Starting phenix.real_space_refine on Thu Jul 2 17:41:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mbz_63783/07_2026/9mbz_63783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mbz_63783/07_2026/9mbz_63783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mbz_63783/07_2026/9mbz_63783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mbz_63783/07_2026/9mbz_63783.map" model { file = "/net/cci-nas-00/data/ceres_data/9mbz_63783/07_2026/9mbz_63783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mbz_63783/07_2026/9mbz_63783.cif" } resolution = 3.3 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 45 5.16 5 C 5872 2.51 5 N 1595 2.21 5 O 1784 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9296 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1956 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 17, 'TRANS': 222} Chain breaks: 2 Chain: "A" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1547 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain breaks: 4 Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1518 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 15, 'TRANS': 184} Chain breaks: 4 Chain: "C" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1480 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 13, 'TRANS': 179} Chain breaks: 5 Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain breaks: 2 Chain: "J" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.88, per 1000 atoms: 0.20 Number of scatterers: 9296 At special positions: 0 Unit cell: (125.33, 116.2, 138.61, 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 45 16.00 O 1784 8.00 N 1595 7.00 C 5872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 85 " distance=2.03 Simple disulfide: pdb=" SG CYS F 123 " - pdb=" SG CYS F 167 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 261 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 369 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.04 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 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 BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 501 " - " ASN A 459 " " NAG B 501 " - " ASN B 459 " " NAG C 501 " - " ASN C 459 " " NAG D 501 " - " ASN D 459 " " NAG E 1 " - " ASN J 48 " " NAG F 501 " - " ASN F 147 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 448.5 milliseconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 31 sheets defined 10.7% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.643A pdb=" N TRP A 315 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.890A pdb=" N LEU A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.637A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 Processing helix chain 'C' and resid 252 through 258 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'D' and resid 252 through 258 Processing helix chain 'D' and resid 311 through 317 Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.757A pdb=" N LEU D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'J' and resid 64 through 68 Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.591A pdb=" N THR F 70 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'F' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.523A pdb=" N TYR F 136 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE F 145 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL F 134 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.523A pdb=" N TYR F 136 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE F 145 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL F 134 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP F 175 " --> pdb=" O GLY F 171 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 176 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL J 8 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ARG F 178 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP J 9 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N HIS C 457 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 460 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN C 459 " --> pdb=" O VAL D 460 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL D 462 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER C 461 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N MET D 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 225 through 229 removed outlier: 3.522A pdb=" N ALA F 263 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 272 " --> pdb=" O ALA F 