Starting phenix.real_space_refine on Tue Dec 31 17:10:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7b_29805/12_2024/8g7b_29805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7b_29805/12_2024/8g7b_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_29805/12_2024/8g7b_29805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7b_29805/12_2024/8g7b_29805.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7b_29805/12_2024/8g7b_29805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7b_29805/12_2024/8g7b_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-5532/modules/chem_data/mon_lib" Total number of atoms: 15406 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4518 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 31, 'TRANS': 534} Chain breaks: 2 Chain: "B" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4518 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 31, 'TRANS': 534} Chain breaks: 2 Chain: "C" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 877 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "D" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4518 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 31, 'TRANS': 534} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.35, per 1000 atoms: 0.67 Number of scatterers: 15406 At special positions: 0 Unit cell: (163.52, 148.19, 130.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2908 8.00 N 2568 7.00 C 9866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.01 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 165 " " NAG D1301 " - " ASN D 331 " " NAG D1302 " - " ASN D 343 " Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.9 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: 1.98 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: 5.32 Time building geometry restraints manager: 4.23 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.230 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.330 ------------------------------------------------------------------------------- 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 15805 Z= 0.250 Angle : 0.731 14.394 21495 Z= 0.399 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 *********************** 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 : 1.771 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: 0.2563 time to fit residues: 55.8635 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 : 2.002 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0370 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: 1.5662 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15805 Z= 0.312 Angle : 0.665 9.315 21495 Z= 0.347 Chirality : 0.049 0.256 2378 Planarity : 0.005 0.087 2776 Dihedral : 5.997 54.640 2250 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.41 % Favored : 95.44 % Rotamer: Outliers : 3.64 % Allowed : 14.04 % Favored : 82.31 % 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: -2.20 (0.42), residues: 132 sheet: -0.12 (0.20), residues: 632 loop : -1.40 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.006 0.001 ARG A 190 *********************** 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 199 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 137 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 30 SER cc_start: 0.4096 (OUTLIER) cc_final: 0.3835 (p) REVERT: A 104 TRP cc_start: 0.6321 (m-90) cc_final: 0.6067 (m-90) REVERT: A 190 ARG cc_start: 0.7120 (mtt180) cc_final: 0.6572 (mtm180) REVERT: A 495 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.5999 (t80) REVERT: B 468 ILE cc_start: 0.4910 (OUTLIER) cc_final: 0.4625 (tt) REVERT: B 510 VAL cc_start: 0.5934 (OUTLIER) cc_final: 0.5524 (t) REVERT: D 63 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7419 (t) REVERT: D 266 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: D 319 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.3083 (ppt90) REVERT: D 580 GLN cc_start: 0.4905 (OUTLIER) cc_final: 0.4612 (mt0) outliers start: 62 outliers final: 26 residues processed: 184 average time/residue: 0.2693 time to fit residues: 75.5690 Evaluate side-chains 150 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 SER 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 266 TYR Chi-restraints excluded: chain D residue 319 ARG 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 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 245 HIS 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15805 Z= 0.288 Angle : 0.630 9.258 21495 Z= 0.328 Chirality : 0.048 0.230 2378 Planarity : 0.005 0.075 2776 Dihedral : 5.390 53.555 2246 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.83 % Favored : 94.96 % Rotamer: Outliers : 4.17 % Allowed : 14.28 % Favored : 81.55 % 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: -1.59 (0.18), residues: 1906 