Starting phenix.real_space_refine on Sun Feb 8 01:06:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oqn_70767/02_2026/9oqn_70767_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oqn_70767/02_2026/9oqn_70767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oqn_70767/02_2026/9oqn_70767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oqn_70767/02_2026/9oqn_70767.map" model { file = "/net/cci-nas-00/data/ceres_data/9oqn_70767/02_2026/9oqn_70767_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oqn_70767/02_2026/9oqn_70767_trim.cif" } resolution = 3.19 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): 0.02s 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: 5.68, per 1000 atoms: 0.15 Number of scatterers: 36897 At special positions: 0 Unit cell: (108.8, 109.65, 121.55, 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: 2.84 Conformation dependent library (CDL) restraints added in 976.7 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: 0.81 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: 3.610A 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: 3.795A 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: 3.828A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.901A 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: 3.658A 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: 3.609A 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: 3.534A 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: 3.617A 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: 3.901A 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: 3.610A 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: 3.533A 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: 4.215A 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: 3.616A pdb=" N VAL C 308 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.827A 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: 3.658A 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: 3.795A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.640A 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: 4.215A 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: 3.616A pdb=" N VAL D 308 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.828A 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: 3.610A 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: 3.795A 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: 3.901A 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: 3.658A 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: 3.610A 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: 3.639A 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: 4.215A 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: 3.827A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.902A 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: 3.640A 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: 4.214A 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: 3.616A pdb=" N VAL G 308 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.902A 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: 3.598A 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: 3.599A 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: 3.599A 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: 3.599A 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: 3.599A 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: 7.78 Time building geometry restraints manager: 3.87 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: 56 1.23 - 1.42: 7747 1.42 - 1.61: 11552 1.61 - 1.81: 105 Bond restraints: 37352 Sorted by residual: bond pdb=" CB TRP B 74 " pdb=" CG TRP B 74 " ideal model delta sigma weight residual 1.498 1.518 -0.020 3.10e-02 1.04e+03 4.07e-01 bond pdb=" CB TRP F 74 " pdb=" CG TRP F 74 " ideal model delta sigma weight residual 1.498 1.518 -0.020 3.10e-02 1.04e+03 4.02e-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 3.98e-01 bond pdb=" CG PRO E 110 " pdb=" CD PRO E 110 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.76e-01 bond pdb=" CG PRO G 110 " pdb=" CD PRO G 110 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.73e-01 ... (remaining 37347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 62400 1.04 - 2.08: 4648 2.08 - 3.12: 200 3.12 - 4.15: 64 4.15 - 5.19: 35 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 112.80 110.09 2.71 1.15e+00 7.56e-01 5.57e+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 5.56e+00 angle pdb=" N ILE G 311 " pdb=" CA ILE G 311 " pdb=" C ILE G 311 " ideal model delta sigma weight residual 112.80 110.09 2.71 1.15e+00 7.56e-01 5.54e+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 5.51e+00 angle pdb=" N ILE F 311 " pdb=" CA ILE F 311 " pdb=" C ILE F 311 " ideal model delta sigma weight residual 112.80 110.10 2.70 1.15e+00 7.56e-01 5.51e+00 ... (remaining 67342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 17344 16.16 - 32.32: 995 32.32 - 48.48: 292 48.48 - 64.64: 101 64.64 - 80.79: 21 Dihedral angle restraints: 18753 sinusoidal: 10192 harmonic: 8561 Sorted by residual: dihedral pdb=" CA GLU A 9 " pdb=" C GLU A 9 " pdb=" N TYR A 10 " pdb=" CA TYR A 10 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU E 9 " pdb=" C GLU E 9 " pdb=" N TYR E 10 " pdb=" CA TYR E 10 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU B 9 " pdb=" C GLU B 9 " pdb=" N TYR B 10 " pdb=" CA TYR B 10 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 18750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2530 0.039 - 0.079: 533 0.079 - 0.118: 156 0.118 - 0.158: 8 0.158 - 0.197: 7 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C1 NAG D 504 " pdb=" ND2 ASN D 255 " pdb=" C2 NAG D 504 " pdb=" O5 NAG D 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.71e-01 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 9.69e-01 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 9.65e-01 ... (remaining 3231 not shown) Planarity restraints: 5432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 122 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 123 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 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 3.34e-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 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 122 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+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 " -0.018 5.00e-02 4.00e+02 ... (remaining 5429 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 19539 2.43 - 2.97: 84899 2.97 - 3.52: 101666 3.52 - 4.06: 127329 4.06 - 4.60: 195365 Nonbonded interactions: 528798 Sorted by model distance: nonbonded pdb=" HE1 TYR E 309 " pdb=" HD1 TYR E 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR D 309 " pdb=" HD1 TYR D 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR A 309 " pdb=" HD1 TYR A 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR C 309 " pdb=" HD1 TYR C 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR G 309 " pdb=" HD1 TYR G 345 " model vdw 1.891 2.100 ... (remaining 528793 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: 2.160 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 30.200 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 0.023 19446 Z= 0.130 Angle : 0.515 5.192 26572 Z= 0.271 Chirality : 0.037 0.197 3234 Planarity : 0.004 0.034 3136 Dihedral : 11.767 80.794 7679 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 1.78 (0.19), residues: 2380 helix: 2.33 (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 B 300 TYR 0.007 0.001 TYR D 10 PHE 0.007 0.001 PHE E 109 TRP 0.007 0.002 TRP E 104 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00297 (19425) covalent geometry : angle 0.51290 (26523) SS BOND : bond 0.00233 ( 14) SS BOND : angle 0.95979 ( 28) hydrogen bonds : bond 0.10207 ( 1212) hydrogen bonds : angle 4.19356 ( 3531) link_NAG-ASN : bond 0.00448 ( 7) link_NAG-ASN : angle 1.39047 ( 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 236 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.936 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 revert: symmetry clash REVERT: D 74 TRP cc_start: 0.7135 (OUTLIER) cc_final: 0.6911 (t60) outliers start: 14 outliers final: 12 residues processed: 229 average time/residue: 0.2838 time to fit residues: 102.5333 Evaluate side-chains 153 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 74 TRP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 74 TRP 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 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: 3.