Starting phenix.real_space_refine on Tue Jan 21 03:42:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7b_29805/01_2025/8g7b_29805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7b_29805/01_2025/8g7b_29805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7b_29805/01_2025/8g7b_29805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7b_29805/01_2025/8g7b_29805.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7b_29805/01_2025/8g7b_29805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7b_29805/01_2025/8g7b_29805.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 916 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 9866 2.51 5 N 2568 2.21 5 O 2908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.45, per 1000 atoms: 0.61 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: 3.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 3812 Ramachandran restraints generated. 1906 Oldfield, 0 Emsley, 1906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 35 sheets defined 7.9% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 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: 6.20 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4911 1.34 - 1.47: 4200 1.47 - 1.59: 6617 1.59 - 1.72: 1 1.72 - 1.85: 76 Bond restraints: 15805 Sorted by residual: bond pdb=" CB PRO A 217 " pdb=" CG PRO A 217 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.71e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.366 0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C SER E 30 " pdb=" N PRO E 31 " ideal model delta sigma weight residual 1.331 1.352 -0.022 1.31e-02 5.83e+03 2.73e+00 bond pdb=" CA SER E 30 " pdb=" C SER E 30 " ideal model delta sigma weight residual 1.524 1.544 -0.021 1.26e-02 6.30e+03 2.66e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 15800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 21238 2.88 - 5.76: 241 5.76 - 8.64: 14 8.64 - 11.52: 1 11.52 - 14.39: 1 Bond angle restraints: 21495 Sorted by residual: angle pdb=" CA PRO A 217 " pdb=" N PRO A 217 " pdb=" CD PRO A 217 " ideal model delta sigma weight residual 112.00 97.61 14.39 1.40e+00 5.10e-01 1.06e+02 angle pdb=" N GLY C 108 " pdb=" CA GLY C 108 " pdb=" C GLY C 108 " ideal model delta sigma weight residual 111.95 116.99 -5.04 9.50e-01 1.11e+00 2.81e+01 angle pdb=" N VAL B 350 " pdb=" CA VAL B 350 " pdb=" C VAL B 350 " ideal model delta sigma weight residual 112.29 108.07 4.22 9.40e-01 1.13e+00 2.01e+01 angle pdb=" C SER E 30 " pdb=" CA SER E 30 " pdb=" CB SER E 30 " ideal model delta sigma weight residual 110.17 118.33 -8.16 1.97e+00 2.58e-01 1.72e+01 angle pdb=" N PRO A 217 " pdb=" CD PRO A 217 " pdb=" CG PRO A 217 " ideal model delta sigma weight residual 103.20 97.15 6.05 1.50e+00 4.44e-01 1.63e+01 ... (remaining 21490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 8220 16.47 - 32.95: 896 32.95 - 49.42: 230 49.42 - 65.90: 40 65.90 - 82.37: 22 Dihedral angle restraints: 9408 sinusoidal: 3789 harmonic: 5619 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -12.20 -73.80 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual 93.00 40.03 52.97 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS D 538 " pdb=" SG CYS D 538 " pdb=" SG CYS D 590 " pdb=" CB CYS D 590 " ideal model delta sinusoidal sigma weight residual -86.00 -132.44 46.44 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 9405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2044 0.070 - 0.140: 314 0.140 - 0.211: 18 0.211 - 0.281: 0 0.281 - 0.351: 2 Chirality restraints: 2378 Sorted by residual: chirality pdb=" C1 NAG D1301 " pdb=" ND2 ASN D 331 " pdb=" C2 NAG D1301 " pdb=" O5 NAG D1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 2375 not shown) Planarity restraints: 2783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " -0.118 5.00e-02 4.00e+02 1.66e-01 4.41e+01 pdb=" N PRO A 217 " 0.287 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 560 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO D 561 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 561 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 561 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 140 " -0.014 2.00e-02 2.50e+03 1.83e-02 