Starting phenix.real_space_refine on Sat Jul 4 03:42:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rys_24747/07_2026/7rys_24747.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rys_24747/07_2026/7rys_24747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rys_24747/07_2026/7rys_24747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rys_24747/07_2026/7rys_24747.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rys_24747/07_2026/7rys_24747.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rys_24747/07_2026/7rys_24747.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rys_24747/07_2026/7rys_24747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rys_24747/07_2026/7rys_24747.cif" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6124 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8528 2.51 5 N 2080 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12900 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 131 Unusual residues: {'PGW': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-3': 6, 'PGW:plan-1': 5, 'PGW:plan-2': 5} Unresolved non-hydrogen planarities: 56 Restraints were copied for chains: B, C, D Time building chain proxies: 2.06, per 1000 atoms: 0.16 Number of scatterers: 12900 At special positions: 0 Unit cell: (108.009, 108.009, 113.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2256 8.00 N 2080 7.00 C 8528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 406.0 milliseconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 62.7% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.109A pdb=" N LEU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 4.193A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.998A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.791A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.735A pdb=" N ALA A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.949A pdb=" N LEU A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 157 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 223 removed outlier: 4.220A pdb=" N ALA A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.639A pdb=" N LEU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.722A pdb=" N ILE A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 292 removed outlier: 3.587A pdb=" N GLU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.508A pdb=" N ILE A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.942A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.591A pdb=" N PHE A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.543A pdb=" N ALA A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 53 removed outlier: 4.110A pdb=" N LEU B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 4.193A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.999A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.791A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 4.735A pdb=" N ALA B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.949A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 223 removed outlier: 4.220A pdb=" N ALA B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.638A pdb=" N LEU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 removed outlier: 3.721A pdb=" N ILE B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 292 removed outlier: 3.586A pdb=" N GLU B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.508A pdb=" N ILE B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.942A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.591A pdb=" N PHE B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 418 removed outlier: 3.543A pdb=" N ALA B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 53 removed outlier: 4.109A pdb=" N LEU C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 4.193A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.997A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.790A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 4.735A pdb=" N ALA C 120 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.949A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 157 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 223 removed outlier: 4.219A pdb=" N ALA C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.639A pdb=" N LEU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 removed outlier: 3.721A pdb=" N ILE C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 292 removed outlier: 3.587A pdb=" N GLU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.508A pdb=" N ILE C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.942A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.591A pdb=" N PHE C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 