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 247 through 249 removed outlier: 4.304A pdb=" N LEU A 264 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 308 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.693A pdb=" N THR A 324 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 321 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 338 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.732A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.732A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 388 through 389 removed outlier: 3.644A pdb=" N CYS A 432 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 446 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE A 443 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 460 through 464 removed outlier: 6.614A pdb=" N VAL A 460 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL B 463 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 462 " --> pdb=" O VAL B 463 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AB6, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.577A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.577A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AB9, first strand: chain 'B' and resid 388 through 389 removed outlier: 3.658A pdb=" N CYS B 432 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 434 " --> pdb=" O THR B 444 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 246 through 249 Processing sheet with id=AC2, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AC3, first strand: chain 'C' and resid 350 through 352 removed outlier: 3.685A pdb=" N THR C 368 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE C 411 " --> pdb=" O GLY C 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 350 through 352 removed outlier: 3.685A pdb=" N THR C 368 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE C 411 " --> pdb=" O GLY C 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 380 through 381 Processing sheet with id=AC6, first strand: chain 'C' and resid 384 through 385 Processing sheet with id=AC7, first strand: chain 'D' and resid 247 through 248 removed outlier: 4.038A pdb=" N LEU D 264 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 321 through 325 removed outlier: 3.798A pdb=" N ALA D 325 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 350 through 352 removed outlier: 5.508A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 350 through 352 removed outlier: 5.508A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 388 through 389 removed outlier: 3.772A pdb=" N CYS D 432 " --> pdb=" O LYS D 446 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AD4, first strand: chain 'J' and resid 74 through 77 325 hydrogen bonds defined for protein. 807 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: 1.63 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1682 1.32 - 1.45: 2372 1.45 - 1.57: 5400 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 9508 Sorted by residual: bond pdb=" CA GLN D 445 " pdb=" C GLN D 445 " ideal model delta sigma weight residual 1.520 1.461 0.060 1.17e-02 7.31e+03 2.60e+01 bond pdb=" CA SER D 356 " pdb=" C SER D 356 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.36e-02 5.41e+03 1.65e+01 bond pdb=" CA PRO D 404 " pdb=" C PRO D 404 " ideal model delta sigma weight residual 1.524 1.487 0.037 9.20e-03 1.18e+04 1.60e+01 bond pdb=" C LEU F 216 " pdb=" N PRO F 217 " ideal model delta sigma weight residual 1.329 1.375 -0.046 1.18e-02 7.18e+03 1.51e+01 bond pdb=" N SER D 356 " pdb=" CA SER D 356 " ideal model delta sigma weight residual 1.459 1.412 0.047 1.25e-02 6.40e+03 1.40e+01 ... (remaining 9503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 12676 2.90 - 5.79: 218 5.79 - 8.69: 39 8.69 - 11.58: 12 11.58 - 14.48: 2 Bond angle restraints: 12947 Sorted by residual: angle pdb=" N GLU F 245 " pdb=" CA GLU F 245 " pdb=" C GLU F 245 " ideal model delta sigma weight residual 112.59 122.42 -9.83 1.22e+00 6.72e-01 6.49e+01 angle pdb=" N ASP B 378 " pdb=" CA ASP B 378 " pdb=" C ASP B 378 " ideal model delta sigma weight residual 110.10 120.88 -10.78 1.49e+00 4.50e-01 5.24e+01 angle pdb=" N ILE F 236 " pdb=" CA ILE F 236 " pdb=" C ILE F 236 " ideal model delta sigma weight residual 108.80 118.66 -9.86 1.46e+00 4.69e-01 4.56e+01 angle pdb=" N LEU F 237 " pdb=" CA LEU F 237 " pdb=" C LEU F 237 " ideal model delta sigma weight residual 112.54 104.86 7.68 1.22e+00 6.72e-01 3.96e+01 angle pdb=" N GLU F 129 " pdb=" CA GLU F 129 " pdb=" C GLU F 129 " ideal model delta sigma weight residual 110.20 101.32 8.88 1.58e+00 4.01e-01 3.16e+01 ... (remaining 12942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5039 17.95 - 35.89: 633 35.89 - 53.84: 155 53.84 - 71.79: 29 71.79 - 89.73: 14 Dihedral angle restraints: 5870 sinusoidal: 2454 harmonic: 3416 Sorted by residual: dihedral pdb=" CB CYS D 471 " pdb=" SG CYS D 471 " pdb=" SG CYS J 14 " pdb=" CB CYS J 14 " ideal model delta sinusoidal sigma weight residual -86.00 -157.49 71.49 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CA HIS F 28 " pdb=" C HIS F 28 " pdb=" N PRO F 29 " pdb=" CA PRO F 29 " ideal model delta harmonic sigma weight residual 180.00 151.89 28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CB CYS J 12 " pdb=" SG CYS J 12 " pdb=" SG CYS J 100 " pdb=" CB CYS J 100 " ideal model delta sinusoidal sigma weight residual -86.00 -125.74 39.74 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 5867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1249 0.065 - 0.129: 229 0.129 - 0.194: 32 0.194 - 0.259: 11 0.259 - 0.323: 8 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CA GLU F 245 " pdb=" N GLU F 245 " pdb=" C GLU F 245 " pdb=" CB GLU F 245 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PRO F 218 " pdb=" N PRO F 218 " pdb=" C PRO F 218 " pdb=" CB PRO F 218 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CG LEU D 268 " pdb=" CB LEU D 268 " pdb=" CD1 LEU D 268 " pdb=" CD2 LEU D 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1526 not shown) Planarity restraints: 1636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 308 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO A 309 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 403 " 0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO C 404 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 404 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 404 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 327 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO D 328 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " -0.034 5.00e-02 4.00e+02 ... (remaining 1633 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1977 2.79 - 3.32: 7512 3.32 - 3.84: 15455 3.84 - 4.37: 17686 4.37 - 4.90: 31514 Nonbonded interactions: 74144 Sorted by model distance: nonbonded pdb=" O ASN A 459 " pdb=" OG1 THR J 58 " model vdw 2.260 3.040 nonbonded pdb=" O PRO F 193 " pdb=" OG SER F 274 " model vdw 2.308 3.040 nonbonded pdb=" OE1 GLN C 402 " pdb=" OG1 THR C 409 " model vdw 2.323 3.040 nonbonded pdb=" OG1 THR C 429 " pdb=" OG1 THR C 447 " model vdw 2.323 3.040 nonbonded pdb=" O THR D 409 " pdb=" OG1 THR D 409 " model vdw 2.345 3.040 ... (remaining 74139 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' and (resid 244 through 267 or resid 278 through 280 or resid 288 thro \ ugh 292 or resid 303 through 307 or resid 314 through 464 or resid 501)) selection = (chain 'B' and (resid 244 through 267 or resid 278 through 280 or resid 288 thro \ ugh 292 or resid 303 through 307 or resid 314 through 325 or resid 334 through 4 \ 64 or resid 501)) selection = (chain 'C' and (resid 244 through 267 or resid 278 through 280 or resid 288 thro \ ugh 292 or resid 303 through 325 or resid 334 through 501)) selection = (chain 'D' and (resid 244 through 267 or resid 278 through 280 or resid 284 or r \ esid 289 through 292 or resid 303 through 307 or resid 314 through 325 or resid \ 334 through 464 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.006 0.071 9532 Z= 0.305 Angle : 0.975 14.477 13003 Z= 0.519 Chirality : 0.057 0.323 1529 Planarity : 0.008 0.104 1630 Dihedral : 16.885 89.733 3590 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.87 % Allowed : 27.55 % Favored : 71.58 % Cbeta Deviations : 0.09 % 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: -2.69 (0.22), residues: 1137 helix: -3.72 (0.31), residues: 112 sheet: -1.16 (0.24), residues: 404 loop : -1.82 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 450 TYR 0.027 0.002 TYR B 395 PHE 0.029 0.002 PHE A 411 TRP 0.016 0.001 TRP F 260 HIS 0.006 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.31 ( 9508) covalent geometry : angle 0.97005 / 0.52 (12947) SS BOND : bond 0.00476 / 0.28 ( 16) SS BOND : angle 1.02336 / 0.60 ( 32) hydrogen bonds : bond 0.26649 / 17.41 ( 266) hydrogen bonds : angle 10.10893 / 7.01 ( 807) link_BETA1-4 : bond 0.01092 / 0.57 ( 1) link_BETA1-4 : angle 2.30913 / 1.22 ( 3) link_BETA1-6 : bond 0.00396 / 0.21 ( 1) link_BETA1-6 : angle 1.08928 / 0.60 ( 3) link_NAG-ASN : bond 0.00991 / 0.53 ( 6) link_NAG-ASN : angle 2.52006 / 1.