Starting phenix.real_space_refine on Sat Sep 12 20:09:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rys_24747/09_2026/7rys_24747.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rys_24747/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7rys_24747/09_2026/7rys_24747.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rys_24747/09_2026/7rys_24747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rys_24747/09_2026/7rys_24747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rys_24747/09_2026/7rys_24747.map" model { file = "/net/cci-nas-00/data/ceres_data/7rys_24747/09_2026/7rys_24747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rys_24747/09_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-2.2.1-6174/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: {'RNAv2': 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: 3.08, per 1000 atoms: 0.24 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: 1.10 Conformation dependent library (CDL) restraints added in 630.8 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: 0.36 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: 2.13 Time building geometry restraints manager: 1.48 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: 17055 2.58 - 5.16: 578 5.16 - 7.73: 123 7.73 - 10.31: 28 10.31 - 12.89: 12 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: 7780 34.90 - 69.79: 156 69.79 - 104.69: 8 104.69 - 139.58: 0 139.58 - 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 - 0.054: 1556 0.054 - 0.108: 401 0.108 - 0.162: 73 0.162 - 0.217: 42 0.217 - 0.271: 12 Chirality restraints: 2084 Sorted by residual: chirality pdb=" C2' CMP A 501 " pdb=" C1' CMP A 501 " pdb=" C3' CMP A 501 " pdb=" O2' CMP A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2' CMP D 501 " pdb=" C1' CMP D 501 " pdb=" C3' CMP D 501 " pdb=" O2' CMP D 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2' CMP C 501 " pdb=" C1' CMP C 501 " pdb=" C3' CMP C 501 " pdb=" O2' CMP C 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.81e+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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.120 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.170 ------------------------------------------------------------------------------- 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 : 1.152 12.890 17796 Z= 0.658 Chirality : 0.058 0.271 2084 Planarity : 0.008 0.067 2156 Dihedral : 15.853 174.480 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 0.00729 / 0.44 (13156) covalent geometry : angle 1.15175 / 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 : 0.573 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: 0.1312 time to fit residues: 42.0779 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 : 0.494 ------------------------------------------------------------------------------- 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: 10.0000 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 364 GLN C 131 ASN C 253 GLN D 131 ASN D 253 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.214191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.195648 restraints weight = 14886.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.194956 restraints weight = 17965.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.194255 restraints weight = 17641.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.193987 restraints weight = 16398.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.193789 restraints weight = 14418.561| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1636 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= 0.128 Angle : 0.728 8.608 17796 Z= 0.331 Chirality : 0.042 0.161 2084 Planarity : 0.005 0.047 2156 Dihedral : 12.723 149.450 2052 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.68 % Allowed : 10.66 % Favored : 88.66 % 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: -0.73 (0.22), residues: 1532 helix: 0.26 (0.18), residues: 944 sheet: -1.88 (0.36), residues: 124 loop : -1.42 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 136 TYR 0.013 0.001 TYR D 357 PHE 0.021 0.002 PHE D 365 TRP 0.007 0.001 TRP C 264 HIS 0.005 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (13156) covalent geometry : angle 0.72836 / 0.33 (17796) hydrogen bonds : bond 0.04305 / 2.78 ( 668) hydrogen bonds : angle 4.38654 / 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 217 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.486 Fit side-chains REVERT: A 103 PRO cc_start: 0.6900 (Cg_endo) cc_final: 0.6679 (Cg_exo) REVERT: A 261 ASP cc_start: 0.7457 (t70) cc_final: 0.7113 (t0) REVERT: B 114 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8062 (tttp) REVERT: B 261 ASP cc_start: 0.7555 (t70) cc_final: 0.7206 (t0) REVERT: B 342 ASN cc_start: 0.8575 (t0) cc_final: 0.8263 (t0) REVERT: C 261 ASP cc_start: 0.7597 (t70) cc_final: 0.7324 (t0) REVERT: D 210 MET cc_start: 0.6730 (mpp) cc_final: 0.6305 (mpp) REVERT: D 342 ASN cc_start: 0.8432 (t0) cc_final: 0.8231 (t0) outliers start: 9 outliers final: 3 residues processed: 213 average time/residue: 0.1254 time to fit residues: 37.9078 Evaluate side-chains 164 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 72 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 HIS C 99 HIS D 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.210179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.191566 restraints weight = 14807.