 0.8104 (mtm180) REVERT: A 386 LYS cc_start: 0.3661 (mtmt) cc_final: 0.3244 (mtmt) REVERT: B 131 CYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5596 (m) REVERT: B 305 SER cc_start: 0.9354 (t) cc_final: 0.9067 (p) REVERT: B 558 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7863 (mmtt) REVERT: C 80 LEU cc_start: -0.1235 (OUTLIER) cc_final: -0.1478 (tp) REVERT: D 266 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8867 (m-80) REVERT: D 319 ARG cc_start: 0.5231 (OUTLIER) cc_final: 0.3544 (ppt90) REVERT: D 328 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.4913 (tpp-160) REVERT: D 571 ASP cc_start: 0.5643 (p0) cc_final: 0.5228 (p0) REVERT: D 580 GLN cc_start: 0.4843 (OUTLIER) cc_final: 0.4426 (mt0) outliers start: 64 outliers final: 47 residues processed: 172 average time/residue: 0.2494 time to fit residues: 66.0386 Evaluate side-chains 165 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 136 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 187 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.233898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161303 restraints weight = 21490.247| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 4.43 r_work: 0.3729 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15833 Z= 0.119 Angle : 0.565 9.403 21558 Z= 0.291 Chirality : 0.046 0.224 2378 Planarity : 0.005 0.063 2776 Dihedral : 4.807 55.126 2246 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.46 % Favored : 95.33 % Rotamer: Outliers : 3.53 % Allowed : 16.27 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1906 helix: -2.00 (0.40), residues: 138 sheet: 0.03 (0.21), residues: 577 loop : -1.32 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.007 0.001 HIS A 69 PHE 0.017 0.001 PHE A 400 TYR 0.014 0.001 TYR D 265 ARG 0.011 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 7) link_NAG-ASN : angle 2.06281 ( 21) hydrogen bonds : bond 0.03023 ( 469) hydrogen bonds : angle 6.04489 ( 1221) SS BOND : bond 0.00217 ( 21) SS BOND : angle 0.79574 ( 42) covalent geometry : bond 0.00278 (15805) covalent geometry : angle 0.56080 (21495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 117 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7964 (p0) cc_final: 0.7695 (p0) REVERT: A 106 PHE cc_start: 0.4925 (m-80) cc_final: 0.4690 (m-80) REVERT: A 158 ARG cc_start: 0.6237 (OUTLIER) cc_final: 0.5813 (ptp90) REVERT: A 190 ARG cc_start: 0.8317 (mtt180) cc_final: 0.8049 (mtm180) REVERT: A 386 LYS cc_start: 0.3691 (mtmt) cc_final: 0.3333 (mtmt) REVERT: A 508 TYR cc_start: 0.6670 (m-80) cc_final: 0.6145 (m-80) REVERT: B 95 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7957 (p) REVERT: B 102 ARG cc_start: 0.7853 (mmt-90) cc_final: 0.7370 (mpt180) REVERT: B 131 CYS cc_start: 0.5786 (OUTLIER) cc_final: 0.5569 (m) REVERT: B 305 SER cc_start: 0.9324 (t) cc_final: 0.9034 (p) REVERT: B 558 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7831 (mmtm) REVERT: C 80 LEU cc_start: -0.1226 (OUTLIER) cc_final: -0.1488 (tp) REVERT: D 266 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8768 (m-80) REVERT: D 319 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.3551 (ppt90) REVERT: D 328 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.4794 (tpp-160) REVERT: D 580 GLN cc_start: 0.4896 (OUTLIER) cc_final: 0.4504 (mt0) outliers start: 60 outliers final: 42 residues processed: 166 average time/residue: 0.2630 time to fit residues: 65.9701 Evaluate side-chains 162 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.232531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.159793 restraints weight = 21170.767| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 4.56 r_work: 0.3707 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15833 Z= 0.153 Angle : 0.583 9.508 21558 Z= 0.300 Chirality : 0.046 0.228 2378 Planarity : 0.005 0.061 2776 Dihedral : 4.762 54.158 2246 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.04 % Favored : 94.75 % Rotamer: Outliers : 3.58 % Allowed : 16.16 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 1906 helix: -1.88 (0.41), residues: 139 sheet: -0.12 (0.21), residues: 601 loop : -1.27 