Starting phenix.real_space_refine on Sun Feb 8 01:10:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oqh_70761/02_2026/9oqh_70761_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oqh_70761/02_2026/9oqh_70761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oqh_70761/02_2026/9oqh_70761_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oqh_70761/02_2026/9oqh_70761_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oqh_70761/02_2026/9oqh_70761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oqh_70761/02_2026/9oqh_70761.map" } resolution = 2.58 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= 0.001 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 77 5.16 5 C 12754 2.51 5 N 2898 2.21 5 O 3234 1.98 5 H 17927 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36897 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 5.52, per 1000 atoms: 0.15 Number of scatterers: 36897 At special positions: 0 Unit cell: (109.65, 109.65, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 7 15.00 O 3234 8.00 N 2898 7.00 C 12754 6.00 H 17927 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " 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 NAG-ASN " NAG A 504 " - " ASN A 255 " " NAG B 504 " - " ASN B 255 " " NAG C 504 " - " ASN C 255 " " NAG D 504 " - " ASN D 255 " " NAG E 504 " - " ASN E 255 " " NAG F 504 " - " ASN F 255 " " NAG G 504 " - " ASN G 255 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 901.4 milliseconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 70.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.608A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 100 through 131 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 removed outlier: 3.796A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 254 removed outlier: 4.214A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.616A pdb=" N VAL A 308 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.659A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.611A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 100 through 131 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 removed outlier: 3.532A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.796A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 254 removed outlier: 4.216A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.615A pdb=" N VAL B 308 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 356 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.657A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.611A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 100 through 131 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 254 removed outlier: 4.214A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.617A pdb=" N VAL C 308 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 356 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.659A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.610A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 100 through 131 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.797A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.214A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 305 through 312 removed outlier: 3.618A pdb=" N VAL D 308 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.903A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 356 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.658A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.612A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 100 through 131 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 206 removed outlier: 3.794A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 305 through 312 removed outlier: 3.616A pdb=" N VAL E 308 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.900A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 356 Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.657A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.609A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 100 through 131 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 254 removed outlier: 4.214A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 305 through 312 removed outlier: 3.615A pdb=" N VAL F 308 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.903A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 356 Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.658A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.610A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 100 through 131 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 removed outlier: 3.533A pdb=" N ILE G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 305 through 312 removed outlier: 3.614A pdb=" N VAL G 308 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.903A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 356 Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.658A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.599A pdb=" N VAL A 245 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.600A pdb=" N VAL B 245 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL C 245 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL D 245 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL E 