helix: -2.47 (0.36), residues: 151 sheet: -0.09 (0.21), residues: 598 loop : -1.42 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.008 0.001 HIS A 69 PHE 0.021 0.002 PHE D 338 TYR 0.019 0.002 TYR D 266 ARG 0.005 0.001 ARG D 328 *********************** 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 197 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 126 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: E 25 SER cc_start: 0.6825 (m) cc_final: 0.6620 (p) REVERT: E 27 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.7316 (p) REVERT: A 190 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6678 (mtm180) REVERT: A 226 LEU cc_start: 0.5157 (OUTLIER) cc_final: 0.4743 (mp) REVERT: A 368 LEU cc_start: 0.8020 (mt) cc_final: 0.7765 (mt) REVERT: A 495 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.6089 (t80) REVERT: B 131 CYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5202 (m) REVERT: B 468 ILE cc_start: 0.4867 (OUTLIER) cc_final: 0.4553 (tt) REVERT: D 319 ARG cc_start: 0.5041 (OUTLIER) cc_final: 0.3233 (ppt90) REVERT: D 580 GLN cc_start: 0.4890 (OUTLIER) cc_final: 0.4597 (mt0) outliers start: 71 outliers final: 46 residues processed: 187 average time/residue: 0.2594 time to fit residues: 75.0863 Evaluate side-chains 160 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 SER 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 159 VAL Chi-restraints excluded: chain A residue 226 LEU 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 583 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 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 468 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 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 332 ILE 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 170 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 173 optimal weight: 0.0970 chunk 183 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN C 5 GLN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15805 Z= 0.258 Angle : 0.602 9.428 21495 Z= 0.313 Chirality : 0.047 0.222 2378 Planarity : 0.005 0.074 2776 Dihedral : 5.161 54.237 2246 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.02 % Rotamer: Outliers : 3.70 % Allowed : 15.57 % Favored : 80.73 % 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 (0.18), residues: 1906 helix: -2.23 (0.40), residues: 137 sheet: -0.11 (0.21), residues: 616 loop : -1.34 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.006 0.001 HIS A 69 PHE 0.019 0.002 PHE A 86 TYR 0.017 0.001 TYR D 266 ARG 0.005 0.001 ARG A 237 *********************** 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 181 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 118 time to evaluate : 1.677 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6025 (mmm-85) cc_final: 0.4927 (mmm-85) REVERT: A 190 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6924 (mtm180) REVERT: A 205 SER cc_start: 0.8260 (p) cc_final: 0.8002 (t) REVERT: A 386 LYS cc_start: 0.3934 (mtmt) cc_final: 0.3448 (mtmt) REVERT: A 495 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6223 (t80) REVERT: A 537 LYS cc_start: 0.7307 (mtpp) cc_final: 0.7088 (tttt) REVERT: A 586 ASP cc_start: 0.7758 (p0) cc_final: 0.7108 (p0) REVERT: B 131 CYS cc_start: 0.5620 (OUTLIER) cc_final: 0.5322 (m) REVERT: D 266 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: D 319 ARG cc_start: 0.5148 (OUTLIER) cc_final: 0.3225 (ppt90) REVERT: D 580 GLN cc_start: 0.4833 (OUTLIER) cc_final: 0.4571 (mt0) outliers start: 63 outliers final: 47 residues processed: 171 average time/residue: 0.2642 time to fit residues: 69.3262 Evaluate side-chains 163 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 111 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR 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 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 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 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG 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 94 SER 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 580 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15805 Z= 0.236 Angle : 0.584 9.677 21495 Z= 0.303 Chirality : 0.047 0.225 2378 Planarity : 0.005 0.071 2776 Dihedral : 4.990 54.350 2246 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.51 % Favored : 95.28 % Rotamer: Outliers : 4.17 % Allowed : 15.45 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1906 helix: -2.06 (0.41), residues: 130 sheet: -0.04 (0.21), residues: 600 loop : -1.34 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.006 0.001 HIS A 69 PHE 0.017 0.002 PHE A 400 TYR 0.016 0.001 TYR D 265 ARG 0.005 0.000 ARG D 328 *********************** 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 189 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 