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.7812 (mmm) cc_final: 0.7483 (mmm) REVERT: B 321 PHE cc_start: 0.3672 (OUTLIER) cc_final: 0.3362 (m-80) REVERT: D 279 PHE cc_start: 0.7969 (m-80) cc_final: 0.7758 (m-80) REVERT: D 357 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7413 (pm20) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.0897 time to fit residues: 16.4253 Evaluate side-chains 128 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 217 PRO Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 124 HIS C 402 GLN J 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.185187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.170354 restraints weight = 10595.421| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.83 r_work: 0.3619 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9532 Z= 0.150 Angle : 0.650 10.735 13003 Z= 0.315 Chirality : 0.041 0.225 1529 Planarity : 0.006 0.070 1630 Dihedral : 6.199 58.722 1427 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.56 % Allowed : 24.95 % Favored : 71.48 % 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: -2.15 (0.23), residues: 1137 helix: -2.50 (0.38), residues: 119 sheet: -0.84 (0.24), residues: 405 loop : -1.58 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.013 0.001 TYR F 243 PHE 0.015 0.001 PHE C 374 TRP 0.007 0.001 TRP C 315 HIS 0.003 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9508) covalent geometry : angle 0.64395 / 0.31 (12947) SS BOND : bond 0.00352 / 0.22 ( 16) SS BOND : angle 1.39395 / 0.94 ( 32) hydrogen bonds : bond 0.04332 / 2.87 ( 266) hydrogen bonds : angle 6.45698 / 4.39 ( 807) link_BETA1-4 : bond 0.00398 / 0.21 ( 1) link_BETA1-4 : angle 1.49846 / 0.77 ( 3) link_BETA1-6 : bond 0.00363 / 0.19 ( 1) link_BETA1-6 : angle 1.26982 / 0.69 ( 3) link_NAG-ASN : bond 0.00349 / 0.18 ( 6) link_NAG-ASN : angle 1.54971 / 1.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 166 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7499 (ttm170) REVERT: B 321 PHE cc_start: 0.3728 (OUTLIER) cc_final: 0.3295 (m-80) REVERT: D 401 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7400 (mtm-85) REVERT: J 89 ASN cc_start: 0.7595 (m-40) cc_final: 0.6826 (m110) outliers start: 37 outliers final: 18 residues processed: 154 average time/residue: 0.0906 time to fit residues: 18.6908 Evaluate side-chains 137 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 106 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 362 ASN C 402 GLN J 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.184915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.171150 restraints weight = 10559.858| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 0.86 r_work: 0.4100 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 9532 Z= 0.297 Angle : 0.764 10.454 13003 Z= 0.371 Chirality : 0.045 0.212 1529 Planarity : 0.006 0.060 1630 Dihedral : 6.042 59.617 1417 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.97 % Allowed : 24.18 % Favored : 69.85 % 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: -2.06 (0.23), residues: 1137 helix: -1.85 (0.40), residues: 119 sheet: -1.01 (0.24), residues: 421 loop : -1.47 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 418 TYR 0.016 0.002 TYR A 472 PHE 0.028 0.002 PHE C 374 TRP 0.009 0.002 TRP C 315 HIS 0.009 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.30 ( 9508) covalent geometry : angle 0.75738 / 0.37 (12947) SS BOND : bond 0.00769 / 0.52 ( 16) SS BOND : angle 1.65858 / 1.10 ( 32) hydrogen bonds : bond 0.04544 / 2.96 ( 266) hydrogen bonds : angle 6.53100 / 4.38 ( 807) link_BETA1-4 : bond 0.00277 / 0.15 ( 1) link_BETA1-4 : angle 1.28775 / 0.66 ( 3) link_BETA1-6 : bond 0.00166 / 0.09 ( 1) link_BETA1-6 : angle 1.28949 / 0.70 ( 3) link_NAG-ASN : bond 0.00356 / 0.18 ( 6) link_NAG-ASN : angle 1.91084 / 1.