418 removed outlier: 3.543A pdb=" N ALA C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 53 removed outlier: 4.109A pdb=" N LEU D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 4.194A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.997A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 113 removed outlier: 3.792A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 122 removed outlier: 4.736A pdb=" N ALA D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.949A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 223 removed outlier: 4.220A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.638A pdb=" N LEU D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.721A pdb=" N ILE D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.587A pdb=" N GLU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.507A pdb=" N ILE D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.941A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.591A pdb=" N PHE D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.543A pdb=" N ALA D 408 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 removed outlier: 7.105A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 338 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 339 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.701A pdb=" N VAL A 381 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 322 removed outlier: 7.105A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 338 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 339 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.700A pdb=" N VAL B 381 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 322 removed outlier: 7.105A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 338 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 339 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.700A pdb=" N VAL C 381 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 322 removed outlier: 7.105A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 338 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR D 339 " --> pdb=" O PHE D 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.701A pdb=" N VAL D 381 " --> pdb=" O ILE D 328 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2043 1.32 - 1.44: 3259 1.44 - 1.57: 7790 1.57 - 1.69: 16 1.69 - 1.81: 48 Bond restraints: 13156 Sorted by residual: bond pdb=" C10 PGW D 503 " pdb=" C9 PGW D 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" C10 PGW B 503 " pdb=" C9 PGW B 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C10 PGW A 503 " pdb=" C9 PGW A 503 " ideal model delta sigma weight residual 1.333 1.508 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C10 PGW C 503 " pdb=" C9 PGW C 503 " ideal model delta sigma weight residual 1.333 1.508 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" C GLY B 332 " pdb=" N GLU B 333 " ideal model delta sigma weight residual 1.330 1.424 -0.094 1.38e-02 5.25e+03 4.61e+01 ... (remaining 13151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 17071 2.58 - 5.16: 578 5.16 - 7.73: 119 7.73 - 10.31: 20 10.31 - 12.89: 8 Bond angle restraints: 17796 Sorted by residual: angle pdb=" N TYR C 259 " pdb=" CA TYR C 259 " pdb=" C TYR C 259 " ideal model delta sigma weight residual 111.14 104.24 6.90 1.08e+00 8.57e-01 4.08e+01 angle pdb=" N TYR D 259 " pdb=" CA TYR D 259 " pdb=" C TYR D 259 " ideal model delta sigma weight residual 111.14 104.25 6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" N TYR A 259 " pdb=" CA TYR A 259 " pdb=" C TYR A 259 " ideal model delta sigma weight residual 111.14 104.26 6.88 1.08e+00 8.57e-01 4.06e+01 angle pdb=" N TYR B 259 " pdb=" CA TYR B 259 " pdb=" C TYR B 259 " ideal model delta sigma weight residual 111.14 104.30 6.84 1.08e+00 8.57e-01 4.01e+01 angle pdb=" N LEU A 98 " pdb=" CA LEU A 98 " pdb=" C LEU A 98 " ideal model delta sigma weight residual 113.19 106.71 6.48 1.19e+00 7.06e-01 2.97e+01 ... (remaining 17791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.90: 7776 34.90 - 69.79: 156 69.79 - 104.69: 8 104.69 - 139.58: 4 139.58 - 174.48: 8 Dihedral angle restraints: 7952 sinusoidal: 3384 harmonic: 4568 Sorted by residual: dihedral pdb=" C07 PGW B 503 " pdb=" C06 PGW B 503 " pdb=" C10 PGW B 503 " pdb=" C9 PGW B 503 " ideal model delta sinusoidal sigma weight residual 110.06 -64.42 174.