Starting phenix.real_space_refine on Sat Jun 14 14:38:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7b_29805/06_2025/8g7b_29805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7b_29805/06_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_29805/06_2025/8g7b_29805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7b_29805/06_2025/8g7b_29805.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7b_29805/06_2025/8g7b_29805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7b_29805/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.32, per 1000 atoms: 0.73 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: 4.00 Conformation dependent library (CDL) restraints added in 2.1 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: 2.28 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: 5.96 Time building geometry restraints manager: 4.77 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: 0.000 Normalize map: mean=0, sd=1: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.790 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.460 ------------------------------------------------------------------------------- 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 : 1.612 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: 0.2577 time to fit residues: 56.0137 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 : 1.567 ------------------------------------------------------------------------------- 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 = 0.239054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.168906 restraints weight = 21504.681| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 4.06 r_work: 0.3744 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 6.82269 ( 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 : 1.930 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6520 (m-90) cc_final: 0.6240 (m-90) REVERT: A 118 LEU cc_start: 0.6614 (tt) cc_final: 0.6367 (tp) REVERT: A 190 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7618 (mtm180) REVERT: A 227 VAL cc_start: 0.7378 (p) cc_final: 0.7137 (p) REVERT: A 495 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.5961 (t80) REVERT: B 215 ASP cc_start: 0.6388 (p0) cc_final: 0.6151 (p0) REVERT: B 468 ILE cc_start: 0.4687 (OUTLIER) cc_final: 0.4456 (tt) REVERT: B 510 VAL cc_start: 0.5486 (OUTLIER) cc_final: 0.5187 (t) REVERT: D 63 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8043 (t) REVERT: D 328 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.5229 (mmt180) REVERT: D 580 GLN cc_start: 0.5090 (OUTLIER) cc_final: 0.4828 (mt0) outliers start: 60 outliers final: 25 residues processed: 181 average time/residue: 0.2659 time to fit residues: 73.5356 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 : 1.644 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 0.0980 chunk 105 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 114 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.4807 r_free = 0.4807 target = 0.238820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.166186 restraints weight = 21436.677| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 4.07 r_work: 0.3795 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15833 Z= 0.113 Angle : 0.590 9.202 21558 Z= 0.303 Chirality : 0.046 0.226 2378 Planarity : 0.005 0.076 2776 Dihedral : 5.276 55.696 2246 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.99 % Favored : 95.80 % Rotamer: Outliers : 2.64 % Allowed : 15.16 % 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: -1.44 (0.18), residues: 1906 helix: -2.22 (0.40), residues: 139 sheet: 0.08 (0.21), residues: 573 loop : -1.37 (0.17), residues: 1194 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 0.021 0.001 PHE D 338 TYR 0.012 0.001 TYR D 265 ARG 0.007 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 7) link_NAG-ASN : angle 2.61898 ( 21) hydrogen bonds : bond 0.03287 ( 469) hydrogen bonds : angle 6.43695 ( 1221) SS BOND : bond 0.00307 ( 21) SS BOND : angle 0.62437 ( 42) covalent geometry : bond 0.00257 (15805) covalent geometry : angle 0.58480 (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 179 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: E 100 LYS cc_start: 0.7339 (tttt) cc_final: 0.7113 (tttt) REVERT: A 190 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7368 (mtm180) REVERT: A 201 PHE cc_start: 0.4253 (t80) cc_final: 0.4005 (t80) REVERT: A 408 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7508 (tmm160) REVERT: A 495 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.5797 (t80) REVERT: A 541 PHE cc_start: 0.8478 (p90) cc_final: 0.8202 (p90) REVERT: B 131 CYS cc_start: 0.5513 (OUTLIER) cc_final: 0.5057 (m) REVERT: B 468 ILE cc_start: 0.4647 (OUTLIER) cc_final: 0.4405 (tt) REVERT: B 558 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7702 (mmtt) REVERT: D 319 ARG cc_start: 0.4921 (OUTLIER) cc_final: 0.3282 (ppt90) REVERT: D 580 GLN cc_start: 0.5017 (OUTLIER) cc_final: 0.4692 (mt0) outliers start: 45 outliers final: 26 residues processed: 170 average time/residue: 0.2587 time to fit residues: 67.4911 Evaluate side-chains 149 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 408 ARG 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 131 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR 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 210 ILE 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: 5.9990 chunk 157 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 121 optimal weight: 0.2980 chunk 170 optimal weight: 9.9990 chunk 155 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.8704 ------------------------------------------------------------------------------- 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 245 HIS A 394 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 409 GLN C 5 GLN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.230422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.157867 restraints weight = 21299.446| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 4.43 r_work: 0.3660 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 15833 Z= 0.306 Angle : 0.735 11.617 21558 Z= 0.381 Chirality : 0.052 0.234 2378 Planarity : 0.006 0.072 2776 Dihedral : 5.608 50.745 2246 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.24 % Favored : 93.55 % Rotamer: Outliers : 4.35 % Allowed : 14.51 % Favored : 81.14 % 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: -1.67 (0.18), residues: 1906 helix: -2.40 (0.37), residues: 151 sheet: -0.22 (0.21), residues: 582 loop : -1.43 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 64 HIS 0.006 0.001 HIS A 69 PHE 0.025 0.003 PHE A 86 TYR 0.027 0.002 TYR D 265 ARG 0.006 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 7) link_NAG-ASN : angle 2.84572 ( 21) hydrogen bonds : bond 0.04140 ( 469) hydrogen bonds : angle 6.64152 ( 1221) SS BOND : bond 0.00542 ( 21) SS BOND : angle 1.05456 ( 42) covalent geometry : bond 0.00744 (15805) covalent geometry : angle 0.72918 (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 202 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 128 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.4916 (t80) cc_final: 0.4609 (t80) REVERT: A 190 ARG cc_start: 0.8272 (mtt180) cc_final: 0.8043 (mtm180) REVERT: A 226 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5143 (mp) REVERT: A 383 SER cc_start: 0.8708 (m) cc_final: 0.8329 (t) REVERT: A 386 LYS cc_start: 0.3752 (mtmt) cc_final: 0.3484 (mtmt) REVERT: A 408 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7586 (tmm160) REVERT: A 495 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.5995 (t80) REVERT: A 537 LYS cc_start: 0.7575 (mtpp) cc_final: 0.7257 (tttt) REVERT: B 131 CYS cc_start: 0.5842 (OUTLIER) cc_final: 0.5531 (m) REVERT: B 443 SER cc_start: 0.6232 (p) cc_final: 0.6003 (m) REVERT: D 63 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8030 (t) REVERT: D 266 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: D 319 ARG cc_start: 0.5149 (OUTLIER) cc_final: 0.4796 (ppt90) REVERT: D 328 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.4931 (tpp-160) REVERT: D 580 GLN cc_start: 0.5004 (OUTLIER) cc_final: 0.4475 (mt0) outliers start: 74 outliers final: 50 residues processed: 189 average time/residue: 0.2701 time to fit residues: 76.8619 Evaluate side-chains 173 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 115 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 289 VAL Chi-restraints excluded: chain A residue 350 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 495 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 549 THR 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 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 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 160 TYR 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 281 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: 4.9990 chunk 74 optimal weight: 0.9980 chunk 179 optimal weight: 0.1980 chunk 131 optimal weight: 0.0570 chunk 183 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 0.0770 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.234434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.164051 restraints weight = 