245 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL F 245 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.601A pdb=" N VAL G 245 " --> pdb=" O GLN G 95 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3531 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: 9.80 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17892 1.03 - 1.23: 57 1.23 - 1.42: 7745 1.42 - 1.62: 11553 1.62 - 1.81: 105 Bond restraints: 37352 Sorted by residual: bond pdb=" CA PHE E 79 " pdb=" C PHE E 79 " ideal model delta sigma weight residual 1.523 1.515 0.009 1.30e-02 5.92e+03 4.30e-01 bond pdb=" CB TRP D 74 " pdb=" CG TRP D 74 " ideal model delta sigma weight residual 1.498 1.518 -0.020 3.10e-02 1.04e+03 4.08e-01 bond pdb=" C GLU D 310 " pdb=" N ILE D 311 " ideal model delta sigma weight residual 1.338 1.331 0.007 1.05e-02 9.07e+03 4.01e-01 bond pdb=" CG1 ILE C 60 " pdb=" CD1 ILE C 60 " ideal model delta sigma weight residual 1.513 1.489 0.024 3.90e-02 6.57e+02 3.93e-01 bond pdb=" CB TRP G 74 " pdb=" CG TRP G 74 " ideal model delta sigma weight residual 1.498 1.517 -0.019 3.10e-02 1.04e+03 3.91e-01 ... (remaining 37347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 62381 1.05 - 2.10: 4673 2.10 - 3.14: 195 3.14 - 4.19: 72 4.19 - 5.24: 26 Bond angle restraints: 67347 Sorted by residual: angle pdb=" N ILE D 311 " pdb=" CA ILE D 311 " pdb=" C ILE D 311 " ideal model delta sigma weight residual 112.80 110.03 2.77 1.15e+00 7.56e-01 5.80e+00 angle pdb=" N ILE G 311 " pdb=" CA ILE G 311 " pdb=" C ILE G 311 " ideal model delta sigma weight residual 112.80 110.08 2.72 1.15e+00 7.56e-01 5.61e+00 angle pdb=" N ILE C 311 " pdb=" CA ILE C 311 " pdb=" C ILE C 311 " ideal model delta sigma weight residual 112.80 110.09 2.71 1.15e+00 7.56e-01 5.56e+00 angle pdb=" N ILE A 311 " pdb=" CA ILE A 311 " pdb=" C ILE A 311 " ideal model delta sigma weight residual 112.80 110.09 2.71 1.15e+00 7.56e-01 5.53e+00 angle pdb=" N ILE B 311 " pdb=" CA ILE B 311 " pdb=" C ILE B 311 " ideal model delta sigma weight residual 112.80 110.10 2.70 1.15e+00 7.56e-01 5.53e+00 ... (remaining 67342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 17342 16.17 - 32.33: 996 32.33 - 48.50: 295 48.50 - 64.66: 99 64.66 - 80.83: 21 Dihedral angle restraints: 18753 sinusoidal: 10192 harmonic: 8561 Sorted by residual: dihedral pdb=" CA GLU C 9 " pdb=" C GLU C 9 " pdb=" N TYR C 10 " pdb=" CA TYR C 10 " ideal model delta harmonic sigma weight residual -180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU D 9 " pdb=" C GLU D 9 " pdb=" N TYR D 10 " pdb=" CA TYR D 10 " ideal model delta harmonic sigma weight residual 180.00 -163.57 -16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU G 9 " pdb=" C GLU G 9 " pdb=" N TYR G 10 " pdb=" CA TYR G 10 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 18750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2541 0.040 - 0.080: 525 0.080 - 0.121: 149 0.121 - 0.161: 12 0.161 - 0.201: 7 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C1 NAG F 504 " pdb=" ND2 ASN F 255 " pdb=" C2 NAG F 504 " pdb=" O5 NAG F 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C1 NAG G 504 " pdb=" ND2 ASN G 255 " pdb=" C2 NAG G 504 " pdb=" O5 NAG G 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 255 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 3231 not shown) Planarity restraints: 5432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 122 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO F 123 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 123 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 123 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 122 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO D 123 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 122 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO B 123 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.018 5.00e-02 4.00e+02 ... (remaining 5429 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 19398 2.43 - 2.97: 84936 2.97 - 3.52: 101672 3.52 - 4.06: 127322 4.06 - 4.60: 195435 Nonbonded interactions: 528763 Sorted by model distance: nonbonded pdb=" HE1 TYR C 309 " pdb=" HD1 TYR C 345 " model vdw 1.890 2.100 nonbonded pdb=" HE1 TYR A 309 " pdb=" HD1 TYR A 345 " model vdw 1.890 2.100 nonbonded pdb=" HE1 TYR B 309 " pdb=" HD1 TYR B 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR G 309 " pdb=" HD1 TYR G 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR D 309 " pdb=" HD1 TYR D 345 " model vdw 1.891 2.100 ... (remaining 528758 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.340 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: 0.250 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 34.160 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.003 0.024 19446 Z= 0.141 Angle : 0.518 5.239 26572 Z= 0.274 Chirality : 0.037 0.201 3234 Planarity : 0.004 0.034 3136 Dihedral : 11.768 80.829 7679 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.76 % Allowed : 4.18 % Favored : 95.06 % 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: 1.79 (0.19), residues: 2380 helix: 2.34 (0.14), residues: 1610 sheet: None (None), residues: 0 loop : -1.43 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 300 TYR 0.008 0.001 TYR D 10 