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 PGW C 503 " pdb=" C06 PGW C 503 " pdb=" C10 PGW C 503 " pdb=" C9 PGW C 503 " ideal model delta sinusoidal sigma weight residual 110.06 -64.39 174.45 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 PGW A 503 " pdb=" C06 PGW A 503 " pdb=" C10 PGW A 503 " pdb=" C9 PGW A 503 " ideal model delta sinusoidal sigma weight residual 110.06 -64.39 174.45 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1443 0.048 - 0.096: 462 0.096 - 0.144: 107 0.144 - 0.192: 44 0.192 - 0.240: 28 Chirality restraints: 2084 Sorted by residual: chirality pdb=" CA LEU C 98 " pdb=" N LEU C 98 " pdb=" C LEU C 98 " pdb=" CB LEU C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU A 98 " pdb=" N LEU A 98 " pdb=" C LEU A 98 " pdb=" CB LEU A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LEU B 98 " pdb=" N LEU B 98 " pdb=" C LEU B 98 " pdb=" CB LEU B 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2081 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 503 " -0.067 2.00e-02 2.50e+03 6.68e-02 4.47e+01 pdb=" C10 PGW C 503 " 0.067 2.00e-02 2.50e+03 pdb=" C8 PGW C 503 " -0.067 2.00e-02 2.50e+03 pdb=" C9 PGW C 503 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " 0.067 2.00e-02 2.50e+03 6.68e-02 4.46e+01 pdb=" C10 PGW A 503 " -0.067 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " 0.067 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " -0.067 2.00e-02 2.50e+03 6.67e-02 4.45e+01 pdb=" C10 PGW B 503 " 0.067 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " -0.067 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " 0.066 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2428 2.78 - 3.31: 12335 3.31 - 3.84: 19546 3.84 - 4.37: 22523 4.37 - 4.90: 38964 Nonbonded interactions: 95796 Sorted by model distance: nonbonded pdb=" OE1 GLU B 308 " pdb=" OH TYR B 404 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU A 308 " pdb=" OH TYR A 404 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU C 308 " pdb=" OH TYR C 404 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU D 308 " pdb=" OH TYR D 404 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.254 3.040 ... (remaining 95791 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 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 : 0.007 0.176 13156 Z= 0.444 Angle : 1.122 12.890 17796 Z= 0.655 Chirality : 0.056 0.240 2084 Planarity : 0.008 0.067 2156 Dihedral : 16.255 174.480 5000 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.30 % Allowed : 1.80 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.21), residues: 1532 helix: -0.45 (0.17), residues: 936 sheet: -1.24 (0.42), residues: 112 loop : -1.61 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 399 TYR 0.014 0.002 TYR A 259 PHE 0.030 0.003 PHE D 340 TRP 0.011 0.001 TRP D 264 HIS 0.007 0.002 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.44 (13156) covalent geometry : angle 1.12188 / 0.66 (17796) hydrogen bonds : bond 0.18075 / 11.56 ( 668) hydrogen bonds : angle 6.62188 / 4.97 ( 1932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 0.646 Fit side-chains REVERT: A 229 LYS cc_start: 0.8680 (tptt) cc_final: 0.8464 (tptt) REVERT: A 261 ASP cc_start: 0.7486 (t70) cc_final: 0.7195 (t0) REVERT: B 261 ASP cc_start: 0.7680 (t70) cc_final: 0.7390 (t0) REVERT: C 261 ASP cc_start: 0.7734 (t70) cc_final: 0.7444 (t0) REVERT: D 341 ILE cc_start: 0.8245 (mm) cc_final: 0.8039 (mm) outliers start: 4 outliers final: 0 residues processed: 227 average time/residue: 0.1332 time to fit residues: 42.5438 Evaluate side-chains 167 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 0.0000 chunk 91 optimal weight: 0.0040 chunk 149 optimal weight: 7.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 253 GLN B 131 ASN B 253 GLN B 364 GLN C 131 ASN C 253 GLN D 131 ASN D 253 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.214174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.195994 restraints weight = 14851.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.192278 restraints weight = 21221.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.190141 restraints weight = 22728.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.189569 restraints weight = 19848.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.188217 restraints weight = 19292.192| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13156 Z= 0.132 Angle : 0.699 8.641 17796 Z= 0.330 Chirality : 0.042 0.143 2084 Planarity : 0.005 0.047 2156 Dihedral : 14.111 148.981 2052 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.83 % Allowed : 10.66 % Favored : 88.51 % 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: -0.87 (0.22), residues: 1532 helix: 0.13 (0.18), residues: 968 sheet: -1.88 (0.36), residues: 124 loop : -1.54 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 417 TYR 0.014 0.001 TYR D 357 PHE 0.021 0.002 PHE D 365 TRP 0.009 0.001 TRP C 264 HIS 0.005 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (13156) covalent geometry : angle 0.69911 / 0.33 (17796) hydrogen bonds : bond 0.04283 / 2.77 ( 668) hydrogen bonds : angle 4.38801 / 3.26 ( 1932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.484 Fit side-chains REVERT: A 103 PRO cc_start: 0.6869 (Cg_endo) cc_final: 0.6657 (Cg_exo) REVERT: A 261 ASP cc_start: 0.7512 (t70) cc_final: 0.7160 (t0) REVERT: B 114 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8080 (tttp) REVERT: B 261 ASP cc_start: 0.7612 (t70) cc_final: 0.7247 (t0) REVERT: B 342 ASN cc_start: 0.8637 (t0) cc_final: 0.8330 (t0) REVERT: C 261 ASP cc_start: 0.7639 (t70) cc_final: 0.7358 (t0) REVERT: D 210 MET cc_start: 0.6834 (mpp) cc_final: 0.6429 (mpp) REVERT: D 342 ASN cc_start: 0.8504 (t0) cc_final: 0.8288 (t0) outliers start: 11 outliers final: 3 residues processed: 215 average time/residue: 0.1293 time to fit residues: 39.3282 Evaluate side-chains 165 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 140 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 0.0270 chunk 72 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS C 99 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.212668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.194483 restraints weight = 14830.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.191648 restraints weight = 21244.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.190164 restraints weight = 17215.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.188810 restraints weight = 16189.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.187041 restraints weight = 18530.360| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13156 Z= 0.122 Angle : 0.650 8.108 17796 Z= 0.305 Chirality : 0.041 0.141 2084 Planarity : 0.005 0.048 2156 Dihedral : 11.953 133.297 2052 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.98 % Allowed : 12.84 % Favored : 86.19 % 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: -0.37 (0.22), residues: 1532 helix: 0.50 (0.18), residues: 956 sheet: -1.67 (0.37), residues: 124 loop : -1.22 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 399 TYR 0.010 0.001 TYR D 175 PHE 0.021 0.001 PHE D 365 TRP 0.006 0.001 TRP B 264 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13156) covalent geometry : angle 0.64990 / 0.31 (17796) hydrogen bonds : bond 0.03809 / 2.46 ( 668) hydrogen bonds : angle 4.13066 / 3.06 ( 1932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7522 (t70) cc_final: 0.7190 (t0) REVERT: B 114 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8181 (mttp) REVERT: B 261 ASP cc_start: 0.7581 (t70) cc_final: 0.7224 (t0) REVERT: C 261 ASP cc_start: 0.7619 (t70) cc_final: 0.7316 (t0) outliers start: 13 outliers final: 10 residues processed: 191 average time/residue: 0.1353 time to fit residues: 36.0744 Evaluate side-chains 170 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 8.9990 chunk 19 optimal weight: 0.0570 chunk 109 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 24 optimal weight: 0.0010 chunk 6 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.6908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.211336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.193886 restraints weight = 14956.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.192434 restraints weight = 17733.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.191547 restraints weight = 17298.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.190671 restraints weight = 16107.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.190076 restraints weight = 17563.921| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13156 Z= 0.127 Angle : 0.641 7.889 17796 Z= 0.300 Chirality : 0.041 0.146 2084 Planarity : 0.005 0.053 2156 Dihedral : 10.510 133.537 2052 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.50 % Allowed : 13.59 % Favored : 84.91 % 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: -0.20 (0.22), residues: 1532 helix: 0.61 (0.18), residues: 960 sheet: -1.61 (0.37), residues: 124 loop : -1.13 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.011 0.001 TYR D 175 PHE 0.018 0.001 PHE D 365 TRP 0.006 0.001 TRP A 264 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13156) covalent geometry : angle 0.64108 / 0.30 (17796) hydrogen bonds : bond 0.03612 / 2.35 ( 668) hydrogen bonds : angle 4.01418 / 2.98 ( 1932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6735 (mpp) REVERT: A 261 ASP cc_start: 0.7508 (t70) cc_final: 0.7156 (t0) REVERT: B 114 LYS cc_start: 0.8635 (mmmm) cc_final: 0.8250 (mttp) REVERT: B 261 ASP cc_start: 0.7544 (t70) cc_final: 0.7207 (t0) REVERT: C 261 ASP cc_start: 0.7550 (t70) cc_final: 0.7223 (t0) REVERT: D 210 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6473 (mpp) outliers start: 20 outliers final: 10 residues processed: 189 average time/residue: 0.1351 time to fit residues: 35.7010 Evaluate side-chains 168 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN D 99 HIS D 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.208926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.189615 restraints weight = 14809.