21586.632| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 4.01 r_work: 0.3722 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15833 Z= 0.116 Angle : 0.583 9.263 21558 Z= 0.302 Chirality : 0.046 0.218 2378 Planarity : 0.005 0.071 2776 Dihedral : 5.164 55.331 2246 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.88 % Favored : 95.91 % Rotamer: Outliers : 3.11 % Allowed : 16.10 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.18), residues: 1906 helix: -2.26 (0.38), residues: 145 sheet: -0.07 (0.21), residues: 595 loop : -1.40 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.019 0.001 PHE E 29 TYR 0.012 0.001 TYR A 495 ARG 0.004 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 7) link_NAG-ASN : angle 2.38357 ( 21) hydrogen bonds : bond 0.03186 ( 469) hydrogen bonds : angle 6.33511 ( 1221) SS BOND : bond 0.00196 ( 21) SS BOND : angle 0.76196 ( 42) covalent geometry : bond 0.00267 (15805) covalent geometry : angle 0.57819 (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 166 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 113 time to evaluate : 1.887 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7957 (mtm180) REVERT: A 205 SER cc_start: 0.8883 (p) cc_final: 0.8597 (t) REVERT: A 237 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7361 (ttt-90) REVERT: A 319 ARG cc_start: 0.6536 (mmt180) cc_final: 0.6266 (mmp-170) REVERT: A 386 LYS cc_start: 0.3642 (mtmt) cc_final: 0.3253 (mtmt) REVERT: A 495 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.5895 (t80) REVERT: B 131 CYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5518 (m) REVERT: B 558 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7729 (mmtt) REVERT: C 80 LEU cc_start: -0.1069 (OUTLIER) cc_final: -0.1326 (tp) REVERT: D 266 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8686 (m-80) REVERT: D 319 ARG cc_start: 0.5244 (OUTLIER) cc_final: 0.3617 (ppt90) REVERT: D 328 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.4921 (tpp-160) REVERT: D 580 GLN cc_start: 0.4892 (OUTLIER) cc_final: 0.4410 (mt0) outliers start: 53 outliers final: 34 residues processed: 159 average time/residue: 0.2975 time to fit residues: 73.3555 Evaluate side-chains 147 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 320 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 495 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 157 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 34 optimal weight: 0.0070 chunk 102 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 120 optimal weight: 0.6980 chunk 187 optimal weight: 0.0020 overall best weight: 0.4806 ------------------------------------------------------------------------------- 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** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.234682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.161995 restraints weight = 21420.473| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 4.49 r_work: 0.3748 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2889 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= 0.110 Angle : 0.568 9.393 21558 Z= 0.292 Chirality : 0.046 0.226 2378 Planarity : 0.005 0.068 2776 Dihedral : 4.893 55.142 2246 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 2.88 % Allowed : 16.33 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 1906 helix: -2.11 (0.39), residues: 145 sheet: 0.02 (0.21), residues: 590 loop : -1.35 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS A 69 PHE 0.023 0.001 PHE E 29 TYR 0.012 0.001 TYR D 265 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 7) link_NAG-ASN : angle 2.17229 ( 21) hydrogen bonds : bond 0.02967 ( 469) hydrogen bonds : angle 6.14085 ( 1221) SS BOND : bond 0.00249 ( 21) SS BOND : angle 0.97843 ( 42) covalent geometry : bond 0.00254 (15805) covalent geometry : angle 0.56295 (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 166 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7909 (mtm180) REVERT: A 205 SER cc_start: 0.8857 (p) cc_final: 0.8614 (t) REVERT: A 386 LYS cc_start: 0.3643 (mtmt) cc_final: 0.3226 (mtmt) REVERT: A 437 ASN cc_start: 0.7717 (t0) cc_final: 0.7386 (t0) REVERT: A 495 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6086 (t80) REVERT: B 95 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7949 (p) REVERT: B 131 CYS cc_start: 0.5831 (OUTLIER) cc_final: 0.5548 (m) REVERT: B 305 SER cc_start: 0.9295 (t) cc_final: 0.9017 (p) REVERT: B 558 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7820 (mmtt) REVERT: C 80 LEU cc_start: -0.1184 (OUTLIER) cc_final: -0.1465 (tp) REVERT: D 266 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8693 (m-80) REVERT: D 319 ARG cc_start: 0.5288 (OUTLIER) cc_final: 0.3465 (ppt90) REVERT: D 328 ARG cc_start: 0.5894 (OUTLIER) cc_final: 0.4799 (tpp-160) REVERT: D 580 GLN cc_start: 0.4894 (OUTLIER) cc_final: 0.4492 (mt0) outliers start: 49 outliers final: 38 residues processed: 158 average time/residue: 0.2536 time to fit residues: 61.6166 Evaluate side-chains 157 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 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 547 THR Chi-restraints excluded: chain A residue 581 THR 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 131 CYS 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 433 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 136 CYS Chi-restraints excluded: chain D residue 210 ILE 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 546 LEU 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: 1.9990 chunk 93 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 136 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ** 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 = 0.4730 r_free = 0.4730 target = 0.231518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157577 restraints weight = 21459.360| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 4.37 r_work: 0.3658 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15833 Z= 0.185 Angle : 0.617 9.920 21558 Z= 0.319 Chirality : 0.047 0.228 2378 Planarity : 0.005 0.063 2776 Dihedral : 4.977 53.131 2246 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.35 % Favored : 94.44 % Rotamer: Outliers : 3.58 % Allowed : 15.86 % Favored : 80.55 % 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: -1.48 (0.19), residues: 1906 helix: -2.06 (0.40), residues: 138 sheet: -0.19 (0.21), residues: 597 loop : -1.30 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 64 HIS 0.006 0.001 HIS A 69 PHE 0.021 0.002 PHE E 29 TYR 0.021 0.002 TYR D 265 ARG 0.006 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 7) link_NAG-ASN : angle 2.18222 ( 21) hydrogen bonds : bond 0.03381 ( 469) hydrogen bonds : angle 6.12480 ( 1221) SS BOND : bond 0.00412 ( 21) SS BOND : angle 1.14015 ( 42) covalent geometry : bond 0.00451 (15805) covalent geometry : angle 0.61179 (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 174 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 113 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.5127 (t80) cc_final: 0.4717 (t80) REVERT: A 190 ARG cc_start: 0.8333 (mtt180) cc_final: 0.8042 (mtm180) REVERT: A 386 LYS cc_start: 0.3620 (mtmt) cc_final: 0.3219 (mtmt) REVERT: A 495 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6005 (t80) REVERT: A 537 LYS cc_start: 0.7540 (mtpp) cc_final: 0.7267 (ttpt) REVERT: B 131 CYS cc_start: 0.5931 (OUTLIER) cc_final: 0.5659 (m) REVERT: B 305 SER cc_start: 0.9391 (t) cc_final: 0.9126 (p) REVERT: B 558 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7875 (mmtt) REVERT: C 80 LEU cc_start: -0.1223 (OUTLIER) cc_final: -0.1475 (tp) REVERT: D 266 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: D 319 ARG cc_start: 0.5243 (OUTLIER) cc_final: 0.3540 (ppt90) REVERT: D 328 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.4831 (tpp-160) REVERT: D 580 GLN cc_start: 0.4774 (OUTLIER) cc_final: 0.4378 (mt0) outliers start: 61 outliers final: 43 residues processed: 162 average time/residue: 0.2589 time to fit residues: 64.3522 Evaluate side-chains 156 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 299 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 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 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 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 32 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 180 optimal weight: 0.0980 chunk 159 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** 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 = 0.4750 r_free = 0.4750 target = 0.233730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.159237 restraints weight = 21246.978| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 4.56 r_work: 0.3664 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15833 Z= 0.115 Angle : 0.566 9.367 21558 Z= 0.292 Chirality : 0.046 0.222 2378 Planarity : 0.005 0.061 2776 Dihedral : 4.776 55.489 2246 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 3.17 % Allowed : 16.80 % Favored : 80.02 % 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: -1.37 (0.19), residues: 1906 helix: -1.85 (0.41), residues: 139 sheet: -0.01 (0.21), residues: 590 loop : -1.30 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.022 0.001 PHE