118 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7267 (mtt180) cc_final: 0.6976 (mtm180) REVERT: A 203 ILE cc_start: 0.6593 (tt) cc_final: 0.6342 (tt) REVERT: A 226 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5260 (mp) REVERT: A 383 SER cc_start: 0.8814 (t) cc_final: 0.8585 (m) REVERT: A 386 LYS cc_start: 0.3812 (mtmt) cc_final: 0.3387 (mtmm) REVERT: A 495 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6203 (t80) REVERT: A 586 ASP cc_start: 0.7712 (p0) cc_final: 0.7164 (p0) REVERT: B 131 CYS cc_start: 0.5653 (OUTLIER) cc_final: 0.5401 (m) REVERT: C 80 LEU cc_start: -0.0581 (OUTLIER) cc_final: -0.0914 (tp) REVERT: D 266 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: D 319 ARG cc_start: 0.5279 (OUTLIER) cc_final: 0.3241 (ppt90) REVERT: D 571 ASP cc_start: 0.5276 (p0) cc_final: 0.5073 (p0) REVERT: D 580 GLN cc_start: 0.4720 (OUTLIER) cc_final: 0.4478 (mt0) outliers start: 71 outliers final: 51 residues processed: 179 average time/residue: 0.2604 time to fit residues: 72.7040 Evaluate side-chains 172 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 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 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.1980 chunk 165 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 45 optimal weight: 0.0980 chunk 183 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 239 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15805 Z= 0.175 Angle : 0.565 9.393 21495 Z= 0.292 Chirality : 0.046 0.225 2378 Planarity : 0.004 0.067 2776 Dihedral : 4.869 55.140 2246 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 3.23 % Allowed : 16.63 % Favored : 80.14 % 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: -1.34 (0.19), residues: 1906 helix: -2.01 (0.42), residues: 130 sheet: 0.06 (0.21), residues: 592 loop : -1.30 (0.17), residues: 1184 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 0.016 0.001 PHE A 400 TYR 0.014 0.001 TYR D 265 ARG 0.004 0.000 ARG D 328 *********************** 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 180 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7281 (mtt180) cc_final: 0.6869 (mtm180) REVERT: A 383 SER cc_start: 0.8809 (t) cc_final: 0.8565 (m) REVERT: A 386 LYS cc_start: 0.3798 (mtmt) cc_final: 0.3378 (mtmm) REVERT: A 495 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.5938 (t80) REVERT: A 586 ASP cc_start: 0.7650 (p0) cc_final: 0.7157 (p0) REVERT: B 95 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7493 (p) REVERT: B 131 CYS cc_start: 0.5631 (OUTLIER) cc_final: 0.5381 (m) REVERT: B 558 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7524 (mmtm) REVERT: B 567 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7736 (mtt180) REVERT: C 80 LEU cc_start: -0.0724 (OUTLIER) cc_final: -0.1035 (tp) REVERT: D 94 SER cc_start: 0.8526 (t) cc_final: 0.8322 (m) REVERT: D 319 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.3305 (ppt90) REVERT: D 328 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.4819 (tpp-160) REVERT: D 571 ASP cc_start: 0.5301 (p0) cc_final: 0.5062 (p0) REVERT: D 580 GLN cc_start: 0.4692 (OUTLIER) cc_final: 0.4213 (mt0) outliers start: 55 outliers final: 37 residues processed: 172 average time/residue: 0.2628 time to fit residues: 69.1186 Evaluate side-chains 155 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN 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 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 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 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 B residue 567 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 134 optimal weight: 0.0870 chunk 154 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 113 optimal weight: 0.0370 overall best weight: 1.3438 ------------------------------------------------------------------------------- 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 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 148 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15805 Z= 0.256 Angle : 0.593 9.506 21495 Z= 0.306 Chirality : 0.047 0.227 2378 Planarity : 0.005 0.062 2776 Dihedral : 4.894 53.674 2246 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.04 % Favored : 94.75 % Rotamer: Outliers : 4.00 % Allowed : 15.98 % 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: -1.39 (0.19), residues: 1906 helix: -1.90 (0.42), residues: 131 sheet: -0.10 (0.21), residues: 601 loop : -1.28 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.004 0.001 HIS A 207 PHE 0.019 0.002 PHE D 86 TYR 0.018 0.001 TYR D 265 ARG 0.005 0.000 ARG D 328 *********************** 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 180 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 112 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7361 (mtt180) cc_final: 