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7948 (tp) REVERT: B 321 PHE cc_start: 0.3460 (OUTLIER) cc_final: 0.3150 (m-80) REVERT: B 417 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8846 (tp) REVERT: D 401 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7628 (mtm-85) REVERT: J 59 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7397 (tpt90) outliers start: 62 outliers final: 38 residues processed: 169 average time/residue: 0.0837 time to fit residues: 19.5979 Evaluate side-chains 159 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 ARG Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 95 optimal weight: 0.0870 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 GLN C 362 ASN C 402 GLN J 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.206627 restraints weight = 9666.379| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 0.41 r_work: 0.3799 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work: 0.3654 rms_B_bonded: 2.64 restraints_weight: 0.1250 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9532 Z= 0.151 Angle : 0.653 11.913 13003 Z= 0.307 Chirality : 0.041 0.168 1529 Planarity : 0.005 0.055 1630 Dihedral : 5.692 59.457 1416 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.62 % Allowed : 25.63 % Favored : 69.75 % 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: -1.84 (0.24), residues: 1137 helix: -1.34 (0.44), residues: 119 sheet: -0.88 (0.24), residues: 420 loop : -1.40 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 16 TYR 0.012 0.001 TYR F 243 PHE 0.014 0.001 PHE D 374 TRP 0.008 0.001 TRP F 150 HIS 0.003 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 9508) covalent geometry : angle 0.63467 / 0.30 (12947) SS BOND : bond 0.00392 / 0.25 ( 16) SS BOND : angle 1.18920 / 0.75 ( 32) hydrogen bonds : bond 0.03469 / 2.29 ( 266) hydrogen bonds : angle 6.08444 / 4.08 ( 807) link_BETA1-4 : bond 0.00317 / 0.17 ( 1) link_BETA1-4 : angle 1.23053 / 0.63 ( 3) link_BETA1-6 : bond 0.00401 / 0.21 ( 1) link_BETA1-6 : angle 1.30726 / 0.71 ( 3) link_NAG-ASN : bond 0.00614 / 0.48 ( 6) link_NAG-ASN : angle 3.89280 / 2.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 108 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7876 (mm-40) REVERT: A 451 LEU cc_start: 0.8052 (mm) cc_final: 0.7795 (mm) REVERT: B 321 PHE cc_start: 0.3516 (OUTLIER) cc_final: 0.3152 (m-80) REVERT: D 401 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7594 (mtm-85) REVERT: J 89 ASN cc_start: 0.8475 (m-40) cc_final: 0.6741 (m110) outliers start: 48 outliers final: 37 residues processed: 157 average time/residue: 0.0847 time to fit residues: 18.7362 Evaluate side-chains 155 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 362 ASN Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 101 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 350 HIS C 362 ASN J 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.179611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.162096 restraints weight = 10549.549| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 0.90 r_work: 0.3584 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9532 Z= 0.170 Angle : 0.646 10.543 13003 Z= 0.304 Chirality : 0.041 0.161 1529 Planarity : 0.005 0.054 1630 Dihedral : 5.519 59.381 1416 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.26 % Allowed : 24.47 % Favored : 69.27 % 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: -1.73 (0.24), residues: 1137 helix: -0.99 (0.47), residues: 113 sheet: -0.88 (0.24), residues: 419 loop : -1.32 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 16 TYR 0.012 0.001 TYR A 472 PHE 0.016 0.001 PHE C 374 TRP 0.008 0.001 TRP F 150 HIS 0.004 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 9508) covalent geometry : angle 0.62988 / 0.30 (12947) SS BOND : bond 0.00445 / 0.29 ( 16) SS BOND : angle 1.14278 / 0.72 ( 32) hydrogen bonds : bond 0.03371 / 2.23 ( 266) hydrogen bonds : angle 5.91828 / 3.96 ( 807) link_BETA1-4 : bond 0.00286 / 0.15 ( 1) link_BETA1-4 : angle 1.23042 / 0.63 ( 3) link_BETA1-6 : bond 0.00306 / 0.16 ( 1) link_BETA1-6 : angle 1.23685 / 0.67 ( 3) link_NAG-ASN : bond 0.00508 / 0.38 ( 6) link_NAG-ASN : angle 3.62157 / 2.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 116 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 LEU cc_start: 0.8004 (mm) cc_final: 0.7789 (mm) REVERT: B 321 PHE cc_start: 0.3759 (OUTLIER) cc_final: 0.3334 (m-80) REVERT: B 417 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8848 (tp) REVERT: D 401 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7574 (mtm-85) REVERT: J 59 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7211 (tpt90) REVERT: J 89 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.6854 (m110) outliers start: 65 outliers final: 48 residues processed: 167 average time/residue: 0.0875 time to fit residues: 20.3930 Evaluate side-chains 168 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 115 