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.188652 restraints weight = 20700.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.186609 restraints weight = 24115.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.186035 restraints weight = 18548.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.185382 restraints weight = 17758.550| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13156 Z= 0.143 Angle : 0.697 8.763 17796 Z= 0.315 Chirality : 0.043 0.168 2084 Planarity : 0.005 0.048 2156 Dihedral : 10.421 100.950 2052 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.13 % Allowed : 13.06 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.22), residues: 1532 helix: 0.38 (0.18), residues: 956 sheet: -1.74 (0.37), residues: 124 loop : -1.24 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.013 0.001 TYR D 175 PHE 0.020 0.001 PHE D 365 TRP 0.006 0.001 TRP B 264 HIS 0.003 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (13156) covalent geometry : angle 0.69688 / 0.31 (17796) hydrogen bonds : bond 0.04087 / 2.65 ( 668) hydrogen bonds : angle 4.20998 / 3.10 ( 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 193 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 210 MET cc_start: 0.6590 (mtt) cc_final: 0.6312 (mpp) REVERT: A 261 ASP cc_start: 0.7545 (t70) cc_final: 0.7199 (t0) REVERT: B 114 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8221 (mttp) REVERT: B 210 MET cc_start: 0.6644 (mtt) cc_final: 0.6437 (mpp) REVERT: B 261 ASP cc_start: 0.7609 (t70) cc_final: 0.7230 (t0) REVERT: B 277 LYS cc_start: 0.8236 (pttt) cc_final: 0.7389 (mttp) REVERT: C 261 ASP cc_start: 0.7610 (t70) cc_final: 0.7295 (t0) outliers start: 15 outliers final: 11 residues processed: 188 average time/residue: 0.1319 time to fit residues: 34.8991 Evaluate side-chains 173 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR 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 206 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 140 LEU 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: 0.0060 chunk 19 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN D 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.210780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.191965 restraints weight = 14762.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.187916 restraints weight = 19657.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.185557 restraints weight = 22922.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.184533 restraints weight = 20823.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.183073 restraints weight = 20805.423| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13156 Z= 0.121 Angle : 0.672 8.547 17796 Z= 0.300 Chirality : 0.042 0.160 2084 Planarity : 0.005 0.052 2156 Dihedral : 8.593 80.157 2052 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.28 % Allowed : 13.96 % Favored : 84.76 % 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: -0.23 (0.22), residues: 1532 helix: 0.60 (0.18), residues: 960 sheet: -1.63 (0.37), residues: 124 loop : -1.17 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 399 TYR 0.009 0.001 TYR D 175 PHE 0.017 0.001 PHE D 365 TRP 0.005 0.001 TRP B 176 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13156) covalent geometry : angle 0.67232 / 0.30 (17796) hydrogen bonds : bond 0.03626 / 2.36 ( 668) hydrogen bonds : angle 3.99898 / 2.96 ( 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 190 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6649 (mtt) cc_final: 0.6426 (mpp) REVERT: A 261 ASP cc_start: 0.7579 (t70) cc_final: 0.7251 (t0) REVERT: B 114 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8291 (tttp) REVERT: B 210 MET cc_start: 0.6660 (mtt) cc_final: 0.6445 (mpp) REVERT: B 261 ASP cc_start: 0.7599 (t70) cc_final: 0.7248 (t0) REVERT: B 277 LYS cc_start: 0.8240 (pttt) cc_final: 0.7395 (mttp) REVERT: C 261 ASP cc_start: 0.7603 (t70) cc_final: 0.7264 (t0) outliers start: 17 outliers final: 9 residues processed: 183 average time/residue: 0.1372 time to fit residues: 34.8191 Evaluate side-chains 166 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 206 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 140 LEU 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: 6.9990 chunk 56 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 0.0270 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 0.0870 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 99 HIS D 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.208204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.190221 restraints weight = 14848.