5.89e+00 pdb=" CG PHE A 140 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 140 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 140 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 140 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 140 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 140 " 0.001 2.00e-02 2.50e+03 ... (remaining 2780 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 151 2.60 - 3.18: 12900 3.18 - 3.75: 22340 3.75 - 4.33: 32475 4.33 - 4.90: 53275 Nonbonded interactions: 121141 Sorted by model distance: nonbonded pdb=" OD1 ASN E 32 " pdb=" OG SER E 53 " model vdw 2.030 3.040 nonbonded pdb=" OG SER B 359 " pdb=" OD1 ASN B 394 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR E 96 " pdb=" OH TYR A 351 " model vdw 2.132 3.040 nonbonded pdb=" NH2 ARG D 454 " pdb=" O SER D 469 " model vdw 2.155 3.120 nonbonded pdb=" OG1 THR B 553 " pdb=" OD1 ASP B 586 " model vdw 2.156 3.040 ... (remaining 121136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 592 or resid 1301 through 1302)) selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.600 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.790 ------------------------------------------------------------------------------- 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 : 1.643 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: 0.2671 time to fit residues: 58.7722 Evaluate side-chains 119 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.236631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163242 restraints weight = 21484.087| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 4.53 r_work: 0.3716 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 30 SER cc_start: 0.4145 (OUTLIER) cc_final: 0.3854 (p) REVERT: A 104 TRP cc_start: 0.6514 (m-90) cc_final: 0.6240 (m-90) REVERT: A 118 LEU cc_start: 0.6650 (tt) cc_final: 0.6384 (tp) REVERT: A 190 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7686 (mtm180) REVERT: A 227 VAL cc_start: 0.7396 (p) cc_final: 0.7158 (p) REVERT: A 495 TYR cc_start: 0.6617 (OUTLIER) cc_final: 0.5982 (t80) REVERT: B 215 ASP cc_start: 0.6322 (p0) cc_final: 0.6086 (p0) REVERT: B 468 ILE cc_start: 0.4682 (OUTLIER) cc_final: 0.4448 (tt) REVERT: B 510 VAL cc_start: 0.5426 (OUTLIER) cc_final: 0.5144 (t) REVERT: D 63 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8061 (t) REVERT: D 319 ARG cc_start: 0.4967 (OUTLIER) cc_final: 0.3130 (ppt90) REVERT: D 580 GLN cc_start: 0.5046 (OUTLIER) cc_final: 0.4761 (mt0) outliers start: 62 outliers final: 26 residues processed: 184 average time/residue: 0.2711 time to fit residues: 75.9540 Evaluate side-chains 149 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 114 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 422 ASN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.237406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.164093 restraints weight = 21397.902| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 4.41 r_work: 0.3740 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15805 Z= 0.194 Angle : 0.591 9.176 21495 Z= 0.306 Chirality : 0.046 0.225 2378 Planarity : 0.005 0.072 2776 Dihedral : 5.231 55.071 2246 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 3.11 % Allowed : 14.98 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 1906 helix: -2.22 (0.40), residues: 139 sheet: 0.01 (0.21), residues: 588 loop : -1.35 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.008 0.001 HIS A 69 PHE 0.019 0.001 PHE D 338 TYR 0.013 0.001 TYR D 265 ARG 0.004 0.000 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 181 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: E 27 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7130 (p) REVERT: E 100 LYS cc_start: 0.7287 (tttt) cc_final: 0.7077 (tttt) REVERT: A 190 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7593 (mtm180) REVERT: A 201 PHE cc_start: 0.4363 (t80) cc_final: 0.4110 (t80) REVERT: A 368 LEU cc_start: 0.7934 (mt) cc_final: 0.7647 (mt) REVERT: A 495 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.5905 (t80) REVERT: A 541 PHE cc_start: 0.8531 (p90) cc_final: 0.8280 (p90) REVERT: A 586 ASP cc_start: 0.7493 (p0) cc_final: 