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 ARG Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 103 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.180676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.161598 restraints weight = 10608.867| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 0.91 r_work: 0.3572 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9532 Z= 0.145 Angle : 0.621 10.262 13003 Z= 0.293 Chirality : 0.040 0.155 1529 Planarity : 0.005 0.050 1630 Dihedral : 5.358 59.450 1416 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.17 % Allowed : 25.34 % Favored : 68.50 % 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: -1.68 (0.24), residues: 1137 helix: -0.77 (0.49), residues: 112 sheet: -0.90 (0.24), residues: 417 loop : -1.27 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 105 TYR 0.011 0.001 TYR A 472 PHE 0.015 0.001 PHE D 374 TRP 0.008 0.001 TRP F 150 HIS 0.003 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9508) covalent geometry : angle 0.60794 / 0.29 (12947) SS BOND : bond 0.00371 / 0.22 ( 16) SS BOND : angle 1.04276 / 0.64 ( 32) hydrogen bonds : bond 0.03202 / 2.13 ( 266) hydrogen bonds : angle 5.72427 / 3.84 ( 807) link_BETA1-4 : bond 0.00178 / 0.09 ( 1) link_BETA1-4 : angle 1.19600 / 0.61 ( 3) link_BETA1-6 : bond 0.00215 / 0.11 ( 1) link_BETA1-6 : angle 1.19498 / 0.64 ( 3) link_NAG-ASN : bond 0.00477 / 0.36 ( 6) link_NAG-ASN : angle 3.25971 / 2.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 108 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7885 (mm-40) REVERT: B 321 PHE cc_start: 0.3783 (OUTLIER) cc_final: 0.3363 (m-80) REVERT: B 417 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8791 (tp) REVERT: D 401 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7540 (mtm-85) REVERT: D 422 GLU cc_start: 0.8342 (tp30) cc_final: 0.7504 (mp0) REVERT: J 59 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7180 (tpt90) REVERT: J 89 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.6839 (m110) outliers start: 64 outliers final: 49 residues processed: 169 average time/residue: 0.0764 time to fit residues: 17.7981 Evaluate side-chains 170 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 ASN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 ARG Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.178322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.160936 restraints weight = 10591.293| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 0.89 r_work: 0.3570 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9532 Z= 0.196 Angle : 0.657 10.225 13003 Z= 0.311 Chirality : 0.042 0.190 1529 Planarity : 0.005 0.050 1630 Dihedral : 5.413 59.700 1416 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.94 % Allowed : 24.76 % Favored : 68.30 % 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: -1.73 (0.24), residues: 1137 helix: -0.82 (0.47), residues: 118 sheet: -0.95 (0.24), residues: 414 loop : -1.30 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 57 TYR 0.013 0.001 TYR A 472 PHE 0.019 0.002 PHE C 374 TRP 0.007 0.001 TRP D 281 HIS 0.005 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 9508) covalent geometry : angle 0.64493 / 0.31 (12947) SS BOND : bond 0.00530 / 0.34 ( 16) SS BOND : angle 1.14151 / 0.72 ( 32) hydrogen bonds : bond 0.03439 / 2.27 ( 266) hydrogen bonds : angle 5.78817 / 3.89 ( 807) link_BETA1-4 : bond 0.00271 / 0.14 ( 1) link_BETA1-4 : angle 1.19059 / 0.61 ( 3) link_BETA1-6 : bond 0.00213 / 0.11 ( 1) link_BETA1-6 : angle 1.23383 / 0.66 ( 3) link_NAG-ASN : bond 0.00442 / 0.32 ( 6) link_NAG-ASN : angle 3.06760 / 2.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 116 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: F 108 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7919 (mm-40) REVERT: B 321 PHE cc_start: 0.3854 (OUTLIER) cc_final: 0.3462 (m-80) REVERT: B 417 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8802 (tp) REVERT: D 401 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7550 (mtm-85) REVERT: D 422 GLU cc_start: 0.8251 (tp30) cc_final: 0.7462 (mp0) REVERT: J 59 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7211 (tpt90) REVERT: J 89 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.6974 (m110) outliers start: 72 outliers final: 52 residues processed: 173 average time/residue: 0.0797 time to fit residues: 19.3657 Evaluate side-chains 175 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 117 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 