E 29 TYR 0.012 0.001 TYR D 265 ARG 0.003 0.000 ARG D 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 7) link_NAG-ASN : angle 1.94743 ( 21) hydrogen bonds : bond 0.02990 ( 469) hydrogen bonds : angle 5.99636 ( 1221) SS BOND : bond 0.00257 ( 21) SS BOND : angle 0.75488 ( 42) covalent geometry : bond 0.00266 (15805) covalent geometry : angle 0.56221 (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 164 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 110 time to evaluate : 1.758 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8352 (mtt180) cc_final: 0.8045 (mtm180) REVERT: A 386 LYS cc_start: 0.3571 (mtmt) cc_final: 0.2881 (mtmt) REVERT: A 495 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6014 (t80) REVERT: A 508 TYR cc_start: 0.6476 (m-80) cc_final: 0.6188 (m-10) REVERT: A 537 LYS cc_start: 0.7491 (mtpp) cc_final: 0.7234 (ttpt) REVERT: B 95 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 131 CYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5701 (m) REVERT: B 305 SER cc_start: 0.9391 (t) cc_final: 0.9116 (p) REVERT: B 558 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7818 (mmtm) REVERT: C 80 LEU cc_start: -0.1251 (OUTLIER) cc_final: -0.1498 (tp) REVERT: D 266 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: D 319 ARG cc_start: 0.5352 (OUTLIER) cc_final: 0.3730 (ppt90) REVERT: D 328 ARG cc_start: 0.5872 (OUTLIER) cc_final: 0.4801 (ttp-170) REVERT: D 580 GLN cc_start: 0.4840 (OUTLIER) cc_final: 0.4479 (mt0) outliers start: 54 outliers final: 41 residues processed: 155 average time/residue: 0.2551 time to fit residues: 61.2383 Evaluate side-chains 156 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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: 0.0010 chunk 150 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 178 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 409 GLN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** 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 = 0.4757 r_free = 0.4757 target = 0.233422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.158451 restraints weight = 21302.899| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 4.21 r_work: 0.3737 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15833 Z= 0.132 Angle : 0.568 9.469 21558 Z= 0.293 Chirality : 0.046 0.230 2378 Planarity : 0.005 0.059 2776 Dihedral : 4.673 54.559 2246 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.88 % Favored : 94.91 % Rotamer: Outliers : 2.82 % Allowed : 17.27 % 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: -1.33 (0.19), residues: 1906 helix: -1.68 (0.42), residues: 138 sheet: -0.01 (0.21), residues: 604 loop : -1.30 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 64 HIS 0.004 0.001 HIS A 69 PHE 0.022 0.002 PHE E 67 TYR 0.016 0.001 TYR D 265 ARG 0.003 0.000 ARG D 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 7) link_NAG-ASN : angle 1.82628 ( 21) hydrogen bonds : bond 0.03011 ( 469) hydrogen bonds : angle 5.90347 ( 1221) SS BOND : bond 0.00301 ( 21) SS BOND : angle 0.80067 ( 42) covalent geometry : bond 0.00315 (15805) covalent geometry : angle 0.56523 (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 160 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.5049 (t80) cc_final: 0.4691 (t80) REVERT: A 190 ARG cc_start: 0.8323 (mtt180) cc_final: 0.8014 (mtm180) REVERT: A 386 LYS cc_start: 0.3603 (mtmt) cc_final: 0.3161 (mtmt) REVERT: A 495 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.6007 (t80) REVERT: A 508 TYR cc_start: 0.6478 (m-80) cc_final: 0.6151 (m-10) REVERT: A 537 LYS cc_start: 0.7524 (mtpp) cc_final: 0.7268 (ttpt) REVERT: B 95 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.7994 (p) REVERT: B 131 CYS cc_start: 0.5838 (OUTLIER) cc_final: 0.5634 (m) REVERT: B 305 SER cc_start: 0.9363 (t) cc_final: 0.9089 (p) REVERT: B 558 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7887 (mmtm) REVERT: D 266 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: D 319 ARG cc_start: 0.5389 (OUTLIER) cc_final: 0.3600 (ppt90) outliers start: 48 outliers final: 40 residues processed: 153 average time/residue: 0.2551 time to fit residues: 59.8620 Evaluate side-chains 151 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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 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 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 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 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 224 GLU 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 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 135 