Starting phenix.real_space_refine on Wed Mar 4 20:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7b_29805/03_2026/8g7b_29805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7b_29805/03_2026/8g7b_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_29805/03_2026/8g7b_29805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7b_29805/03_2026/8g7b_29805.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7b_29805/03_2026/8g7b_29805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7b_29805/03_2026/8g7b_29805.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.49, per 1000 atoms: 0.23 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: 1.21 Conformation dependent library (CDL) restraints added in 684.9 milliseconds 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: 0.50 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: 2.62 Time building geometry restraints manager: 1.62 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 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: 6.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.630 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 15833 Z= 0.171 Angle : 0.739 14.394 21558 Z= 0.401 Chirality : 0.050 0.351 2378 Planarity : 0.006 0.166 2776 Dihedral : 14.799 82.369 5743 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 0.35 % Allowed : 15.04 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG E 66 TYR 0.027 0.002 TYR A 495 PHE 0.038 0.002 PHE A 140 TRP 0.027 0.002 TRP A 64 HIS 0.009 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00386 (15805) covalent geometry : angle 0.73134 (21495) SS BOND : bond 0.00614 ( 21) SS BOND : angle 0.96303 ( 42) hydrogen bonds : bond 0.13382 ( 469) hydrogen bonds : angle 8.01886 ( 1221) link_NAG-ASN : bond 0.00554 ( 7) link_NAG-ASN : angle 3.30555 ( 21) *********************** 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 : 0.541 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: 0.6357 (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: 0.1137 time to fit residues: 24.8182 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 : 0.685 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** A 422 ASN ** 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 = 0.4794 r_free = 0.4794 target = 0.238638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.165558 restraints weight = 21508.588| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 4.44 r_work: 0.3837 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15833 Z= 0.149 Angle : 0.636 9.517 21558 Z= 0.329 Chirality : 0.048 0.240 2378 Planarity : 0.005 0.088 2776 Dihedral : 6.091 55.792 2250 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.91 % Rotamer: Outliers : 2.82 % Allowed : 14.57 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.18), residues: 1906 helix: -2.14 (0.43), residues: 132 sheet: -0.01 (0.21), residues: 587 loop : -1.39 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 457 TYR 0.016 0.002 TYR D 265 PHE 0.018 0.002 PHE C 67 TRP 0.015 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00352 (15805) covalent geometry : angle 0.62848 (21495) SS BOND : bond 0.00416 ( 21) SS BOND : angle 0.68941 ( 42) hydrogen bonds : bond 0.03547 ( 469) hydrogen bonds : angle 6.81537 ( 1221) link_NAG-ASN : bond 0.00546 ( 7) link_NAG-ASN : angle 3.10157 ( 21) *********************** 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 182 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.7333 (p) cc_final: 0.7016 (m) REVERT: A 467 ASP cc_start: 0.6743 (t70) cc_final: 0.6419 (t70) REVERT: A 495 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.5717 (t80) REVERT: B 468 ILE cc_start: 0.4650 (OUTLIER) cc_final: 0.4450 (tt) REVERT: B 510 VAL cc_start: 0.5498 (OUTLIER) cc_final: 0.5206 (t) REVERT: D 580 GLN cc_start: 0.5039 (OUTLIER) cc_final: 0.4687 (mt0) outliers start: 48 outliers final: 23 residues processed: 167 average time/residue: 0.1070 time to fit residues: 28.1273 Evaluate side-chains 148 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 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 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 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 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 172 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 153 optimal weight: 0.0370 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 179 optimal weight: 30.0000 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 D 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.231824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156756 restraints weight = 21606.550| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 4.59 r_work: 0.3730 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15833 Z= 0.256 Angle : 0.711 10.515 21558 Z= 0.368 Chirality : 