PHE 0.007 0.001 PHE F 109 TRP 0.007 0.002 TRP E 104 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00309 (19425) covalent geometry : angle 0.51605 (26523) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.96754 ( 28) hydrogen bonds : bond 0.10206 ( 1212) hydrogen bonds : angle 4.19481 ( 3531) link_NAG-ASN : bond 0.00433 ( 7) link_NAG-ASN : angle 1.35903 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 202 average time/residue: 1.3051 time to fit residues: 297.4203 Evaluate side-chains 132 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 337 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 5 GLN C 280 ASN D 280 ASN E 280 ASN F 280 ASN G 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.092664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.069134 restraints weight = 139151.464| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.61 r_work: 0.3040 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19446 Z= 0.192 Angle : 0.543 5.471 26572 Z= 0.284 Chirality : 0.038 0.184 3234 Planarity : 0.004 0.040 3136 Dihedral : 7.725 65.822 3888 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.63 % Allowed : 7.28 % Favored : 91.09 % 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 (0.19), residues: 2380 helix: 2.56 (0.14), residues: 1554 sheet: None (None), residues: 0 loop : -1.07 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 75 TYR 0.016 0.001 TYR C 10 PHE 0.011 0.001 PHE G 67 TRP 0.009 0.002 TRP E 74 HIS 0.003 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00429 (19425) covalent geometry : angle 0.54141 (26523) SS BOND : bond 0.00285 ( 14) SS BOND : angle 1.03711 ( 28) hydrogen bonds : bond 0.03794 ( 1212) hydrogen bonds : angle 4.04970 ( 3531) link_NAG-ASN : bond 0.00182 ( 7) link_NAG-ASN : angle 1.36301 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 243 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8221 (mt-10) REVERT: C 5 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8035 (tm-30) REVERT: C 9 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8065 (tm-30) REVERT: D 9 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8075 (tm-30) REVERT: E 9 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8061 (tm-30) REVERT: F 9 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7981 (tm-30) REVERT: G 9 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7985 (tm-30) outliers start: 30 outliers final: 16 residues processed: 145 average time/residue: 1.3549 time to fit residues: 221.1815 Evaluate side-chains 127 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 337 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 151 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.088803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.063689 restraints weight = 142557.532| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.55 r_work: 0.2906 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 19446 Z= 0.332 Angle : 0.613 6.337 26572 Z= 0.325 Chirality : 0.040 0.209 3234 Planarity : 0.004 0.041 3136 Dihedral : 7.934 69.021 3878 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.09 % Allowed : 9.67 % Favored : 89.24 % 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: 2.10 (0.19), residues: 2380 helix: 2.57 (0.14), residues: 1512 sheet: -0.39 (0.53), residues: 84 loop : -0.83 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 75 TYR 0.017 0.002 TYR G 10 PHE 0.019 0.002 PHE F 67 TRP 0.015 0.002 TRP E 74 HIS 0.005 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00743 (19425) covalent geometry : angle 0.61135 (26523) SS BOND : bond 0.00421 ( 14) SS BOND : angle 1.45911 ( 28) hydrogen bonds : bond 0.04363 ( 1212) hydrogen bonds : angle 4.35991 ( 3531) link_NAG-ASN : bond 0.00147 ( 7) link_NAG-ASN : angle 1.16125 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 9 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 9 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8224 (tm-30) REVERT: D 9 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 9 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8319 (tm-30) REVERT: F 9 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8339 (tm-30) REVERT: G 9 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8242 (tm-30) outliers start: 20 outliers final: 15 residues processed: 112 average time/residue: 1.5987 time to fit residues: 199.2450 Evaluate side-chains 112 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 337 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 49 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 216 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.090694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.066476 restraints weight = 140008.939| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.54 r_work: 0.2972 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19446 Z= 0.126 Angle : 0.507 5.255 26572 Z= 0.263 Chirality : 0.036 0.187 3234 Planarity : 0.004 0.039 3136 Dihedral : 7.058 63.540 3872 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.41 % Allowed : 10.10 % Favored : 88.48 % 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: 2.24 (0.19), residues: 2380 helix: 2.68 (0.14), residues: 1512 sheet: -0.32 (0.57), residues: 84 loop : -0.79 