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.017 0.002 PHE E 67 TYR 0.017 0.001 TYR D 265 ARG 0.009 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 7) link_NAG-ASN : angle 2.00323 ( 21) hydrogen bonds : bond 0.03123 ( 469) hydrogen bonds : angle 5.98367 ( 1221) SS BOND : bond 0.00325 ( 21) SS BOND : angle 0.94782 ( 42) covalent geometry : bond 0.00366 (15805) covalent geometry : angle 0.57859 (21495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 113 time to evaluate : 1.593 Fit side-chains REVERT: A 81 ASN cc_start: 0.8035 (p0) cc_final: 0.7728 (p0) REVERT: A 102 ARG cc_start: 0.6864 (mmm-85) cc_final: 0.6021 (mmm160) REVERT: A 106 PHE cc_start: 0.5053 (m-80) cc_final: 0.4797 (m-80) REVERT: A 190 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8082 (mtm180) REVERT: A 386 LYS cc_start: 0.3722 (mtmt) cc_final: 0.3349 (mtmt) REVERT: A 495 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.4528 (t80) REVERT: A 537 LYS cc_start: 0.7527 (mtpp) cc_final: 0.7270 (ttpt) REVERT: B 95 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8028 (p) REVERT: B 131 CYS cc_start: 0.5858 (OUTLIER) cc_final: 0.5634 (m) REVERT: B 305 SER cc_start: 0.9373 (t) cc_final: 0.9093 (p) REVERT: B 558 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7898 (mmtt) REVERT: C 80 LEU cc_start: -0.1197 (OUTLIER) cc_final: -0.1460 (tp) REVERT: D 266 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8791 (m-80) REVERT: D 319 ARG cc_start: 0.5298 (OUTLIER) cc_final: 0.3605 (ppt90) REVERT: D 328 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.4814 (tpp-160) REVERT: D 580 GLN cc_start: 0.4763 (OUTLIER) cc_final: 0.4397 (mt0) outliers start: 61 outliers final: 48 residues processed: 163 average time/residue: 0.2528 time to fit residues: 63.6833 Evaluate side-chains 166 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 110 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 32 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.231706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.158404 restraints weight = 21333.597| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 4.52 r_work: 0.3654 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15833 Z= 0.170 Angle : 0.592 9.500 21558 Z= 0.306 Chirality : 0.047 0.225 2378 Planarity : 0.005 0.058 2776 Dihedral : 4.826 54.037 2246 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.02 % Rotamer: Outliers : 3.41 % Allowed : 16.92 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1906 helix: -1.82 (0.40), residues: 145 sheet: -0.17 (0.21), residues: 590 loop : -1.23 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.020 0.002 PHE A 86 TYR 0.017 0.001 TYR D 265 ARG 0.009 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 7) link_NAG-ASN : angle 1.93690 ( 21) hydrogen bonds : bond 0.03298 ( 469) hydrogen bonds : angle 5.99976 ( 1221) SS BOND : bond 0.00344 ( 21) SS BOND : angle 0.90729 ( 42) covalent geometry : bond 0.00408 (15805) covalent geometry : angle 0.58858 (21495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 112 time to evaluate : 1.709 Fit side-chains REVERT: A 81 ASN cc_start: 0.8051 (p0) cc_final: 0.7750 (p0) REVERT: A 102 ARG cc_start: 0.6930 (mmm-85) cc_final: 0.6077 (mmm160) REVERT: A 106 PHE cc_start: 0.5173 (m-80) cc_final: 0.4904 (m-80) REVERT: A 170 TYR cc_start: 0.5098 (t80) cc_final: 0.4705 (t80) REVERT: A 190 ARG cc_start: 0.8429 (mtt180) cc_final: 0.8126 (mtm180) REVERT: A 203 ILE cc_start: 0.7483 (tt) cc_final: 0.7125 (tt) REVERT: A 237 ARG cc_start: 0.7353 (ttt-90) cc_final: 0.7124 (ttt90) REVERT: A 386 LYS cc_start: 0.3689 (mtmt) cc_final: 0.3200 (mtmt) REVERT: A 495 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.4616 (t80) REVERT: A 508 TYR cc_start: 0.6742 (m-80) cc_final: 0.6286 (m-80) REVERT: A 537 LYS cc_start: 0.7607 (mtpp) cc_final: 0.7323 (ttpt) REVERT: B 95 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8047 (p) REVERT: B 131 CYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5725 (m) REVERT: B 305 SER cc_start: 0.9382 (t) cc_final: 0.9119 (p) REVERT: B 558 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7860 (mmtm) REVERT: D 266 