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.184793 restraints weight = 20050.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.182529 restraints weight = 24449.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.181785 restraints weight = 21693.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.181252 restraints weight = 20330.123| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13156 Z= 0.160 Angle : 0.662 7.776 17796 Z= 0.313 Chirality : 0.043 0.135 2084 Planarity : 0.005 0.058 2156 Dihedral : 10.309 133.566 2052 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.03 % Allowed : 15.39 % Favored : 82.58 % 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: -0.16 (0.22), residues: 1532 helix: 0.65 (0.18), residues: 956 sheet: -1.43 (0.38), residues: 124 loop : -1.17 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.013 0.001 TYR B 175 PHE 0.015 0.001 PHE D 365 TRP 0.006 0.001 TRP D 15 HIS 0.003 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (13156) covalent geometry : angle 0.66249 / 0.31 (17796) hydrogen bonds : bond 0.03887 / 2.54 ( 668) hydrogen bonds : angle 4.06337 / 2.99 ( 1932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6736 (mpp) REVERT: A 261 ASP cc_start: 0.7516 (t70) cc_final: 0.7190 (t0) REVERT: A 397 PHE cc_start: 0.7080 (t80) cc_final: 0.6785 (t80) REVERT: B 210 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6341 (mpp) REVERT: B 261 ASP cc_start: 0.7627 (t70) cc_final: 0.7254 (t0) REVERT: C 261 ASP cc_start: 0.7615 (t70) cc_final: 0.7259 (t0) outliers start: 27 outliers final: 19 residues processed: 184 average time/residue: 0.1316 time to fit residues: 34.4424 Evaluate side-chains 177 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 136 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 99 HIS D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.210533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.191928 restraints weight = 14674.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.190044 restraints weight = 21627.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.188140 restraints weight = 23670.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.187078 restraints weight = 21662.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.185097 restraints weight = 26414.699| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13156 Z= 0.125 Angle : 0.653 8.564 17796 Z= 0.305 Chirality : 0.041 0.139 2084 Planarity : 0.005 0.057 2156 Dihedral : 9.845 133.335 2052 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.05 % Allowed : 16.74 % Favored : 82.21 % 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: 0.09 (0.22), residues: 1532 helix: 0.85 (0.18), residues: 956 sheet: -1.19 (0.40), residues: 124 loop : -1.13 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 399 TYR 0.010 0.001 TYR B 357 PHE 0.015 0.001 PHE D 365 TRP 0.006 0.001 TRP B 176 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13156) covalent geometry : angle 0.65305 / 0.30 (17796) hydrogen bonds : bond 0.03413 / 2.22 ( 668) hydrogen bonds : angle 3.86805 / 2.85 ( 1932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.7135 (mpp) cc_final: 0.6655 (mpp) REVERT: A 261 ASP cc_start: 0.7501 (t70) cc_final: 0.7207 (t0) REVERT: A 388 ASP cc_start: 0.7401 (p0) cc_final: 0.6977 (p0) REVERT: A 397 PHE cc_start: 0.6966 (t80) cc_final: 0.6656 (t80) REVERT: B 210 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6562 (mpp) REVERT: B 261 ASP cc_start: 0.7593 (t70) cc_final: 0.7258 (t0) REVERT: D 99 HIS cc_start: 0.5099 (m-70) cc_final: 0.4893 (m170) REVERT: D 210 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6320 (mpp) outliers start: 14 outliers final: 12 residues processed: 173 average time/residue: 0.1320 time to fit residues: 32.3118 Evaluate side-chains 162 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 210 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 146 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 110 optimal weight: 0.0870 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.209726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.192904 restraints weight = 14638.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.189289 restraints weight = 21506.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.187932 restraints weight = 22660.