0.7155 (p0) REVERT: B 131 CYS cc_start: 0.5627 (OUTLIER) cc_final: 0.5227 (m) REVERT: B 468 ILE cc_start: 0.4615 (OUTLIER) cc_final: 0.4370 (tt) REVERT: D 266 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: D 541 PHE cc_start: 0.6743 (p90) cc_final: 0.6510 (p90) REVERT: D 580 GLN cc_start: 0.5027 (OUTLIER) cc_final: 0.4718 (mt0) outliers start: 53 outliers final: 29 residues processed: 172 average time/residue: 0.2567 time to fit residues: 69.6313 Evaluate side-chains 147 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 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 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 0.0970 chunk 111 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 121 optimal weight: 0.0270 chunk 170 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- 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** B 388 ASN C 5 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.235188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163139 restraints weight = 21316.190| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 4.48 r_work: 0.3711 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2113 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= 0.231 Angle : 0.587 9.466 21495 Z= 0.303 Chirality : 0.046 0.229 2378 Planarity : 0.005 0.072 2776 Dihedral : 5.027 54.388 2246 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.46 % Favored : 95.33 % Rotamer: Outliers : 3.76 % Allowed : 14.86 % Favored : 81.37 % 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: -1.45 (0.18), residues: 1906 helix: -2.19 (0.39), residues: 145 sheet: 0.03 (0.22), residues: 571 loop : -1.35 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.006 0.001 HIS A 69 PHE 0.017 0.002 PHE A 400 TYR 0.017 0.001 TYR D 265 ARG 0.004 0.000 ARG B 102 *********************** 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 186 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6557 (m-90) cc_final: 0.6352 (m-90) REVERT: A 106 PHE cc_start: 0.5037 (m-80) cc_final: 0.4821 (m-80) REVERT: A 190 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7818 (mtm180) REVERT: A 226 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.5282 (mp) REVERT: A 368 LEU cc_start: 0.7942 (mt) cc_final: 0.7719 (mt) REVERT: A 386 LYS cc_start: 0.3553 (mtmt) cc_final: 0.3249 (mtmt) REVERT: A 495 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.5978 (t80) REVERT: A 586 ASP cc_start: 0.7624 (p0) cc_final: 0.6911 (p0) REVERT: B 131 CYS cc_start: 0.5773 (OUTLIER) cc_final: 0.5402 (m) REVERT: B 468 ILE cc_start: 0.4701 (OUTLIER) cc_final: 0.4409 (tt) REVERT: D 319 ARG cc_start: 0.4999 (OUTLIER) cc_final: 0.3330 (ppt90) REVERT: D 328 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4784 (tpp-160) REVERT: D 580 GLN cc_start: 0.4993 (OUTLIER) cc_final: 0.4473 (mt0) outliers start: 64 outliers final: 43 residues processed: 175 average time/residue: 0.2656 time to fit residues: 71.1464 Evaluate side-chains 164 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 394 ASN 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 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 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 468 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 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 289 VAL Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 62 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 179 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.234428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.165741 restraints weight = 21644.111| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 4.23 r_work: 0.3733 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15805 Z= 0.239 Angle : 0.579 9.465 21495 Z= 0.300 Chirality : 0.046 0.226 2378 Planarity : 0.005 0.070 2776 Dihedral : 4.938 54.317 2246 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.62 % Favored : 95.17 % Rotamer: Outliers : 3.94 % Allowed : 15.10 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 1906 helix: -2.05 (0.41), residues: 137 sheet: -0.04 (0.21), residues: 595 loop : -1.32 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 PHE 0.020 0.002 PHE E 29 