0.051 0.248 2378 Planarity : 0.006 0.070 2776 Dihedral : 5.713 51.294 2246 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.93 % Favored : 93.86 % Rotamer: Outliers : 4.58 % Allowed : 14.22 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 1906 helix: -2.51 (0.36), residues: 151 sheet: -0.16 (0.21), residues: 591 loop : -1.45 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 466 TYR 0.024 0.002 TYR D 265 PHE 0.027 0.003 PHE A 86 TRP 0.022 0.002 TRP A 64 HIS 0.007 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00620 (15805) covalent geometry : angle 0.70497 (21495) SS BOND : bond 0.00518 ( 21) SS BOND : angle 0.87649 ( 42) hydrogen bonds : bond 0.04118 ( 469) hydrogen bonds : angle 6.69963 ( 1221) link_NAG-ASN : bond 0.00629 ( 7) link_NAG-ASN : angle 3.01160 ( 21) *********************** 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 211 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 133 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7893 (mtm180) REVERT: A 226 LEU cc_start: 0.5497 (OUTLIER) cc_final: 0.5085 (mp) REVERT: A 368 LEU cc_start: 0.8064 (mt) cc_final: 0.7845 (mt) REVERT: A 386 LYS cc_start: 0.3700 (mtmt) cc_final: 0.3465 (mtmt) REVERT: A 495 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.5827 (t80) REVERT: A 537 LYS cc_start: 0.7484 (mtpp) cc_final: 0.7174 (tttt) REVERT: B 131 CYS cc_start: 0.5674 (OUTLIER) cc_final: 0.5345 (m) REVERT: B 468 ILE cc_start: 0.4640 (OUTLIER) cc_final: 0.4364 (tt) REVERT: D 63 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8131 (t) REVERT: D 266 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8852 (m-80) REVERT: D 319 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.3391 (ppt90) REVERT: D 328 ARG cc_start: 0.5830 (OUTLIER) cc_final: 0.4831 (tpp-160) REVERT: D 580 GLN cc_start: 0.5091 (OUTLIER) cc_final: 0.4546 (mt0) outliers start: 78 outliers final: 42 residues processed: 202 average time/residue: 0.1152 time to fit residues: 35.9858 Evaluate side-chains 160 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 299 THR 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 495 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 549 THR 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 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 236 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 B residue 567 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 70 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 0.1980 chunk 166 optimal weight: 0.7980 chunk 121 optimal weight: 0.0870 chunk 125 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN C 5 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.235107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.164516 restraints weight = 21538.071| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.94 r_work: 0.3772 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15833 Z= 0.116 Angle : 0.588 9.328 21558 Z= 0.303 Chirality : 0.046 0.219 2378 Planarity : 0.005 0.072 2776 Dihedral : 5.273 55.603 2246 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.83 % Favored : 95.96 % Rotamer: Outliers : 2.76 % Allowed : 16.16 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 1906 helix: -2.23 (0.40), residues: 137 sheet: -0.04 (0.21), residues: 594 loop : -1.39 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.021 0.001 TYR A 473 PHE 0.018 0.001 PHE D 338 TRP 0.014 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00267 (15805) covalent geometry : angle 0.58262 (21495) SS BOND : bond 0.00317 ( 21) SS BOND : angle 0.73965 ( 42) hydrogen bonds : bond 0.03140 ( 469) hydrogen bonds : angle 6.40453 ( 1221) link_NAG-ASN : bond 0.00513 ( 7) link_NAG-ASN : angle 2.55060 ( 21) *********************** 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 166 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: E 82 MET cc_start: 0.6360 (mtp) cc_final: 0.6010 (mtm) REVERT: A 83 VAL cc_start: 0.5604 (OUTLIER) cc_final: 0.4194 (t) REVERT: A 104 TRP cc_start: 0.6540 (m-90) cc_final: 0.6334 (m-90) REVERT: A 190 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7791 (mtm180) REVERT: A 237 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7032 (ttt-90) REVERT: A 386 LYS cc_start: 0.3578 (mtmt) cc_final: 0.3316 (mtmt) REVERT: A 495 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6056 (t80) REVERT: A 508 TYR cc_start: 0.6602 (m-80) cc_final: 0.6190 (m-80) REVERT: B 131 CYS cc_start: 0.5664 (OUTLIER) cc_final: 0.5380 (m) REVERT: B 558 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7713 (mmtt) REVERT: D 319 ARG cc_start: 0.5208 (OUTLIER) cc_final: 0.3466 (ppt90) REVERT: D 328 ARG cc_start: 0.5833 (OUTLIER) cc_final: 0.4872 (tpp-160) REVERT: D 580 GLN cc_start: 0.5056 (OUTLIER) cc_final: 0.4561 (mt0) outliers start: 47 outliers final: 27 residues