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 235 optimal weight: 0.0970 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 353 ASN B 280 ASN B 353 ASN C 280 ASN C 353 ASN D 280 ASN D 353 ASN E 280 ASN E 353 ASN F 280 ASN F 353 ASN G 280 ASN G 353 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.092132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.073891 restraints weight = 174395.018| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.50 r_work: 0.3225 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1394 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= 0.139 Angle : 0.509 5.502 26572 Z= 0.263 Chirality : 0.036 0.179 3234 Planarity : 0.004 0.033 3136 Dihedral : 7.636 65.125 3890 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.20 % Allowed : 7.66 % Favored : 91.15 % 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: 1.87 (0.19), residues: 2380 helix: 2.40 (0.14), residues: 1596 sheet: None (None), residues: 0 loop : -1.33 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 217 TYR 0.012 0.001 TYR G 345 PHE 0.015 0.001 PHE F 67 TRP 0.009 0.001 TRP F 74 HIS 0.001 0.000 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00302 (19425) covalent geometry : angle 0.50767 (26523) SS BOND : bond 0.00184 ( 14) SS BOND : angle 0.85602 ( 28) hydrogen bonds : bond 0.03574 ( 1212) hydrogen bonds : angle 4.04846 ( 3531) link_NAG-ASN : bond 0.00282 ( 7) link_NAG-ASN : angle 1.35217 ( 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 168 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.715 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: A 337 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: D 74 TRP cc_start: 0.7710 (OUTLIER) cc_final: 0.7402 (t60) REVERT: E 37 MET cc_start: 0.8722 (ttm) cc_final: 0.8353 (ttp) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 0.3040 time to fit residues: 76.3955 Evaluate side-chains 151 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 295 LEU 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 216 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 151 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 232 optimal weight: 0.0070 chunk 115 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 ASN E 353 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.088566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069406 restraints weight = 175962.744| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.48 r_work: 0.3090 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 19446 Z= 0.257 Angle : 0.572 5.131 26572 Z= 0.301 Chirality : 0.038 0.187 3234 Planarity : 0.004 0.041 3136 Dihedral : 7.263 61.033 3876 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.60 % Allowed : 8.53 % Favored : 90.87 % 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: 1.85 (0.18), residues: 2380 helix: 2.39 (0.14), residues: 1547 sheet: None (None), residues: 0 loop : -1.11 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 29 TYR 0.017 0.001 TYR A 10 PHE 0.008 0.001 PHE F 141 TRP 0.012 0.002 TRP D 74 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00553 (19425) covalent geometry : angle 0.57048 (26523) SS BOND : bond 0.00261 ( 14) SS BOND : angle 1.16064 ( 28) hydrogen bonds : bond 0.03852 ( 1212) hydrogen bonds : angle 4.29256 ( 3531) link_NAG-ASN : bond 0.00104 ( 7) link_NAG-ASN : angle 1.12512 ( 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 171 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.9455 (tm-30) cc_final: 0.9251 (tm-30) REVERT: B 56 GLN cc_start: 0.8250 (pp30) cc_final: 0.7962 (pp30) REVERT: B 57 GLU cc_start: 0.8055 (pm20) cc_final: 0.7605 (pm20) REVERT: B 352 GLU cc_start: 0.9466 (tm-30) cc_final: 0.9240 (tm-30) REVERT: D 352 GLU cc_start: 0.9439 (tm-30) cc_final: 0.9221 (tm-30) REVERT: E 37 MET cc_start: 0.8787 (ttm) cc_final: 0.8404 (ttp) REVERT: F 57 GLU cc_start: 0.8040 (pm20) cc_final: 0.7671 (pm20) REVERT: G 352 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9238 (tm-30) outliers start: 11 outliers final: 7 residues processed: 167 average time/residue: 0.2893 time to fit residues: 76.6656 Evaluate side-chains 147 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU 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 E residue 216 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 169 optimal