TYR 0.017 0.001 TYR D 265 ARG 0.006 0.000 ARG A 102 *********************** 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 190 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 123 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5073 (m-80) cc_final: 0.4825 (m-80) REVERT: A 190 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7938 (mtm180) REVERT: A 226 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5228 (mp) REVERT: A 386 LYS cc_start: 0.3728 (mtmt) cc_final: 0.3379 (mtmt) REVERT: A 495 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.5985 (t80) REVERT: A 508 TYR cc_start: 0.6638 (m-80) cc_final: 0.6254 (m-80) REVERT: A 537 LYS cc_start: 0.7403 (mtpp) cc_final: 0.7164 (tttt) REVERT: A 586 ASP cc_start: 0.7727 (p0) cc_final: 0.7094 (p0) REVERT: B 131 CYS cc_start: 0.5819 (OUTLIER) cc_final: 0.5494 (m) REVERT: C 80 LEU cc_start: -0.1179 (OUTLIER) cc_final: -0.1426 (tp) REVERT: D 266 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: D 319 ARG cc_start: 0.5151 (OUTLIER) cc_final: 0.3386 (ppt90) REVERT: D 571 ASP cc_start: 0.5439 (p0) cc_final: 0.5153 (p0) REVERT: D 580 GLN cc_start: 0.5075 (OUTLIER) cc_final: 0.4835 (mt0) outliers start: 67 outliers final: 49 residues processed: 178 average time/residue: 0.2592 time to fit residues: 71.3570 Evaluate side-chains 173 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 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 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 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 157 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 139 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 102 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.234815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.163113 restraints weight = 21451.111| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 4.44 r_work: 0.3747 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15805 Z= 0.197 Angle : 0.566 9.403 21495 Z= 0.292 Chirality : 0.046 0.225 2378 Planarity : 0.004 0.067 2776 Dihedral : 4.773 54.833 2246 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.14 % Favored : 95.65 % Rotamer: Outliers : 3.64 % Allowed : 15.45 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.89 (0.43), residues: 130 sheet: 0.08 (0.21), residues: 588 loop : -1.30 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.006 0.001 HIS A 69 PHE 0.017 0.001 PHE A 400 TYR 0.015 0.001 TYR D 265 ARG 0.004 0.000 ARG A 102 *********************** 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 189 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 127 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5788 (ptp90) REVERT: A 190 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7969 (mtm180) REVERT: A 226 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5280 (mp) REVERT: A 386 LYS cc_start: 0.3633 (mtmt) cc_final: 0.3235 (mtmt) REVERT: A 495 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.5993 (t80) REVERT: A 508 TYR cc_start: 0.6588 (m-80) cc_final: 0.6192 (m-80) REVERT: A 537 LYS cc_start: 0.7428 (mtpp) cc_final: 0.7195 (tttt) REVERT: A 586 ASP cc_start: 0.7666 (p0) cc_final: 0.7103 (p0) REVERT: B 81 ASN cc_start: 0.8175 (p0) cc_final: 0.7941 (p0) REVERT: B 95 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7937 (p) REVERT: B 102 ARG cc_start: 0.7811 (mmt-90) cc_final: 0.7578 (mmt-90) REVERT: B 131 CYS cc_start: 0.5761 (OUTLIER) cc_final: 0.5481 (m) REVERT: C 80 LEU cc_start: -0.1183 (OUTLIER) cc_final: -0.1462 (tp) REVERT: D 266 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8800 (m-80) REVERT: D 319 ARG cc_start: 0.5281 (OUTLIER) cc_final: 0.3500 (ppt90) REVERT: D 328 ARG cc_start: 0.5859 (OUTLIER) cc_final: 0.4852 (tpp-160) REVERT: D 571 ASP cc_start: 0.5477 (p0) cc_final: 0.5135 (p0) REVERT: D 580 GLN cc_start: 0.5007 (OUTLIER) cc_final: 0.4544 (mt0) outliers start: 62 outliers final: 44 residues processed: 179 average time/residue: 0.2592 time to fit residues: 71.9088 Evaluate side-chains 175 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 158 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR 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 