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.187056 restraints weight = 20425.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.186622 restraints weight = 19674.440| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13156 Z= 0.133 Angle : 0.657 7.963 17796 Z= 0.306 Chirality : 0.041 0.144 2084 Planarity : 0.005 0.052 2156 Dihedral : 9.711 133.435 2052 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.65 % Allowed : 16.97 % Favored : 81.38 % 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: 0.13 (0.22), residues: 1532 helix: 0.86 (0.18), residues: 956 sheet: -1.12 (0.40), residues: 124 loop : -1.09 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.011 0.001 TYR B 175 PHE 0.020 0.001 PHE D 397 TRP 0.005 0.001 TRP D 15 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (13156) covalent geometry : angle 0.65672 / 0.31 (17796) hydrogen bonds : bond 0.03493 / 2.27 ( 668) hydrogen bonds : angle 3.87132 / 2.85 ( 1932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7219 (tpp) cc_final: 0.6950 (mpp) REVERT: A 261 ASP cc_start: 0.7449 (t70) cc_final: 0.7186 (t0) REVERT: A 310 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7297 (mt) REVERT: A 397 PHE cc_start: 0.6926 (t80) cc_final: 0.6680 (t80) REVERT: B 210 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6581 (mpp) REVERT: B 261 ASP cc_start: 0.7535 (t70) cc_final: 0.7214 (t0) REVERT: D 210 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6297 (mpp) outliers start: 22 outliers final: 16 residues processed: 168 average time/residue: 0.1305 time to fit residues: 31.1603 Evaluate side-chains 169 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 130 optimal weight: 0.8980 chunk 81 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.210825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.191774 restraints weight = 14447.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.188378 restraints weight = 20955.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.186140 restraints weight = 19595.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.184637 restraints weight = 19384.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.183282 restraints weight = 20564.687| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13156 Z= 0.122 Angle : 0.649 8.041 17796 Z= 0.302 Chirality : 0.041 0.142 2084 Planarity : 0.005 0.060 2156 Dihedral : 9.456 133.834 2052 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.73 % Allowed : 17.64 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1532 helix: 0.95 (0.18), residues: 956 sheet: -1.06 (0.41), residues: 124 loop : -1.00 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 399 TYR 0.009 0.001 TYR B 175 PHE 0.021 0.001 PHE D 397 TRP 0.005 0.001 TRP B 176 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13156) covalent geometry : angle 0.64928 / 0.30 (17796) hydrogen bonds : bond 0.03262 / 2.12 ( 668) hydrogen bonds : angle 3.77904 / 2.78 ( 1932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.7191 (tpp) cc_final: 0.6965 (mpp) REVERT: A 261 ASP cc_start: 0.7506 (t70) cc_final: 0.7244 (t0) REVERT: A 310 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7338 (mt) REVERT: A 397 PHE cc_start: 0.7067 (t80) cc_final: 0.6751 (t80) REVERT: B 210 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6621 (mpp) REVERT: B 261 ASP cc_start: 0.7555 (t70) cc_final: 0.7247 (t0) REVERT: D 210 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6268 (mpp) outliers start: 23 outliers final: 18 residues processed: 169 average time/residue: 0.1371 time to fit residues: 32.1737 Evaluate side-chains 161 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 18 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 83 optimal weight: 20.0000 chunk 134 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 57 optimal weight: 0.0020 chunk 13 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.211473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.194654 restraints weight = 14627.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.191001 restraints weight = 20709.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.189487 restraints weight = 24243.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188429 restraints weight = 20565.