weight: 50.0000 chunk 62 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.089087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069895 restraints weight = 174888.277| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.50 r_work: 0.3107 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19446 Z= 0.174 Angle : 0.523 5.157 26572 Z= 0.270 Chirality : 0.036 0.176 3234 Planarity : 0.004 0.040 3136 Dihedral : 6.453 57.308 3857 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.49 % Allowed : 10.70 % Favored : 88.81 % 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: 2.02 (0.19), residues: 2380 helix: 2.52 (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 0.004 0.000 ARG F 29 TYR 0.010 0.001 TYR C 230 PHE 0.010 0.001 PHE F 67 TRP 0.009 0.001 TRP F 74 HIS 0.001 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00377 (19425) covalent geometry : angle 0.52102 (26523) SS BOND : bond 0.00172 ( 14) SS BOND : angle 0.88583 ( 28) hydrogen bonds : bond 0.03506 ( 1212) hydrogen bonds : angle 4.14123 ( 3531) link_NAG-ASN : bond 0.00257 ( 7) link_NAG-ASN : angle 1.25604 ( 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 167 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.861 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: A 29 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.6912 (mmp80) REVERT: A 57 GLU cc_start: 0.8116 (pm20) cc_final: 0.7787 (pm20) REVERT: A 337 GLU cc_start: 0.8048 (tp30) cc_final: 0.7836 (tp30) REVERT: B 56 GLN cc_start: 0.8298 (pp30) cc_final: 0.8005 (pp30) REVERT: B 57 GLU cc_start: 0.8094 (pm20) cc_final: 0.7622 (pm20) REVERT: B 352 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9139 (tm-30) REVERT: C 57 GLU cc_start: 0.8067 (pm20) cc_final: 0.7674 (pm20) REVERT: D 352 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9223 (tm-30) REVERT: E 37 MET cc_start: 0.8750 (ttm) cc_final: 0.8367 (ttp) REVERT: F 29 ARG cc_start: 0.7037 (mmt-90) cc_final: 0.6795 (mmt180) REVERT: G 352 GLU cc_start: 0.9471 (tm-30) cc_final: 0.9261 (tm-30) outliers start: 9 outliers final: 9 residues processed: 166 average time/residue: 0.2856 time to fit residues: 76.2584 Evaluate side-chains 151 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 193 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 17 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 228 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.089475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.070422 restraints weight = 173961.286| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.48 r_work: 0.3122 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2608 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= 0.132 Angle : 0.504 5.091 26572 Z= 0.258 Chirality : 0.036 0.168 3234 Planarity : 0.004 0.040 3136 Dihedral : 6.150 54.779 3857 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.36 % Allowed : 9.99 % Favored : 88.65 % 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: 2.09 (0.19), residues: 2380 helix: 2.59 (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 0.005 0.000 ARG B 29 TYR 0.010 0.001 TYR D 230 PHE 0.011 0.001 PHE F 67 TRP 0.008 0.001 TRP B 74 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00293 (19425) covalent geometry : angle 0.50248 (26523) SS BOND : bond 0.00142 ( 14) SS BOND : angle 0.76335 ( 28) hydrogen bonds : bond 0.03360 ( 1212) hydrogen bonds : angle 4.04674 ( 3531) link_NAG-ASN : bond 0.00330 ( 7) link_NAG-ASN : angle 1.40628 ( 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 180 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.062 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: A 57 GLU cc_start: 0.8084 (pm20) cc_final: 0.7729 (pm20) REVERT: A 337 GLU cc_start: 0.8016 (tp30) cc_final: 0.7767 (tp30) REVERT: B 29 ARG cc_start: 0.7264 (mmt-90) cc_final: 0.7006 (mmt-90) REVERT: B 56 GLN cc_start: 0.8260 (pp30) cc_final: 0.7974 (pp30) REVERT: B 57 GLU cc_start: 0.8080 (pm20) cc_final: 0.7609 (pm20) REVERT: B 352 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9204 (tm-30) REVERT: C 147 ASP cc_start: 0.9227 (m-30) cc_final: 0.8892 (t0) REVERT: D 352 GLU cc_start: 0.9445 (tm-30) cc_final: 0.9224 (tm-30) REVERT: E 37 MET cc_start: 0.8750 (ttm) cc_final: 0.8347 (ttp) REVERT: F 29 ARG cc_start: 0.7313 (mmt-90) cc_final: 0.6939 (mmt180) REVERT: G 37 MET cc_start: 0.9064 (ttt) cc_final: 0.8811 (ttm) REVERT: G 352 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9220 (tm-30) outliers start: 25 outliers final: 14 residues processed: 180 average time/residue: 0.2811 time to fit residues: 82.1856 Evaluate side-chains 149 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 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 G residue 136 CYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN E 280 ASN F 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.087793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.069146 restraints weight = 175267.257| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.26 r_work: 0.3098 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19446 Z= 0.258 Angle : 0.562 5.163 26572 Z= 0.295 Chirality : 0.037 0.170 3234 Planarity : 0.004 0.043 3136 Dihedral : 6.436 53.324 3857 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.30 % Allowed : 10.65 % Favored : 88.05 % 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: 1.96 (0.19), residues: 2380 helix: 2.53 (0.14), residues: 1547 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.022 0.001 TYR D 10 PHE 0.007 0.001 PHE D 54 TRP 0.009 0.002 TRP B 74 HIS 0.003 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00553 (19425) covalent geometry : angle 0.56109 (26523) SS BOND : bond 0.00273 ( 14) SS BOND : angle 0.91456 ( 28) hydrogen bonds : bond 0.03583 ( 1212) hydrogen bonds : angle 4.27407 ( 3531) link_NAG-ASN : bond 0.00108 ( 7) link_NAG-ASN : angle 1.26434 ( 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 164 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.030 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: A 57 GLU cc_start: 0.8067 (pm20) cc_final: 0.7792 (pm20) REVERT: B 56 GLN cc_start: 0.8242 (pp30) cc_final: 0.7844 (pp30) REVERT: B 57 GLU cc_start: 0.8123 (pm20) cc_final: 0.7624 (pm20) REVERT: B 352 GLU cc_start: 0.9342 (tm-30) cc_final: 0.9105 (tm-30) REVERT: C 147 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8900 (t0) REVERT: F 29 ARG cc_start: 0.7425 (mmt-90) cc_final: 0.7110 (mmt-90) REVERT: G 37 MET cc_start: 0.9083 (ttt) cc_final: 0.8832 (ttm) outliers start: 24 outliers final: 16 residues processed: 162 average time/residue: 0.2868 time to fit residues: 75.1524 Evaluate side-chains 150 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain E residue 136 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 G residue 136 CYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 189 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 169 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN D 280 ASN F 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.087927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069217 restraints weight = 174575.555| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.26 r_work: 0.3100 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19446 Z= 0.216 Angle : 0.543 5.521 26572 Z= 0.283 Chirality : 0.037 0.168 3234 Planarity : 0.004 0.043 3136 Dihedral : 6.488 52.151 3857 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.20 % Allowed : 11.19 % Favored : 87.62 % 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: 1.95 (0.19), residues: 2380 helix: 2.49 (0.14), residues: 1554 sheet: None (None), residues: 0 loop : -1.15 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 29 TYR 0.017 0.001 TYR D 10 PHE 0.028 0.001 PHE C 67 TRP 0.008 0.001 TRP B 74 HIS 0.001 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00461 (19425) covalent geometry : angle 0.54151 (26523) SS BOND : bond 0.00229 ( 14) SS BOND : angle 0.85856 ( 28) hydrogen bonds : bond 0.03561 ( 1212) hydrogen bonds : angle 4.20691 ( 3531) link_NAG-ASN : bond 0.00182 ( 7) link_NAG-ASN : angle 1.27702 ( 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 166 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLN cc_start: 0.8265 (pp30) cc_final: 0.7843 (pp30) REVERT: B 57 GLU cc_start: 0.8208 (pm20) cc_final: 0.7708 (pm20) REVERT: B 352 GLU cc_start: 0.9349 (tm-30) cc_final: 0.9116 (tm-30) REVERT: C 57 GLU cc_start: 0.8077 (pm20) cc_final: 0.7758 (pm20) REVERT: C 147 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.8907 (t0) REVERT: F 29 ARG cc_start: 0.7502 (mmt-90) cc_final: 0.7295 (mmt-90) REVERT: G 