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 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 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 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 546 LEU Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 187 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 148 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.232853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.161342 restraints weight = 21503.460| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 4.67 r_work: 0.3661 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15805 Z= 0.266 Angle : 0.594 10.034 21495 Z= 0.306 Chirality : 0.047 0.228 2378 Planarity : 0.005 0.062 2776 Dihedral : 4.853 53.673 2246 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.81 % Rotamer: Outliers : 3.76 % Allowed : 15.80 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 1906 helix: -1.89 (0.42), residues: 130 sheet: -0.09 (0.21), residues: 617 loop : -1.30 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.008 0.001 HIS A 69 PHE 0.018 0.002 PHE D 86 TYR 0.019 0.001 TYR D 265 ARG 0.003 0.000 ARG A 319 *********************** 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 186 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.4937 (m-80) cc_final: 0.4734 (m-80) REVERT: A 118 LEU cc_start: 0.6860 (tt) cc_final: 0.6644 (tp) REVERT: A 170 TYR cc_start: 0.5023 (t80) cc_final: 0.4785 (t80) REVERT: A 190 ARG cc_start: 0.8325 (mtt180) cc_final: 0.8055 (mtm180) REVERT: A 386 LYS cc_start: 0.3648 (mtmt) cc_final: 0.3378 (mtmt) REVERT: A 495 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.6082 (t80) REVERT: A 586 ASP cc_start: 0.7773 (p0) cc_final: 0.7202 (p0) REVERT: B 95 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8011 (p) REVERT: B 131 CYS cc_start: 0.5910 (OUTLIER) cc_final: 0.5644 (m) REVERT: C 80 LEU cc_start: -0.1170 (OUTLIER) cc_final: -0.1460 (tp) REVERT: D 266 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8864 (m-80) REVERT: D 319 ARG cc_start: 0.5243 (OUTLIER) cc_final: 0.3436 (ppt90) REVERT: D 328 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.4834 (tpp-160) REVERT: D 580 GLN cc_start: 0.4744 (OUTLIER) cc_final: 0.4333 (mt0) outliers start: 64 outliers final: 48 residues processed: 178 average time/residue: 0.2492 time to fit residues: 69.3356 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 : 1.625 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 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 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 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 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 546 LEU Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.6934 > 50: distance: 38 - 42: 34.699 distance: 44 - 45: 56.489 distance: 46 - 47: 39.739 distance: 48 - 50: 14.527 distance: 50 - 52: 13.056 distance: 54 - 57: 17.436 distance: 55 - 56: 40.506 distance: 57 - 58: 43.831 distance: 57 - 59: 15.914 distance: 61 - 62: 36.279 distance: 61 - 64: 12.738 distance: 62 - 63: 20.329 distance: 64 - 65: 9.797 distance: 65 - 66: 18.938 distance: 65 - 67: 23.979 distance: 66 - 68: 17.889 distance: 67 - 69: 10.335 distance: 68 - 70: 17.765 distance: 69 - 70: 23.828 distance: 71 - 72: 39.903 distance: 72 - 73: 40.884 distance: 73 - 82: 60.500 distance: 75 - 76: 36.749 distance: 76 - 77: 49.036 distance: 77 - 78: 36.097 distance: 78 - 79: 19.019 distance: 79 - 80: 20.063 distance: 79 - 81: 23.064 distance: 82 - 83: 43.958 distance: 83 - 84: 56.013 distance: 83 - 86: 41.134 distance: 84 - 89: 57.877 distance: 89 - 90: 9.871 distance: 90 - 91: 40.849 distance: 90 - 93: 49.861 distance: 94 - 95: 55.659 distance: 95 - 96: 40.993 distance: 98 - 99: 39.458 distance: 98 - 104: 56.274 distance: 99 - 100: 31.260 distance: 99 - 102: 39.050 distance: 100 - 101: 41.142 distance: 100 - 105: 49.854 distance: 103 - 104: 56.779 distance: 107 - 112: 40.784 distance: 109 - 110: 39.922 distance: 109 - 111: 41.491 distance: 114 - 115: 38.069 distance: 118 - 120: 40.315 distance: 121 - 122: 53.416 distance: 122 - 123: 36.169 distance: 122 - 125: 46.317 distance: 123 - 127: 34.498 distance: 125 - 126: 24.455