processed: 161 average time/residue: 0.1144 time to fit residues: 28.2041 Evaluate side-chains 144 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 LEU 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 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 547 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 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 156 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 162 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.232625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.157210 restraints weight = 21392.733| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 4.72 r_work: 0.3630 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15833 Z= 0.186 Angle : 0.622 10.360 21558 Z= 0.320 Chirality : 0.048 0.230 2378 Planarity : 0.005 0.067 2776 Dihedral : 5.128 53.023 2246 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.46 % Favored : 94.33 % Rotamer: Outliers : 3.64 % Allowed : 16.10 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.19), residues: 1906 helix: -2.06 (0.41), residues: 130 sheet: -0.19 (0.21), residues: 606 loop : -1.35 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 44 TYR 0.021 0.002 TYR D 265 PHE 0.020 0.002 PHE D 86 TRP 0.021 0.002 TRP A 64 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00448 (15805) covalent geometry : angle 0.61742 (21495) SS BOND : bond 0.00377 ( 21) SS BOND : angle 0.84638 ( 42) hydrogen bonds : bond 0.03419 ( 469) hydrogen bonds : angle 6.30376 ( 1221) link_NAG-ASN : bond 0.00527 ( 7) link_NAG-ASN : angle 2.43298 ( 21) *********************** 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 181 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 MET cc_start: 0.6683 (mtp) cc_final: 0.6348 (mpp) REVERT: A 106 PHE cc_start: 0.5092 (m-80) cc_final: 0.4888 (m-80) REVERT: A 190 ARG cc_start: 0.8382 (mtt180) cc_final: 0.8162 (mtm180) REVERT: A 203 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.6978 (tt) REVERT: A 205 SER cc_start: 0.9017 (p) cc_final: 0.8736 (t) REVERT: A 386 LYS cc_start: 0.3700 (mtmt) cc_final: 0.3338 (mtmt) REVERT: A 495 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6238 (t80) REVERT: A 537 LYS cc_start: 0.7539 (mtpp) cc_final: 0.7236 (tttt) REVERT: B 131 CYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5677 (m) REVERT: B 305 SER cc_start: 0.9370 (t) cc_final: 0.9086 (p) REVERT: C 80 LEU cc_start: -0.1052 (OUTLIER) cc_final: -0.1295 (tp) REVERT: D 266 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: D 319 ARG cc_start: 0.5275 (OUTLIER) cc_final: 0.3319 (ppt90) REVERT: D 328 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.4935 (tpp-160) REVERT: D 580 GLN cc_start: 0.4884 (OUTLIER) cc_final: 0.4395 (mt0) outliers start: 62 outliers final: 44 residues processed: 173 average time/residue: 0.1090 time to fit residues: 29.3925 Evaluate side-chains 164 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 203 ILE 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 351 TYR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 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 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 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU 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 139 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 154 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.233266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.163233 restraints weight = 21400.608| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 4.58 r_work: 0.3704 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15833 Z= 0.142 Angle : 0.584 9.433 21558 Z= 0.301 Chirality : 0.046 0.223 2378 Planarity : 0.005 0.063 2776 Dihedral : 5.020 54.513 2246 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.62 % Favored : 95.17 % Rotamer: Outliers : 3.35 % Allowed : 17.10 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.19), residues: 1906 helix: -1.98 (0.42), residues: 130 sheet: -0.17 (0.21), residues: 591 loop : -1.34 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.015 0.001 TYR D 265 PHE 0.022 0.002 PHE E 29 TRP 0.015 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00337 (15805) covalent geometry : angle 0.57885 (21495) SS BOND : bond 0.00337 ( 21) SS BOND : angle 0.88604 ( 42) hydrogen bonds : bond 0.03189 ( 469) hydrogen bonds : angle 6.19023 ( 1221) link_NAG-ASN : bond 0.00467 ( 7) link_NAG-ASN : angle 2.26990 ( 21) *********************** 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 168 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7938 (mtm180) REVERT: A 203 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6950 (tt) REVERT: A 205 SER cc_start: 0.8943 (p) cc_final: 0.8666 (t) REVERT: A 237 ARG cc_start: 0.7572 (mtt180) cc_final: 0.7323 (ttt-90) REVERT: A 319 ARG cc_start: 0.6551 (mmt180) cc_final: 0.6236 (mmt180) REVERT: A 324 GLU cc_start: 0.7723 (pm20) cc_final: 0.6820 (pm20) REVERT: A 386 LYS cc_start: 0.3720 (mtmt) cc_final: 0.3368 (mtmt) REVERT: A 495 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6250 (t80) REVERT: A 537 LYS cc_start: 0.7499 (mtpp) cc_final: 0.7252 (tttt) REVERT: B 131 CYS cc_start: 0.5837 (OUTLIER) cc_final: 0.5629 (m) REVERT: B 305 SER cc_start: 0.9356 (t) cc_final: 0.9076 (p) REVERT: B 558 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7803 (mmtm) REVERT: C 80 LEU cc_start: -0.1097 (OUTLIER) cc_final: -0.1346 (tp) REVERT: D 266 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8738 (m-80) REVERT: D 319 ARG cc_start: 0.5348 (OUTLIER) cc_final: 0.3315 (ppt90) REVERT: D 328 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.4834 (tpp-160) REVERT: D 571 ASP cc_start: 0.5543 (p0) cc_final: 0.5234 (p0) REVERT: D 580 GLN cc_start: 0.4864 (OUTLIER) cc_final: 0.4458 (mt0) outliers start: 57 outliers final: 38 residues processed: 162 average time/residue: 0.1098 time to fit residues: 27.4551 Evaluate side-chains 155 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 547 THR 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 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 433 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU 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 88 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.232475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160793 restraints weight = 21203.590| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 4.88 r_work: 0.3644 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15833 Z= 0.152 Angle : 0.582 9.473 21558 Z= 0.300 Chirality : 0.046 0.226 2378 Planarity : 0.005 0.059 2776 Dihedral : 4.925 54.268 2246 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.04 % Favored : 94.75 % Rotamer: Outliers : 3.58 % Allowed : 17.33 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 1906 helix: -1.91 (0.42), residues: 130 sheet: -0.21 (0.21), residues: 601 loop : -1.28 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 328 TYR 0.016 0.001 TYR D 265 PHE 0.022 0.002 PHE E 29 TRP 0.020 0.002 TRP A 64 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00363 (15805) covalent geometry : angle 0.57785 (21495) SS BOND : bond 0.00326 ( 21) SS BOND : angle 0.86538 ( 42) hydrogen bonds : bond 0.03157 ( 469) hydrogen bonds : angle 6.09973 ( 1221) link_NAG-ASN : bond 0.00449 ( 7) link_NAG-ASN : angle 2.11994 ( 21) *********************** 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 172 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 111 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8423 (mtt180) cc_final: 0.7948 (mtm180) REVERT: A 203 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6968 (tt) REVERT: A 205 SER cc_start: 0.9014 (p) cc_final: 0.8730 (t) REVERT: A 324 GLU cc_start: 0.7746 (pm20) cc_final: 0.7315 (pm20) REVERT: A 386 LYS cc_start: 0.3647 (mtmt) cc_final: 0.3186 (mtmt) REVERT: A 495 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.5996 (t80) REVERT: A 537 LYS cc_start: 0.7586 (mtpp) cc_final: 0.7312 (ttpt) REVERT: B 131 CYS cc_start: 0.5967 (OUTLIER) cc_final: 0.5731 (m) REVERT: B 305 SER cc_start: 0.9407 (t) cc_final: 0.9141 (p) REVERT: B 558 LYS cc_start: 0.8276 (mmtm) cc_final: 0.7844 (mmtm) REVERT: C 80 LEU cc_start: -0.1147 (OUTLIER) cc_final: -0.1400 (tp) REVERT: D 266 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: D 319 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.3458 (ppt90) REVERT: D 328 ARG cc_start: 0.5857 (OUTLIER) cc_final: 0.4793 (tpp-160) REVERT: D 580 GLN cc_start: 0.4837 (OUTLIER) cc_final: 0.4445 (mt0) outliers start: 61 outliers final: 47 residues processed: 165 average time/residue: 0.1131 time to fit residues: 28.4932 Evaluate side-chains 161 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 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 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 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 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 318 PHE Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 116 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 149 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 166 optimal weight: 30.0000 chunk 184 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.232593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.163324 restraints weight = 21419.626| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 4.26 r_work: 0.3671 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15833 Z= 0.144 Angle : 0.578 9.457 21558 Z= 0.298 Chirality : 0.046 0.225 2378 Planarity : 0.005 0.057 2776 Dihedral : 4.856 54.525 2246 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.51 % Favored : 95.28 % Rotamer: Outliers : 3.29 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.19), residues: 1906 helix: -1.76 (0.42), residues: 131 sheet: -0.17 (0.21), residues: 599 loop : -1.28 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 328 TYR 0.015 0.001 TYR D 265 PHE 0.022 0.001 PHE E 29 TRP 0.018 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00345 (15805) covalent geometry : angle 0.57442 (21495) SS BOND : bond 0.00313 ( 21) SS BOND : angle 0.77725 ( 42) hydrogen bonds : bond 0.03145 ( 469) hydrogen bonds : angle 6.04458 ( 1221) link_NAG-ASN : bond 0.00435 ( 7) link_NAG-ASN : angle 2.02236 ( 21) *********************** 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 167 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 111 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: E 82 MET cc_start: 0.6581 (mtp) cc_final: 0.6077 (mtm) REVERT: A 190 ARG cc_start: 0.8396 (mtt180) cc_final: 0.7989 (mtm180) REVERT: A 205 SER cc_start: 0.8964 (p) cc_final: 0.8693 (t) REVERT: A 386 LYS cc_start: 0.3654 (mtmt) cc_final: 0.3201 (mtmt) REVERT: A 495 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6026 (t80) REVERT: A 537 LYS cc_start: 0.7601 (mtpp) cc_final: 0.7349 (ttpt) REVERT: B 95 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8005 (p) REVERT: B 131 CYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5702 (m) REVERT: B 305 SER cc_start: 0.9392 (t) cc_final: 0.9124 (p) REVERT: B 558 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7847 (mmtm) REVERT: C 80 LEU cc_start: -0.1137 (OUTLIER) cc_final: -0.1396 (tp) REVERT: D 266 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: D 319 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.3438 (ppt90) REVERT: D 328 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.4785 (ttp-170) REVERT: D 580 GLN cc_start: 0.4869 (OUTLIER) cc_final: 0.4486 (mt0) outliers start: 56 outliers final: 44 residues processed: 161 average time/residue: 0.1139 time to fit residues: 28.3760 Evaluate side-chains 158 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 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 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 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU 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 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 D 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.232905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.161753 restraints weight = 21267.203| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 4.06 r_work: 0.3729 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15833 Z= 0.131 Angle : 0.567 9.418 21558 Z= 0.293 Chirality : 0.046 0.226 2378 Planarity : 0.005 0.055 2776 Dihedral : 4.778 54.970 2246 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.35 % Favored : 95.44 % Rotamer: Outliers : 3.35 % Allowed : 17.51 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.19), residues: 1906 helix: -1.68 (0.42), residues: 137 sheet: -0.03 (0.21), residues: 596 loop : -1.28 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 237 TYR 0.014 0.001 TYR D 265 PHE 0.021 0.001 PHE E 29 TRP 0.017 0.001 TRP A 64 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00311 (15805) covalent geometry : angle 0.56406 (21495) SS BOND : bond 0.00285 ( 21) SS BOND : angle 0.72564 ( 42) hydrogen bonds : bond 0.03049 ( 469) hydrogen bonds : angle 5.98987 ( 1221) link_NAG-ASN : bond 0.00422 ( 7) link_NAG-ASN : angle 1.87665 ( 21) *********************** 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 169 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 112 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 MET cc_start: 0.6456 (mtp) cc_final: 0.6141 (mtm) REVERT: A 190 ARG cc_start: 0.8396 (mtt180) cc_final: 0.8002 (mtm180) REVERT: A 203 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7044 (tt) REVERT: A 205 SER cc_start: 0.8918 (p) cc_final: 0.8667 (t) REVERT: A 386 LYS cc_start: 0.3699 (mtmt) cc_final: 0.3122 (mtmt) REVERT: A 495 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.5959 (t80) REVERT: A 537 LYS cc_start: 0.7615 (mtpp) cc_final: 0.7398 (ttpt) REVERT: B 95 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 305 SER cc_start: 0.9371 (t) cc_final: 0.9114 (p) REVERT: B 558 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7872 (mmtm) REVERT: C 80 LEU cc_start: -0.1181 (OUTLIER) cc_final: -0.1438 (tp) REVERT: D 266 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8669 (m-80) REVERT: D 319 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.3408 (ppt90) REVERT: D 328 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.4694 (tpp80) REVERT: D 580 GLN cc_start: 0.4995 (OUTLIER) cc_final: 0.4685 (mt0) outliers start: 57 outliers final: 45 residues processed: 161 average time/residue: 0.1139 time to fit residues: 28.4800 Evaluate side-chains 161 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 203 ILE 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 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 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 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 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 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 319 ARG Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 580 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 19 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 49 optimal weight: 0.0070 chunk 132 optimal weight: 8.