37 MET cc_start: 0.9070 (ttt) cc_final: 0.8810 (ttm) REVERT: G 230 TYR cc_start: 0.9253 (t80) cc_final: 0.9038 (t80) outliers start: 22 outliers final: 19 residues processed: 163 average time/residue: 0.2980 time to fit residues: 78.0440 Evaluate side-chains 158 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain E residue 136 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 280 ASN Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 147 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 179 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN D 353 ASN E 353 ASN F 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.088398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069647 restraints weight = 173329.199| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.30 r_work: 0.3111 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19446 Z= 0.163 Angle : 0.527 5.575 26572 Z= 0.274 Chirality : 0.036 0.166 3234 Planarity : 0.004 0.042 3136 Dihedral : 6.377 56.408 3857 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.25 % Allowed : 10.97 % Favored : 87.78 % 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: 2.05 (0.19), residues: 2380 helix: 2.55 (0.14), residues: 1547 sheet: None (None), residues: 0 loop : -1.05 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.026 0.001 TYR G 10 PHE 0.018 0.001 PHE A 67 TRP 0.008 0.001 TRP G 74 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00355 (19425) covalent geometry : angle 0.52572 (26523) SS BOND : bond 0.00204 ( 14) SS BOND : angle 0.79382 ( 28) hydrogen bonds : bond 0.03477 ( 1212) hydrogen bonds : angle 4.08301 ( 3531) link_NAG-ASN : bond 0.00255 ( 7) link_NAG-ASN : angle 1.33756 ( 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 163 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLN cc_start: 0.8252 (pp30) cc_final: 0.7840 (pp30) REVERT: B 57 GLU cc_start: 0.8210 (pm20) cc_final: 0.7739 (pm20) REVERT: B 352 GLU cc_start: 0.9340 (tm-30) cc_final: 0.8998 (tm-30) REVERT: C 57 GLU cc_start: 0.8046 (pm20) cc_final: 0.7762 (pm20) REVERT: D 352 GLU cc_start: 0.9401 (tm-30) cc_final: 0.9142 (tm-30) REVERT: E 37 MET cc_start: 0.8722 (ttm) cc_final: 0.8336 (ttp) REVERT: G 37 MET cc_start: 0.9080 (ttt) cc_final: 0.8819 (ttm) REVERT: G 230 TYR cc_start: 0.9233 (t80) cc_final: 0.9022 (t80) outliers start: 23 outliers final: 18 residues processed: 161 average time/residue: 0.2873 time to fit residues: 75.5170 Evaluate side-chains 151 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 136 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 G residue 136 CYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 177 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 148 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN C 353 ASN E 280 ASN F 280 ASN G 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.088326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069482 restraints weight = 173723.676| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.28 r_work: 0.3109 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19446 Z= 0.182 Angle : 0.533 5.748 26572 Z= 0.277 Chirality : 0.037 0.163 3234 Planarity : 0.004 0.043 3136 Dihedral : 6.370 59.120 3857 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.25 % Allowed : 10.97 % Favored : 87.78 % 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: 2.05 (0.18), residues: 2380 helix: 2.57 (0.14), residues: 1547 sheet: None (None), residues: 0 loop : -1.08 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.018 0.001 TYR F 10 PHE 0.019 0.001 PHE F 67 TRP 0.008 0.001 TRP G 74 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00394 (19425) covalent geometry : angle 0.53118 (26523) SS BOND : bond 0.00233 ( 14) SS BOND : angle 0.86715 ( 28) hydrogen bonds : bond 0.03456 ( 1212) hydrogen bonds : angle 4.05754 ( 3531) link_NAG-ASN : bond 0.00219 ( 7) link_NAG-ASN : angle 1.35466 ( 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 159 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 GLN cc_start: 0.8247 (pp30) cc_final: 0.7825 (pp30) REVERT: B 57 GLU cc_start: 0.8237 (pm20) cc_final: 0.7739 (pm20) REVERT: B 352 GLU cc_start: 0.9333 (tm-30) cc_final: 0.9078 (tm-30) REVERT: C 57 GLU cc_start: 0.8067 (pm20) cc_final: 0.7812 (pm20) REVERT: D 352 GLU cc_start: 0.9383 (tm-30) cc_final: 