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.187518 restraints weight = 20628.981| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13156 Z= 0.120 Angle : 0.658 12.027 17796 Z= 0.303 Chirality : 0.041 0.138 2084 Planarity : 0.005 0.061 2156 Dihedral : 9.281 133.395 2052 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.58 % Allowed : 17.94 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1532 helix: 0.98 (0.18), residues: 960 sheet: -1.00 (0.41), residues: 124 loop : -0.96 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 399 TYR 0.009 0.001 TYR A 175 PHE 0.014 0.001 PHE B 397 TRP 0.005 0.001 TRP B 176 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13156) covalent geometry : angle 0.65829 / 0.30 (17796) hydrogen bonds : bond 0.03168 / 2.04 ( 668) hydrogen bonds : angle 3.73757 / 2.76 ( 1932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6989 (mpp) REVERT: A 261 ASP cc_start: 0.7469 (t70) cc_final: 0.7257 (t0) REVERT: A 310 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7325 (mt) REVERT: A 397 PHE cc_start: 0.6997 (t80) cc_final: 0.6725 (t80) REVERT: B 210 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6680 (mpp) REVERT: B 261 ASP cc_start: 0.7488 (t70) cc_final: 0.7221 (t0) REVERT: D 210 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6285 (mpp) outliers start: 21 outliers final: 15 residues processed: 163 average time/residue: 0.1114 time to fit residues: 26.0268 Evaluate side-chains 167 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 0.0870 chunk 110 optimal weight: 0.0370 chunk 59 optimal weight: 0.0050 chunk 81 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 109 optimal weight: 0.8980 chunk 123 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 overall best weight: 0.0626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.214153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.195376 restraints weight = 14694.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.192507 restraints weight = 20388.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.190912 restraints weight = 24196.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.190161 restraints weight = 20420.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.189200 restraints weight = 20034.995| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13156 Z= 0.116 Angle : 0.664 11.666 17796 Z= 0.303 Chirality : 0.041 0.158 2084 Planarity : 0.004 0.044 2156 Dihedral : 8.985 133.442 2052 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.13 % Allowed : 18.77 % Favored : 80.11 % 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: 0.51 (0.23), residues: 1532 helix: 1.15 (0.18), residues: 956 sheet: -0.96 (0.41), residues: 124 loop : -0.92 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 399 TYR 0.009 0.001 TYR B 357 PHE 0.013 0.001 PHE D 365 TRP 0.004 0.000 TRP C 176 HIS 0.001 0.000 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (13156) covalent geometry : angle 0.66355 / 0.30 (17796) hydrogen bonds : bond 0.02871 / 1.83 ( 668) hydrogen bonds : angle 3.60267 / 2.67 ( 1932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.7011 (tpp) cc_final: 0.6742 (mpp) REVERT: A 310 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7388 (mt) REVERT: B 81 ARG cc_start: 0.3639 (ptt180) cc_final: 0.3313 (ptt180) REVERT: B 210 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6673 (mpp) REVERT: B 261 ASP cc_start: 0.7509 (t70) cc_final: 0.7265 (t0) REVERT: B 388 ASP cc_start: 0.7654 (p0) cc_final: 0.7376 (p0) REVERT: D 210 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6395 (mpp) outliers start: 15 outliers final: 11 residues processed: 163 average time/residue: 0.1065 time to fit residues: 24.7504 Evaluate side-chains 162 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.211906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.195733 restraints weight = 14648.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.194500 restraints weight = 17869.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.193271 restraints weight = 21277.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.191363 restraints weight = 20052.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.189515 restraints weight = 23844.291| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13156 Z= 0.123 Angle : 0.669 11.771 17796 Z= 0.308 Chirality : 0.041 0.138 2084 Planarity : 0.005 0.044 2156 Dihedral : 8.980 133.591 2052 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.43 % Allowed : 18.54 % Favored : 80.03 % 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: 0.49 (0.23), residues: 1532 helix: 1.13 (0.18), residues: 956 sheet: -0.97 (0.41), residues: 124 loop : -0.90 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 399 TYR 0.009 0.001 TYR A 175 PHE 0.016 0.001 PHE A 397 TRP 0.003 0.001 TRP B 264 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13156) covalent geometry : angle 0.66945 / 0.31 (17796) hydrogen bonds : bond 0.03099 / 1.99 ( 668) hydrogen bonds : angle 3.64360 / 2.68 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.65 seconds wall clock time: 33 minutes 43.55 seconds (2023.55 seconds total)