ASN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 ARG Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 68 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.179175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.161552 restraints weight = 10499.127| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 0.88 r_work: 0.3579 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9532 Z= 0.164 Angle : 0.636 10.221 13003 Z= 0.300 Chirality : 0.041 0.176 1529 Planarity : 0.005 0.050 1630 Dihedral : 5.284 59.814 1414 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.55 % Allowed : 24.86 % Favored : 68.59 % 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: -1.68 (0.24), residues: 1137 helix: -0.68 (0.49), residues: 112 sheet: -0.93 (0.24), residues: 414 loop : -1.28 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 57 TYR 0.012 0.001 TYR A 472 PHE 0.017 0.001 PHE C 374 TRP 0.007 0.001 TRP F 150 HIS 0.004 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 ( 9508) covalent geometry : angle 0.62559 / 0.30 (12947) SS BOND : bond 0.00429 / 0.26 ( 16) SS BOND : angle 1.04978 / 0.65 ( 32) hydrogen bonds : bond 0.03228 / 2.14 ( 266) hydrogen bonds : angle 5.71691 / 3.84 ( 807) link_BETA1-4 : bond 0.00287 / 0.15 ( 1) link_BETA1-4 : angle 1.16340 / 0.60 ( 3) link_BETA1-6 : bond 0.00257 / 0.14 ( 1) link_BETA1-6 : angle 1.24036 / 0.67 ( 3) link_NAG-ASN : bond 0.00454 / 0.31 ( 6) link_NAG-ASN : angle 2.87934 / 2.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 115 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7475 (tmt-80) REVERT: F 108 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7926 (mm-40) REVERT: B 321 PHE cc_start: 0.3808 (OUTLIER) cc_final: 0.3428 (m-80) REVERT: B 417 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8820 (tp) REVERT: C 461 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8513 (m) REVERT: D 401 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7539 (mtm-85) REVERT: D 422 GLU cc_start: 0.8153 (tp30) cc_final: 0.7451 (mp0) REVERT: J 59 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7188 (tpt90) REVERT: J 89 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.6892 (m110) outliers start: 68 outliers final: 53 residues processed: 168 average time/residue: 0.0874 time to fit residues: 20.1599 Evaluate side-chains 176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 115 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 ASN Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 ARG Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 0.3980 chunk 80 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 20.0000 chunk 54 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 67 optimal weight: 0.0060 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.183897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.165038 restraints weight = 10441.522| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 0.89 r_work: 0.3619 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9532 Z= 0.103 Angle : 0.589 10.259 13003 Z= 0.276 Chirality : 0.040 0.187 1529 Planarity : 0.004 0.049 1630 Dihedral : 4.987 59.890 1414 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.91 % Allowed : 26.49 % Favored : 68.59 % 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: -1.44 (0.24), residues: 1137 helix: -0.57 (0.49), residues: 112 sheet: -0.66 (0.25), residues: 421 loop : -1.20 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 57 TYR 0.012 0.001 TYR F 243 PHE 0.011 0.001 PHE D 374 TRP 0.016 0.001 TRP F 150 HIS 0.002 0.000 HIS F 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 ( 9508) covalent geometry : angle 0.58004 / 0.27 (12947) SS BOND : bond 0.00215 / 0.13 ( 16) SS BOND : angle 0.89977 / 0.54 ( 32) hydrogen bonds : bond 0.02858 / 1.90 ( 266) hydrogen bonds : angle 5.38128 / 3.62 ( 807) link_BETA1-4 : bond 0.00330 / 0.17 ( 1) link_BETA1-4 : angle 1.19246 / 0.61 ( 3) link_BETA1-6 : bond 0.00310 / 0.16 ( 1) link_BETA1-6 : angle 1.20150 / 0.65 ( 3) link_NAG-ASN : bond 0.00406 / 0.31 ( 6) link_NAG-ASN : angle 2.57006 / 1.