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.011 0.001 TYR C 230 PHE 0.010 0.001 PHE G 67 TRP 0.008 0.001 TRP A 74 HIS 0.001 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00276 (19425) covalent geometry : angle 0.50523 (26523) SS BOND : bond 0.00223 ( 14) SS BOND : angle 1.05956 ( 28) hydrogen bonds : bond 0.03709 ( 1212) hydrogen bonds : angle 4.09521 ( 3531) link_NAG-ASN : bond 0.00408 ( 7) link_NAG-ASN : angle 1.32735 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 9 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 31 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8117 (mt-10) REVERT: C 9 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 9 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8330 (tm-30) REVERT: E 9 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8299 (tm-30) REVERT: F 9 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8284 (tm-30) REVERT: F 136 CYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8746 (t) REVERT: G 9 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8223 (tm-30) outliers start: 26 outliers final: 15 residues processed: 121 average time/residue: 1.4917 time to fit residues: 201.4275 Evaluate side-chains 116 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 337 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 193 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062937 restraints weight = 142275.454| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.53 r_work: 0.2877 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 19446 Z= 0.323 Angle : 0.591 5.184 26572 Z= 0.313 Chirality : 0.039 0.212 3234 Planarity : 0.004 0.043 3136 Dihedral : 7.777 67.980 3869 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.98 % Allowed : 11.14 % Favored : 87.89 % 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: 2.10 (0.19), residues: 2380 helix: 2.57 (0.14), residues: 1512 sheet: -0.42 (0.55), residues: 84 loop : -0.82 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 75 TYR 0.013 0.001 TYR G 10 PHE 0.021 0.002 PHE G 67 TRP 0.010 0.002 TRP A 74 HIS 0.005 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00717 (19425) covalent geometry : angle 0.58975 (26523) SS BOND : bond 0.00436 ( 14) SS BOND : angle 1.07704 ( 28) hydrogen bonds : bond 0.04188 ( 1212) hydrogen bonds : angle 4.30766 ( 3531) link_NAG-ASN : bond 0.00132 ( 7) link_NAG-ASN : angle 1.09150 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8275 (tm-30) REVERT: B 9 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8314 (tm-30) REVERT: C 9 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8235 (tm-30) REVERT: D 9 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 337 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8526 (tm-30) REVERT: E 9 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8365 (tm-30) REVERT: F 9 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8367 (tm-30) REVERT: G 9 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8340 (tm-30) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 1.6105 time to fit residues: 201.0501 Evaluate side-chains 105 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 337 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 123 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.089676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065321 restraints weight = 140260.691| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.50 r_work: 0.2947 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19446 Z= 0.149 Angle : 0.514 5.146 26572 Z= 0.267 Chirality : 0.036 0.193 3234 Planarity : 0.004 0.041 3136 Dihedral : 7.049 63.783 3866 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.30 % Allowed : 11.14 % Favored : 87.56 % 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: 2.20 (0.19), residues: 2380 helix: 2.64 (0.14), residues: 1512 sheet: -0.13 (0.57), residues: 84 loop : -0.81 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 29 TYR 0.011 0.001 TYR C 230 PHE 0.011 0.001 PHE G 67 TRP 0.008 0.001 TRP G 74 HIS 0.001 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00330 (19425) covalent geometry : angle 0.51211 (26523) SS BOND : bond 0.00233 ( 14) SS BOND : angle 0.78738 ( 28) hydrogen bonds : bond 0.03697 ( 1212) hydrogen bonds : angle 4.12808 ( 3531) link_NAG-ASN : bond 0.00377 ( 7) link_NAG-ASN : angle 1.26063 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 9 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 31 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 337 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8550 (tm-30) REVERT: C 9 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8175 (tm-30) REVERT: D 9 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8317 (tm-30) REVERT: D 31 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7858 (mp0) REVERT: D 337 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8499 (tm-30) REVERT: E 9 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8317 (tm-30) REVERT: F 9 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8288 (tm-30) REVERT: F 136 CYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8727 (t) REVERT: G 9 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8247 (tm-30) REVERT: G 29 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7923 (mmm-85) outliers start: 24 outliers final: 15 residues processed: 118 average time/residue: 1.5100 time to fit residues: 199.1431 Evaluate side-chains 109 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 189 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 169 optimal weight: 50.0000 chunk 2 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.089258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.065012 restraints weight = 140332.981| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.49 r_work: 0.2934 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19446 Z= 0.186 Angle : 0.522 5.003 26572 Z= 0.273 Chirality : 0.036 0.192 3234 Planarity : 0.004 0.042 3136 Dihedral : 6.890 63.047 3863 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.98 % Allowed : 12.33 % Favored : 86.69 % 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: 2.30 (0.19), residues: 2380 helix: 2.74 (0.14), residues: 1498 sheet: 0.13 (0.57), residues: 84 loop : -0.76 (0.25), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 29 TYR 0.010 0.001 TYR D 230 PHE 0.013 0.001 PHE G 67 TRP 0.008 0.001 TRP A 74 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00413 (19425) covalent geometry : angle 0.52041 (26523) SS BOND : bond 0.00226 ( 14) SS BOND : angle 1.12575 ( 28) hydrogen bonds : bond 0.03689 ( 1212) hydrogen bonds : angle 4.11196 ( 3531) link_NAG-ASN : bond 0.00308 ( 7) link_NAG-ASN : angle 1.21914 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 9 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8265 (tm-30) REVERT: B 31 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8218 (mt-10) REVERT: C 9 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 9 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 31 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7899 (mp0) REVERT: D 337 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8510 (tm-30) REVERT: E 9 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8346 (tm-30) REVERT: F 9 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8321 (tm-30) REVERT: F 136 CYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8735 (t) REVERT: G 9 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8265 (tm-30) REVERT: G 337 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8485 (tm-30) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 1.5885 time to fit residues: 200.4782 Evaluate side-chains 109 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 147 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.089877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.066030 restraints weight = 139370.347| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.47 r_work: 0.2961 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19446 Z= 0.143 Angle : 0.507 5.024 26572 Z= 0.263 Chirality : 0.036 0.181 3234 Planarity : 0.004 0.042 3136 Dihedral : 6.518 60.608 3863 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.14 % Allowed : 12.33 % Favored : 86.53 % 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: 2.37 (0.19), residues: 2380 helix: 2.80 (0.14), residues: 1498 sheet: 0.39 (0.59), residues: 84 loop : -0.78 (0.25), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 29 TYR 0.010 0.001 TYR C 230 PHE 0.009 0.001 PHE F 67 TRP 0.008 0.001 TRP E 74 HIS 0.001 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00319 (19425) covalent geometry : angle 0.50526 (26523) SS BOND : bond 0.00211 ( 14) SS BOND : angle 1.03521 ( 28) hydrogen bonds : bond 0.03479 ( 1212) hydrogen bonds : angle 4.02537 ( 3531) link_NAG-ASN : bond 0.00374 ( 7) link_NAG-ASN : angle 1.31454 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 9 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8272 (tm-30) REVERT: B 31 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8155 (mt-10) REVERT: C 9 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8223 (tm-30) REVERT: D 9 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8334 (tm-30) REVERT: D 29 ARG cc_start: 0.7815 (mmm-85) cc_final: 0.7258 (mmm-85) REVERT: D 31 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7851 (mp0) REVERT: D 337 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8452 (tm-30) REVERT: E 9 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8336 (tm-30) REVERT: E 31 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8342 (mt-10) REVERT: F 9 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8309 (tm-30) REVERT: F 136 CYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8731 (t) REVERT: G 9 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8299 (tm-30) REVERT: G 337 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8482 (tm-30) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 1.6099 time to fit residues: 204.4753 Evaluate side-chains 110 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 177 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 119 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN D 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.064437 restraints weight = 140579.509| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.47 r_work: 0.2921 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19446 Z= 0.226 Angle : 0.540 4.974 26572 Z= 0.284 Chirality : 0.037 0.196 3234 