optimal weight: 0.0060 chunk 144 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.3200 ------------------------------------------------------------------------------- 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 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** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** 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 = 0.4727 r_free = 0.4727 target = 0.231401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.158247 restraints weight = 21430.323| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 4.42 r_work: 0.3663 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15833 Z= 0.157 Angle : 0.585 9.479 21558 Z= 0.302 Chirality : 0.047 0.226 2378 Planarity : 0.005 0.057 2776 Dihedral : 4.756 54.501 2246 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.83 % Favored : 94.96 % Rotamer: Outliers : 2.70 % Allowed : 17.74 % Favored : 79.55 % 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: -1.35 (0.19), residues: 1906 helix: -1.75 (0.42), residues: 132 sheet: -0.11 (0.21), residues: 605 loop : -1.25 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.003 0.001 HIS A 207 PHE 0.020 0.002 PHE E 29 TYR 0.016 0.001 TYR D 265 ARG 0.004 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 7) link_NAG-ASN : angle 1.80874 ( 21) hydrogen bonds : bond 0.03121 ( 469) hydrogen bonds : angle 5.92909 ( 1221) SS BOND : bond 0.00333 ( 21) SS BOND : angle 0.86507 ( 42) covalent geometry : bond 0.00376 (15805) covalent geometry : angle 0.58148 (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 153 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.5132 (t80) cc_final: 0.4710 (t80) REVERT: A 190 ARG cc_start: 0.8399 (mtt180) cc_final: 0.8106 (mtm180) REVERT: A 237 ARG cc_start: 0.7280 (ttt-90) cc_final: 0.7064 (ttt90) REVERT: A 386 LYS cc_start: 0.3667 (mtmt) cc_final: 0.3188 (mtmt) REVERT: A 495 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.5999 (t80) REVERT: A 508 TYR cc_start: 0.6509 (m-80) cc_final: 0.6164 (m-10) REVERT: A 537 LYS cc_start: 0.7594 (mtpp) cc_final: 0.7317 (ttpt) REVERT: B 95 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8056 (p) REVERT: B 131 CYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5767 (m) REVERT: B 305 SER cc_start: 0.9391 (t) cc_final: 0.9129 (p) REVERT: B 558 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7871 (mmtm) REVERT: D 266 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: D 319 ARG cc_start: 0.5457 (OUTLIER) cc_final: 0.3616 (ppt90) REVERT: D 328 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.5729 (tpp-160) outliers start: 46 outliers final: 40 residues processed: 146 average time/residue: 0.2525 time to fit residues: 56.7655 Evaluate side-chains 152 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 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 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 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 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 224 GLU 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 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 0.4980 chunk 91 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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** 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** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.231169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.160093 restraints weight = 21244.159| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 4.38 r_work: 0.3647 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15833 Z= 0.185 Angle : 0.606 9.540 21558 Z= 0.314 Chirality : 0.047 0.227 2378 Planarity : 0.005 0.055 2776 Dihedral : 4.866 53.740 2246 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.72 % Favored : 94.07 % Rotamer: Outliers : 3.23 % Allowed : 17.39 % Favored : 79.38 % 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: -1.39 (0.19), residues: 1906 helix: -1.73 (0.42), residues: 132 sheet: -0.12 (0.21), residues: 583 loop : -1.28 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.005 0.001 HIS D 69 PHE 0.021 0.002 PHE D 86 TYR 0.018 0.002 TYR D 265 ARG 0.009 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 7) link_NAG-ASN : angle 1.80237 ( 21) hydrogen bonds : bond 0.03273 ( 469) hydrogen bonds : angle 5.95625 ( 1221) SS BOND : bond 0.00389 ( 21) SS BOND : angle 0.96676 ( 42) covalent geometry : bond 0.00447 (15805) covalent geometry : angle 0.60296 (21495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11047.59 seconds wall clock time: 189 minutes 24.22 seconds (11364.22 seconds total)