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188576 restraints weight = 17393.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.187535 restraints weight = 16949.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.186905 restraints weight = 15837.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.186392 restraints weight = 17944.628| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13156 Z= 0.155 Angle : 0.692 8.583 17796 Z= 0.312 Chirality : 0.043 0.160 2084 Planarity : 0.005 0.056 2156 Dihedral : 8.360 75.950 2052 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.88 % Allowed : 15.84 % Favored : 82.28 % 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: 0.67 (0.17), residues: 956 sheet: -1.43 (0.38), residues: 124 loop : -1.22 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.013 0.001 TYR A 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 0.00370 / 0.16 (13156) covalent geometry : angle 0.69176 / 0.31 (17796) hydrogen bonds : bond 0.03893 / 2.54 ( 668) hydrogen bonds : angle 4.05406 / 2.98 ( 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 196 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7521 (t70) cc_final: 0.7175 (t0) REVERT: B 114 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8402 (tttp) REVERT: B 210 MET cc_start: 0.6789 (mtt) cc_final: 0.6319 (mpp) REVERT: B 261 ASP cc_start: 0.7556 (t70) cc_final: 0.7181 (t0) outliers start: 25 outliers final: 20 residues processed: 181 average time/residue: 0.1238 time to fit residues: 32.0119 Evaluate side-chains 168 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU 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 206 LEU Chi-restraints excluded: chain B residue 213 LEU 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: 0.6980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 0.0000 chunk 16 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN D 99 HIS D 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.210226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.193702 restraints weight = 14630.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.191071 restraints weight = 22886.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.189505 restraints weight = 26791.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.189246 restraints weight = 21075.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.188808 restraints weight = 19599.802| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13156 Z= 0.121 Angle : 0.680 8.484 17796 Z= 0.304 Chirality : 0.041 0.154 2084 Planarity : 0.005 0.058 2156 Dihedral : 7.774 72.528 2052 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.28 % Allowed : 17.34 % 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: 0.10 (0.22), residues: 1532 helix: 0.88 (0.18), residues: 956 sheet: -1.18 (0.40), residues: 124 loop : -1.19 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 399 TYR 0.009 0.001 TYR B 357 PHE 0.016 0.001 PHE D 365 TRP 0.006 0.001 TRP B 176 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13156) covalent geometry : angle 0.68006 / 0.30 (17796) hydrogen bonds : bond 0.03426 / 2.23 ( 668) hydrogen bonds : angle 3.87501 / 2.86 ( 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: 17 poor density : 165 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7519 (t70) cc_final: 0.7213 (t0) REVERT: A 388 ASP cc_start: 0.7391 (p0) cc_final: 0.6980 (p0) REVERT: A 397 PHE cc_start: 0.7050 (t80) cc_final: 0.6650 (t80) REVERT: B 210 MET cc_start: 0.6829 (mtt) cc_final: 0.6474 (mpp) REVERT: B 261 ASP cc_start: 0.7542 (t70) cc_final: 0.7208 (t0) REVERT: D 99 HIS cc_start: 0.5042 (m-70) cc_final: 0.4824 (m170) REVERT: D 210 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6577 (mpp) outliers start: 17 outliers final: 11 residues processed: 171 average time/residue: 0.1273 time to fit residues: 30.9473 Evaluate side-chains 159 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 289 MET 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.204652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.184972 restraints weight = 14769.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.179875 restraints weight = 20181.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.178049 restraints weight = 23204.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.177083 restraints weight = 20315.