0.6944 (mtm180) REVERT: A 386 LYS cc_start: 0.3619 (mtmt) cc_final: 0.3161 (mtmt) REVERT: A 495 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5087 (t80) REVERT: A 537 LYS cc_start: 0.7410 (mtpp) cc_final: 0.7208 (tttt) REVERT: A 586 ASP cc_start: 0.7751 (p0) cc_final: 0.7263 (p0) REVERT: B 131 CYS cc_start: 0.5703 (OUTLIER) cc_final: 0.5486 (m) REVERT: B 558 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7594 (mmtt) REVERT: C 80 LEU cc_start: -0.0748 (OUTLIER) cc_final: -0.1076 (tp) REVERT: D 266 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: D 319 ARG cc_start: 0.5302 (OUTLIER) cc_final: 0.3139 (ppt90) REVERT: D 580 GLN cc_start: 0.4621 (OUTLIER) cc_final: 0.4413 (mt0) outliers start: 68 outliers final: 54 residues processed: 169 average time/residue: 0.2726 time to fit residues: 70.2151 Evaluate side-chains 166 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 106 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 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 576 VAL 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 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 SER 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 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15805 Z= 0.231 Angle : 0.580 9.462 21495 Z= 0.300 Chirality : 0.046 0.224 2378 Planarity : 0.005 0.060 2776 Dihedral : 4.828 54.630 2246 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.46 % Favored : 95.33 % Rotamer: Outliers : 3.41 % Allowed : 16.80 % Favored : 79.79 % 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: -1.36 (0.19), residues: 1906 helix: -1.86 (0.42), residues: 131 sheet: -0.06 (0.21), residues: 607 loop : -1.28 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.004 0.001 HIS A 207 PHE 0.017 0.001 PHE A 400 TYR 0.016 0.001 TYR D 266 ARG 0.005 0.000 ARG D 328 *********************** 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 170 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 112 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6724 (m-90) cc_final: 0.6502 (m-90) REVERT: A 170 TYR cc_start: 0.4880 (t80) cc_final: 0.4564 (t80) REVERT: A 190 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6940 (mtm180) REVERT: A 386 LYS cc_start: 0.3722 (mtmt) cc_final: 0.3468 (mtmt) REVERT: A 495 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.5095 (t80) REVERT: A 537 LYS cc_start: 0.7454 (mtpp) cc_final: 0.7247 (ttpt) REVERT: A 586 ASP cc_start: 0.7719 (p0) cc_final: 0.7318 (p0) REVERT: B 95 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7585 (p) REVERT: B 558 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7561 (mmtm) REVERT: C 80 LEU cc_start: -0.0761 (OUTLIER) cc_final: -0.1085 (tp) REVERT: D 94 SER cc_start: 0.8591 (t) cc_final: 0.8372 (m) REVERT: D 266 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: D 319 ARG cc_start: 0.5317 (OUTLIER) cc_final: 0.3420 (ppt90) REVERT: D 328 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.4639 (mtt90) REVERT: D 580 GLN cc_start: 0.4649 (OUTLIER) cc_final: 0.4340 (mt0) outliers start: 58 outliers final: 46 residues processed: 164 average time/residue: 0.2551 time to fit residues: 64.7517 Evaluate side-chains 159 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 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 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR 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 305 SER 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 433 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 40.0000 chunk 180 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15805 Z= 0.199 Angle : 0.567 9.593 21495 Z= 0.293 Chirality : 0.046 0.212 2378 Planarity : 0.005 0.057 2776 Dihedral : 4.718 53.658 2246 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.67 % Favored : 95.12 % Rotamer: Outliers : 3.29 % Allowed : 17.04 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1906 helix: -1.78 (0.42), residues: 137 sheet: -0.01 (0.21), residues: 597 loop : -1.27 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 64 HIS 0.003 0.001 HIS A 207 PHE 0.016 0.001 PHE A 400 TYR 0.014 0.001 TYR D 265 ARG 0.005 0.000 ARG D 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 3 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7073 (mm-40) REVERT: A 190 ARG cc_start: 0.7402 (mtt180) cc_final: 0.7017 (mtm180) REVERT: A 386 LYS cc_start: 0.3698 (mtmt) cc_final: 0.3450 (mtmt) REVERT: A 403 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6361 (mtm110) REVERT: A 495 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.4981 (t80) REVERT: A 586 ASP cc_start: 0.7665 (p0) cc_final: 0.7315 (p0) REVERT: B 95 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7563 (p) REVERT: B 558 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7578 (mmtm) REVERT: B 567 