0.9121 (tm-30) REVERT: E 37 MET cc_start: 0.8698 (ttm) cc_final: 0.8311 (ttp) REVERT: G 37 MET cc_start: 0.9070 (ttt) cc_final: 0.8802 (ttm) REVERT: G 56 GLN cc_start: 0.8403 (pp30) cc_final: 0.8189 (pp30) REVERT: G 230 TYR cc_start: 0.9239 (t80) cc_final: 0.9032 (t80) REVERT: G 352 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9152 (tm-30) outliers start: 23 outliers final: 19 residues processed: 156 average time/residue: 0.2863 time to fit residues: 72.5207 Evaluate side-chains 152 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 136 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 G residue 136 CYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 188 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 280 ASN E 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.088802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.070060 restraints weight = 173598.248| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.33 r_work: 0.3124 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19446 Z= 0.147 Angle : 0.519 6.023 26572 Z= 0.268 Chirality : 0.036 0.157 3234 Planarity : 0.004 0.043 3136 Dihedral : 6.147 57.879 3857 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.14 % Allowed : 11.14 % Favored : 87.72 % 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: 2.12 (0.18), residues: 2380 helix: 2.65 (0.14), residues: 1547 sheet: None (None), residues: 0 loop : -1.12 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 29 TYR 0.019 0.001 TYR F 10 PHE 0.013 0.001 PHE A 67 TRP 0.009 0.001 TRP G 74 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00323 (19425) covalent geometry : angle 0.51712 (26523) SS BOND : bond 0.00179 ( 14) SS BOND : angle 0.79230 ( 28) hydrogen bonds : bond 0.03359 ( 1212) hydrogen bonds : angle 3.96638 ( 3531) link_NAG-ASN : bond 0.00282 ( 7) link_NAG-ASN : angle 1.43272 ( 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 155 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7234 (mmt-90) cc_final: 0.7025 (mmt180) REVERT: B 56 GLN cc_start: 0.8237 (pp30) cc_final: 0.7808 (pp30) REVERT: B 57 GLU cc_start: 0.8216 (pm20) cc_final: 0.7710 (pm20) REVERT: B 352 GLU cc_start: 0.9329 (tm-30) cc_final: 0.8985 (tm-30) REVERT: C 57 GLU cc_start: 0.7988 (pm20) cc_final: 0.7738 (pm20) REVERT: D 352 GLU cc_start: 0.9358 (tm-30) cc_final: 0.9091 (tm-30) REVERT: E 37 MET cc_start: 0.8673 (ttm) cc_final: 0.8279 (ttp) REVERT: G 37 MET cc_start: 0.9063 (ttt) cc_final: 0.8802 (ttm) REVERT: G 76 GLN cc_start: 0.8796 (mt0) cc_final: 0.8238 (mt0) REVERT: G 230 TYR cc_start: 0.9228 (t80) cc_final: 0.9021 (t80) REVERT: G 352 GLU cc_start: 0.9403 (tm-30) cc_final: 0.9098 (tm-30) outliers start: 21 outliers final: 20 residues processed: 153 average time/residue: 0.2691 time to fit residues: 67.2729 Evaluate side-chains 152 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 136 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 G residue 136 CYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 234 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 210 optimal weight: 0.0070 chunk 200 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.089602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070914 restraints weight = 173479.379| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.34 r_work: 0.3147 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19446 Z= 0.117 Angle : 0.505 6.007 26572 Z= 0.260 Chirality : 0.036 0.152 3234 Planarity : 0.004 0.042 3136 Dihedral : 5.784 58.135 3857 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.14 % Allowed : 11.08 % Favored : 87.78 % 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: 2.77 (0.14), residues: 1547 sheet: None (None), residues: 0 loop : -1.11 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.015 0.001 TYR C 10 PHE 0.021 0.001 PHE E 67 TRP 0.008 0.001 TRP G 74 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00260 (19425) covalent geometry : angle 0.50301 (26523) SS BOND : bond 0.00150 ( 14) SS BOND : angle 0.74013 ( 28) hydrogen bonds : bond 0.03169 ( 1212) hydrogen bonds : angle 3.81786 ( 3531) link_NAG-ASN : bond 0.00352 ( 7) link_NAG-ASN : angle 1.56886 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6845.77 seconds wall clock time: 117 minutes 25.42 seconds (7045.42 seconds total)