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8817 (m-80) REVERT: D 319 ARG cc_start: 0.5358 (OUTLIER) cc_final: 0.3537 (ppt90) REVERT: D 328 ARG cc_start: 0.5853 (OUTLIER) cc_final: 0.4692 (tpp80) REVERT: D 580 GLN cc_start: 0.4757 (OUTLIER) cc_final: 0.4430 (mt0) outliers start: 58 outliers final: 46 residues processed: 162 average time/residue: 0.2569 time to fit residues: 63.7107 Evaluate side-chains 162 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 135 optimal weight: 0.0010 chunk 144 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 66 optimal weight: 0.0370 chunk 63 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 185 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.234258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.163078 restraints weight = 21444.362| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 4.50 r_work: 0.3697 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15833 Z= 0.106 Angle : 0.559 9.350 21558 Z= 0.288 Chirality : 0.045 0.223 2378 Planarity : 0.004 0.057 2776 Dihedral : 4.652 55.554 2246 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 2.70 % Allowed : 17.63 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1906 helix: -1.64 (0.43), residues: 132 sheet: -0.02 (0.21), residues: 601 loop : -1.24 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.016 0.001 PHE A 400 TYR 0.012 0.001 TYR D 265 ARG 0.009 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 7) link_NAG-ASN : angle 1.73916 ( 21) hydrogen bonds : bond 0.02900 ( 469) hydrogen bonds : angle 5.90062 ( 1221) SS BOND : bond 0.00242 ( 21) SS BOND : angle 0.71713 ( 42) covalent geometry : bond 0.00245 (15805) covalent geometry : angle 0.55580 (21495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: E 82 MET cc_start: 0.6489 (mpp) cc_final: 0.5591 (pmm) REVERT: A 81 ASN cc_start: 0.8114 (p0) cc_final: 0.7764 (p0) REVERT: A 102 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.6022 (mmm160) REVERT: A 190 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8078 (mtm180) REVERT: A 203 ILE cc_start: 0.7369 (tt) cc_final: 0.7040 (tt) REVERT: A 386 LYS cc_start: 0.3575 (mtmt) cc_final: 0.2999 (mtmt) REVERT: A 495 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.4131 (t80) REVERT: A 508 TYR cc_start: 0.6567 (m-80) cc_final: 0.6143 (m-80) REVERT: A 537 LYS cc_start: 0.7515 (mtpp) cc_final: 0.7257 (ttpt) REVERT: B 95 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7939 (p) REVERT: B 305 SER cc_start: 0.9361 (t) cc_final: 0.9085 (p) REVERT: B 558 LYS cc_start: 0.8284 (mmtm) cc_final: 0.7842 (mmtm) REVERT: D 319 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.3708 (ppt90) REVERT: D 328 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.4674 (tpp80) REVERT: D 580 GLN cc_start: 0.4738 (OUTLIER) cc_final: 0.4422 (mt0) outliers start: 46 outliers final: 36 residues processed: 156 average time/residue: 0.2618 time to fit residues: 62.8138 Evaluate side-chains 152 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.231095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.159254 restraints weight = 21249.350| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 4.09 r_work: 0.3670 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15833 Z= 0.175 Angle : 0.601 9.837 21558 Z= 0.310 Chirality : 0.047 0.235 2378 Planarity : 0.005 0.055 2776 Dihedral : 4.747 53.078 2246 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.19 % Favored : 94.60 % Rotamer: Outliers : 2.64 % Allowed : 17.45 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1906 helix: -1.69 (0.43), residues: 132 sheet: -0.12 (0.21), residues: 587 loop : -1.20 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.019 0.002 PHE D 86 TYR 0.022 0.002 TYR D 265 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 7) link_NAG-ASN : angle 1.82771 ( 21) hydrogen bonds : bond 0.03242 ( 469) hydrogen bonds : angle 5.91661 ( 1221) SS BOND : bond 0.00365 ( 21) SS BOND : angle 1.23103 ( 42) covalent geometry : bond 0.00424 (15805) covalent geometry : angle 0.59685 (21495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10751.56 seconds wall clock time: 185 minutes 59.86 seconds (11159.86 seconds total)