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7781 (mtt180) REVERT: D 266 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: D 319 ARG cc_start: 0.5328 (OUTLIER) cc_final: 0.3276 (ppt90) REVERT: D 328 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.4731 (tpp-160) REVERT: D 580 GLN cc_start: 0.4536 (OUTLIER) cc_final: 0.4199 (mt0) outliers start: 56 outliers final: 43 residues processed: 164 average time/residue: 0.2656 time to fit residues: 67.6148 Evaluate side-chains 159 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 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 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 TYR 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 45 SER 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 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.0770 chunk 85 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 189 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 chunk 150 optimal weight: 0.0000 chunk 15 optimal weight: 0.1980 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.3542 ------------------------------------------------------------------------------- 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 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 ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15805 Z= 0.154 Angle : 0.551 9.408 21495 Z= 0.286 Chirality : 0.045 0.232 2378 Planarity : 0.004 0.057 2776 Dihedral : 4.567 56.101 2246 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.25 % Favored : 95.54 % Rotamer: Outliers : 2.41 % Allowed : 18.21 % 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: -1.21 (0.19), residues: 1906 helix: -1.60 (0.45), residues: 124 sheet: 0.10 (0.21), residues: 600 loop : -1.23 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.005 0.001 HIS A 69 PHE 0.016 0.001 PHE A 400 TYR 0.010 0.001 TYR D 266 ARG 0.006 0.000 ARG B 102 ********************** 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 158 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.5541 (mp) cc_final: 0.5137 (mp) REVERT: A 190 ARG cc_start: 0.7357 (mtt180) cc_final: 0.6704 (mpt-90) REVERT: A 386 LYS cc_start: 0.3649 (mtmt) cc_final: 0.3269 (mtmt) REVERT: A 402 ILE cc_start: 0.8208 (mt) cc_final: 0.7981 (mm) REVERT: A 403 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6363 (mtm110) REVERT: A 437 ASN cc_start: 0.7879 (t0) cc_final: 0.7648 (t0) REVERT: A 495 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.4692 (t80) REVERT: A 508 TYR cc_start: 0.6521 (m-80) cc_final: 0.5924 (m-10) REVERT: A 586 ASP cc_start: 0.7572 (p0) cc_final: 0.7335 (p0) REVERT: B 95 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7464 (p) REVERT: B 160 TYR cc_start: 0.6921 (p90) cc_final: 0.6604 (p90) REVERT: B 558 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7560 (mmtm) REVERT: B 567 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7685 (mtt180) REVERT: D 40 ASP cc_start: 0.8237 (m-30) cc_final: 0.7907 (p0) outliers start: 41 outliers final: 32 residues processed: 151 average time/residue: 0.2470 time to fit residues: 58.7142 Evaluate side-chains 147 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 403 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 471 GLU Chi-restraints excluded: chain A residue 495 TYR 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 45 SER Chi-restraints excluded: chain B residue 95 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 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 567 ARG 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 395 VAL Chi-restraints excluded: chain D residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 0.0980 chunk 132 optimal weight: 8.9990 chunk 8 optimal weight: 0.0030 overall best weight: 1.1394 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN B 121 ASN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.232776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.162095 restraints weight = 21247.422| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 3.95 r_work: 0.3683 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15805 Z= 0.229 Angle : 0.580 9.561 21495 Z= 0.301 Chirality : 0.046 0.228 2378 Planarity : 0.005 0.055 2776 Dihedral : 4.593 53.950 2246 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.83 % Favored : 94.96 % Rotamer: Outliers : 2.53 % Allowed : 18.27 % Favored : 79.20 % 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: -1.25 (0.19), residues: 1906 helix: -1.63 (0.45), residues: 124 sheet: 0.05 (0.21), residues: 597 loop : -1.24 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.005 0.001 HIS D 69 PHE 0.020 0.002 PHE E 29 TYR 0.018 0.001 TYR D 265 ARG 0.005 0.000 ARG D 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3690.87 seconds wall clock time: 68 minutes 14.79 seconds (4094.79 seconds total)