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7532 (tmt-80) REVERT: F 108 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8497 (mm-40) REVERT: B 321 PHE cc_start: 0.3813 (OUTLIER) cc_final: 0.3447 (m-80) REVERT: B 370 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (tp) REVERT: D 401 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7502 (mtm-85) REVERT: J 59 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7144 (tpt90) REVERT: J 89 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.6547 (m110) outliers start: 51 outliers final: 38 residues processed: 166 average time/residue: 0.0884 time to fit residues: 20.3618 Evaluate side-chains 164 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 ASN Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 ARG Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.0050 chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 95 optimal weight: 0.2980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 316 ASN J 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.182121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.162952 restraints weight = 10459.783| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 0.90 r_work: 0.3603 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9532 Z= 0.132 Angle : 0.613 10.284 13003 Z= 0.288 Chirality : 0.041 0.226 1529 Planarity : 0.005 0.050 1630 Dihedral : 4.973 59.913 1414 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.91 % Allowed : 27.46 % Favored : 67.63 % 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: -1.37 (0.24), residues: 1137 helix: -0.50 (0.50), residues: 113 sheet: -0.59 (0.25), residues: 415 loop : -1.17 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 57 TYR 0.013 0.001 TYR F 243 PHE 0.015 0.001 PHE D 374 TRP 0.011 0.001 TRP F 150 HIS 0.003 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 9508) covalent geometry : angle 0.60177 / 0.28 (12947) SS BOND : bond 0.00356 / 0.23 ( 16) SS BOND : angle 1.43264 / 0.77 ( 32) hydrogen bonds : bond 0.03002 / 2.01 ( 266) hydrogen bonds : angle 5.37006 / 3.61 ( 807) link_BETA1-4 : bond 0.00368 / 0.19 ( 1) link_BETA1-4 : angle 1.17547 / 0.60 ( 3) link_BETA1-6 : bond 0.00330 / 0.17 ( 1) link_BETA1-6 : angle 1.23405 / 0.67 ( 3) link_NAG-ASN : bond 0.00407 / 0.28 ( 6) link_NAG-ASN : angle 2.56505 / 1.87 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: F 60 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7592 (tmt-80) REVERT: F 108 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7880 (mm-40) REVERT: B 321 PHE cc_start: 0.3796 (OUTLIER) cc_final: 0.3449 (m-80) REVERT: B 370 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8177 (tp) REVERT: C 461 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8416 (m) REVERT: D 401 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7532 (mtm-85) REVERT: D 466 GLU cc_start: 0.7581 (pm20) cc_final: 0.7378 (pm20) REVERT: J 59 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7127 (tpt90) REVERT: J 89 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.6652 (m110) REVERT: J 99 THR cc_start: 0.8137 (t) cc_final: 0.7860 (p) outliers start: 51 outliers final: 38 residues processed: 154 average time/residue: 0.0807 time to fit residues: 17.3663 Evaluate side-chains 158 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 59 ARG Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 72 optimal weight: 0.0270 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.181823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.164430 restraints weight = 10465.396| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 0.86 r_work: 0.3585 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 9532 Z= 0.177 Angle : 0.904 59.200 13003 Z= 0.512 Chirality : 0.046 0.861 1529 Planarity : 0.005 0.050 1630 Dihedral : 5.042 59.930 1414 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 4.91 % Allowed : 27.17 % Favored : 67.92 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.40 (0.24), residues: 1137 helix: -0.50 (0.50), residues: 113 sheet: -0.59 (0.25), residues: 415 loop : -1.22 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 57 TYR 0.013 0.001 TYR F 243 PHE 0.015 0.001 PHE D 374 TRP 0.010 0.001 TRP F 150 HIS 0.003 0.001 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 9508) covalent geometry : angle 0.89799 / 0.51 (12947) SS BOND : bond 0.00356 / 0.23 ( 16) SS BOND : angle 1.33832 / 0.73 ( 32) hydrogen bonds : bond 0.03007 / 2.01 ( 266) hydrogen bonds : angle 5.37536 / 3.61 ( 807) link_BETA1-4 : bond 0.00426 / 0.22 ( 1) link_BETA1-4 : angle 1.18575 / 0.61 ( 3) link_BETA1-6 : bond 0.00404 / 0.21 ( 1) link_BETA1-6 : angle 1.27214 / 0.69 ( 3) link_NAG-ASN : bond 0.00400 / 0.27 ( 6) link_NAG-ASN : angle 2.56646 / 1.87 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.92 seconds wall clock time: 40 minutes 42.96 seconds (2442.96 seconds total)