Planarity : 0.004 0.043 3136 Dihedral : 6.931 62.928 3863 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.09 % Allowed : 12.38 % Favored : 86.53 % 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: 1.98 (0.18), residues: 2380 helix: 2.51 (0.14), residues: 1547 sheet: None (None), residues: 0 loop : -1.08 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 29 TYR 0.010 0.001 TYR D 230 PHE 0.016 0.001 PHE G 67 TRP 0.008 0.002 TRP G 74 HIS 0.003 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00503 (19425) covalent geometry : angle 0.53804 (26523) SS BOND : bond 0.00348 ( 14) SS BOND : angle 1.12360 ( 28) hydrogen bonds : bond 0.03751 ( 1212) hydrogen bonds : angle 4.12799 ( 3531) link_NAG-ASN : bond 0.00247 ( 7) link_NAG-ASN : angle 1.19093 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 9 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8286 (tm-30) REVERT: C 9 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 9 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8354 (tm-30) REVERT: E 9 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8355 (tm-30) REVERT: F 9 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8311 (tm-30) REVERT: F 136 CYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8734 (t) REVERT: G 9 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8293 (tm-30) REVERT: G 337 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8471 (tm-30) outliers start: 20 outliers final: 14 residues processed: 115 average time/residue: 1.6060 time to fit residues: 205.4634 Evaluate side-chains 108 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 188 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065403 restraints weight = 140132.199| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.47 r_work: 0.2959 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19446 Z= 0.160 Angle : 0.518 5.145 26572 Z= 0.270 Chirality : 0.036 0.187 3234 Planarity : 0.004 0.042 3136 Dihedral : 6.608 61.125 3860 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.92 % Allowed : 12.82 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 2380 helix: 2.71 (0.14), residues: 1512 sheet: 0.26 (0.59), residues: 84 loop : -0.84 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 29 TYR 0.010 0.001 TYR C 230 PHE 0.011 0.001 PHE G 67 TRP 0.008 0.001 TRP E 74 HIS 0.001 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00357 (19425) covalent geometry : angle 0.51629 (26523) SS BOND : bond 0.00242 ( 14) SS BOND : angle 1.00897 ( 28) hydrogen bonds : bond 0.03563 ( 1212) hydrogen bonds : angle 4.04898 ( 3531) link_NAG-ASN : bond 0.00342 ( 7) link_NAG-ASN : angle 1.26398 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 9 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 31 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8157 (mt-10) REVERT: B 56 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8142 (pp30) REVERT: C 9 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8236 (tm-30) REVERT: D 9 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 29 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7407 (mmm-85) REVERT: D 337 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8370 (tm-30) REVERT: E 9 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8336 (tm-30) REVERT: E 31 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8340 (mt-10) REVERT: F 9 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8254 (tm-30) REVERT: F 136 CYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8763 (t) REVERT: G 9 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8267 (tm-30) REVERT: G 56 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8851 (pp30) REVERT: G 337 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8495 (tm-30) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 1.5829 time to fit residues: 193.5107 Evaluate side-chains 107 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 234 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 210 optimal weight: 0.5980 chunk 200 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.090215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066170 restraints weight = 139189.058| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.49 r_work: 0.2967 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19446 Z= 0.131 Angle : 0.501 5.539 26572 Z= 0.260 Chirality : 0.035 0.175 3234 Planarity : 0.004 0.042 3136 Dihedral : 6.110 57.871 3857 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.87 % Allowed : 12.93 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.19), residues: 2380 helix: 2.50 (0.14), residues: 1568 sheet: None (None), residues: 0 loop : -1.05 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 29 TYR 0.010 0.001 TYR G 230 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP E 74 HIS 0.001 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00291 (19425) covalent geometry : angle 0.49896 (26523) SS BOND : bond 0.00194 ( 14) SS BOND : angle 0.89153 ( 28) hydrogen bonds : bond 0.03339 ( 1212) hydrogen bonds : angle 3.92168 ( 3531) link_NAG-ASN : bond 0.00385 ( 7) link_NAG-ASN : angle 1.35751 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11297.72 seconds wall clock time: 191 minutes 56.05 seconds (11516.05 seconds total)