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.176129 restraints weight = 21053.344| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.006 0.051 13156 Z= 0.235 Angle : 0.753 8.653 17796 Z= 0.346 Chirality : 0.045 0.164 2084 Planarity : 0.005 0.054 2156 Dihedral : 8.684 68.922 2052 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.85 % Allowed : 17.04 % 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: -0.37 (0.22), residues: 1532 helix: 0.45 (0.17), residues: 980 sheet: -1.38 (0.39), residues: 124 loop : -1.30 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 399 TYR 0.016 0.001 TYR B 175 PHE 0.019 0.002 PHE D 397 TRP 0.006 0.001 TRP D 15 HIS 0.004 0.002 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (13156) covalent geometry : angle 0.75283 / 0.35 (17796) hydrogen bonds : bond 0.04499 / 2.96 ( 668) hydrogen bonds : angle 4.26750 / 3.11 ( 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 201 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.476 Fit side-chains REVERT: A 261 ASP cc_start: 0.7610 (t70) cc_final: 0.7204 (t0) REVERT: A 397 PHE cc_start: 0.7107 (t80) cc_final: 0.6877 (t80) REVERT: B 261 ASP cc_start: 0.7679 (t70) cc_final: 0.7264 (t0) REVERT: C 345 SER cc_start: 0.8396 (p) cc_final: 0.8123 (p) REVERT: D 210 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6629 (mpp) outliers start: 38 outliers final: 25 residues processed: 181 average time/residue: 0.1135 time to fit residues: 30.2186 Evaluate side-chains 174 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 321 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 206 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 381 VAL 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 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 321 ILE Chi-restraints excluded: chain D residue 381 VAL 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: 0.7980 chunk 81 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 150 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 138 optimal weight: 0.1980 chunk 140 optimal weight: 4.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.210396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.191375 restraints weight = 14546.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.187874 restraints weight = 21686.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.186027 restraints weight = 20819.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.185350 restraints weight = 18676.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.184002 restraints weight = 20003.323| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13156 Z= 0.115 Angle : 0.691 11.035 17796 Z= 0.307 Chirality : 0.041 0.157 2084 Planarity : 0.005 0.050 2156 Dihedral : 7.560 64.909 2052 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.20 % Allowed : 18.17 % 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: 0.16 (0.22), residues: 1532 helix: 0.90 (0.18), residues: 956 sheet: -1.10 (0.40), residues: 124 loop : -1.12 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.009 0.001 TYR B 357 PHE 0.016 0.001 PHE A 397 TRP 0.008 0.001 TRP A 15 HIS 0.002 0.000 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (13156) covalent geometry : angle 0.69104 / 0.31 (17796) hydrogen bonds : bond 0.03338 / 2.15 ( 668) hydrogen bonds : angle 3.84548 / 2.83 ( 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 174 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7537 (t70) cc_final: 0.7215 (t0) REVERT: A 397 PHE cc_start: 0.7167 (t80) cc_final: 0.6967 (t80) REVERT: B 261 ASP cc_start: 0.7539 (t70) cc_final: 0.7212 (t0) REVERT: B 310 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7297 (mt) REVERT: B 388 ASP cc_start: 0.7671 (p0) cc_final: 0.7456 (p0) REVERT: C 345 SER cc_start: 0.8258 (p) cc_final: 0.8011 (p) REVERT: C 354 LYS cc_start: 0.6294 (mmtm) cc_final: 0.6049 (mmtm) REVERT: D 210 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6604 (mpp) outliers start: 16 outliers final: 10 residues processed: 162 average time/residue: 0.1258 time to fit residues: 29.1689 Evaluate side-chains 163 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 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 310 ILE 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 338 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: 2.9990 chunk 146 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.206985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.187405 restraints weight = 14769.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.184015 restraints weight = 19875.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.181146 restraints weight = 20077.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.179938 restraints weight = 21393.