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.232723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.159261 restraints weight = 21027.531| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 4.22 r_work: 0.3694 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15833 Z= 0.168 Angle : 0.598 9.721 21558 Z= 0.309 Chirality : 0.047 0.245 2378 Planarity : 0.005 0.055 2776 Dihedral : 4.866 52.877 2246 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.30 % Favored : 94.49 % Rotamer: Outliers : 3.41 % Allowed : 17.57 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 1906 helix: -1.76 (0.42), residues: 131 sheet: -0.11 (0.21), residues: 593 loop : -1.29 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.017 0.001 TYR B 265 PHE 0.019 0.002 PHE E 29 TRP 0.018 0.002 TRP A 64 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00404 (15805) covalent geometry : angle 0.59351 (21495) SS BOND : bond 0.00573 ( 21) SS BOND : angle 1.09055 ( 42) hydrogen bonds : bond 0.03239 ( 469) hydrogen bonds : angle 5.98326 ( 1221) link_NAG-ASN : bond 0.00630 ( 7) link_NAG-ASN : angle 1.93053 ( 21) ********************** 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 172 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 MET cc_start: 0.6666 (mtp) cc_final: 0.6264 (mtm) REVERT: A 170 TYR cc_start: 0.5138 (t80) cc_final: 0.4655 (t80) REVERT: A 190 ARG cc_start: 0.8389 (mtt180) cc_final: 0.8059 (mtm180) REVERT: A 203 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7073 (tt) REVERT: A 386 LYS cc_start: 0.3733 (mtmt) cc_final: 0.3246 (mtmt) REVERT: A 495 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.5881 (t80) REVERT: A 508 TYR cc_start: 0.6809 (m-80) cc_final: 0.6467 (m-80) REVERT: A 537 LYS cc_start: 0.7699 (mtpp) cc_final: 0.7461 (ttpt) REVERT: B 95 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 305 SER cc_start: 0.9393 (t) cc_final: 0.9148 (p) REVERT: B 558 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7886 (mmtm) REVERT: D 266 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: D 319 ARG cc_start: 0.5546 (OUTLIER) cc_final: 0.3525 (ppt90) outliers start: 58 outliers final: 48 residues processed: 164 average time/residue: 0.1127 time to fit residues: 28.9432 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 : 0.595 ------------------------------------------------------------------------------- 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 203 ILE 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 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 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 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 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 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 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 23 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 125 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 0.0020 chunk 69 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.233412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.159732 restraints weight = 21209.454| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 4.43 r_work: 0.3692 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15833 Z= 0.108 Angle : 0.564 9.418 21558 Z= 0.292 Chirality : 0.046 0.226 2378 Planarity : 0.005 0.053 2776 Dihedral : 4.761 55.817 2246 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 2.94 % Allowed : 18.39 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 1906 helix: -1.53 (0.45), residues: 124 sheet: -0.01 (0.21), residues: 594 loop : -1.27 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.012 0.001 TYR B 170 PHE 0.021 0.001 PHE E 29 TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00248 (15805) covalent geometry : angle 0.56065 (21495) SS BOND : bond 0.00284 ( 21) SS BOND : angle 0.94603 ( 42) hydrogen bonds : bond 0.02859 ( 469) hydrogen bonds : angle 5.91394 ( 1221) link_NAG-ASN : bond 0.00416 ( 7) link_NAG-ASN : angle 1.69801 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5140.69 seconds wall clock time: 88 minutes 12.39 seconds (5292.39 seconds total)