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.178884 restraints weight = 22768.946| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13156 Z= 0.168 Angle : 0.711 9.451 17796 Z= 0.319 Chirality : 0.043 0.184 2084 Planarity : 0.005 0.054 2156 Dihedral : 7.895 62.254 2052 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.35 % Allowed : 18.92 % Favored : 79.73 % 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: 0.00 (0.22), residues: 1532 helix: 0.75 (0.18), residues: 956 sheet: -1.10 (0.40), residues: 124 loop : -1.13 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.013 0.001 TYR C 175 PHE 0.014 0.001 PHE A 397 TRP 0.007 0.001 TRP A 15 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (13156) covalent geometry : angle 0.71077 / 0.32 (17796) hydrogen bonds : bond 0.03915 / 2.56 ( 668) hydrogen bonds : angle 4.01240 / 2.93 ( 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 173 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7585 (t70) cc_final: 0.7236 (t0) REVERT: A 397 PHE cc_start: 0.7258 (t80) cc_final: 0.7024 (t80) REVERT: B 261 ASP cc_start: 0.7563 (t70) cc_final: 0.7212 (t0) REVERT: B 310 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7413 (mt) REVERT: C 345 SER cc_start: 0.8332 (p) cc_final: 0.8075 (p) REVERT: D 210 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6659 (mpp) outliers start: 18 outliers final: 16 residues processed: 163 average time/residue: 0.1313 time to fit residues: 30.2278 Evaluate side-chains 167 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 11 TYR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 310 ILE 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 179 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 321 ILE 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: 0.0370 chunk 140 optimal weight: 0.1980 chunk 110 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 0.0010 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 overall best weight: 0.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.211767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.193857 restraints weight = 14788.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.189470 restraints weight = 19475.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.188128 restraints weight = 23072.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.187600 restraints weight = 20908.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.186422 restraints weight = 18980.920| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13156 Z= 0.112 Angle : 0.692 10.188 17796 Z= 0.305 Chirality : 0.041 0.176 2084 Planarity : 0.005 0.045 2156 Dihedral : 7.145 58.958 2052 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.20 % Allowed : 19.29 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.22), residues: 1532 helix: 0.98 (0.18), residues: 956 sheet: -0.94 (0.42), residues: 124 loop : -1.03 (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 C 357 PHE 0.014 0.001 PHE A 397 TRP 0.008 0.001 TRP A 15 HIS 0.002 0.000 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (13156) covalent geometry : angle 0.69164 / 0.31 (17796) hydrogen bonds : bond 0.03135 / 2.01 ( 668) hydrogen bonds : angle 3.74006 / 2.76 ( 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 174 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7518 (t70) cc_final: 0.7213 (t0) REVERT: A 397 PHE cc_start: 0.7205 (t80) cc_final: 0.6982 (t80) REVERT: B 261 ASP cc_start: 0.7522 (t70) cc_final: 0.7240 (t0) REVERT: B 310 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7344 (mt) REVERT: C 89 LEU cc_start: 0.7093 (pp) cc_final: 0.6832 (pp) REVERT: C 345 SER cc_start: 0.8238 (p) cc_final: 0.7977 (p) REVERT: D 210 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6404 (mpp) REVERT: D 399 ARG cc_start: 0.6803 (mtm110) cc_final: 0.6572 (ttm-80) outliers start: 16 outliers final: 10 residues processed: 167 average time/residue: 0.1255 time to fit residues: 30.1695 Evaluate side-chains 164 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 310 ILE 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: 0.7980 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 53 optimal weight: 0.0270 chunk 147 optimal weight: 8.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.210203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.191977 restraints weight = 14729.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.188184 restraints weight = 21184.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.186808 restraints weight = 23951.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.185390 restraints weight = 22469.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.184704 restraints weight = 21710.777| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13156 Z= 0.124 Angle : 0.697 9.655 17796 Z= 0.309 Chirality : 0.042 0.169 2084 Planarity : 0.005 0.045 2156 Dihedral : 7.132 56.460 2052 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.98 % Allowed : 19.74 % Favored : 79.28 % 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: 0.29 (0.22), residues: 1532 helix: 0.97 (0.18), residues: 956 sheet: -0.98 (0.42), residues: 124 loop : -1.02 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 399 TYR 0.010 0.001 TYR C 175 PHE 0.014 0.001 PHE A 397 TRP 0.006 0.001 TRP A 15 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (13156) covalent geometry : angle 0.69738 / 0.31 (17796) hydrogen bonds : bond 0.03301 / 2.13 ( 668) hydrogen bonds : angle 3.77227 / 2.77 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.28 seconds wall clock time: 34 minutes 46.37 seconds (2086.37 seconds total)