Starting phenix.real_space_refine on Sat Sep 28 03:52:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/09_2024/7rys_24747.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/09_2024/7rys_24747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/09_2024/7rys_24747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/09_2024/7rys_24747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/09_2024/7rys_24747.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rys_24747/09_2024/7rys_24747.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12900 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 131 Unusual residues: {'PGW': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 56 Restraints were copied for chains: C, B, D Time building chain proxies: 6.80, per 1000 atoms: 0.53 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.38 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: 3.69 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2043 1.32 - 1.44: 3259 1.44 - 1.57: 7790 1.57 - 1.69: 16 1.69 - 1.81: 48 Bond restraints: 13156 Sorted by residual: bond pdb=" C10 PGW D 503 " pdb=" C9 PGW D 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" C10 PGW B 503 " pdb=" C9 PGW B 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C10 PGW A 503 " pdb=" C9 PGW A 503 " ideal model delta sigma weight residual 1.333 1.508 -0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" C10 PGW C 503 " pdb=" C9 PGW C 503 " ideal model delta sigma weight residual 1.333 1.508 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" C GLY B 332 " pdb=" N GLU B 333 " ideal model delta sigma weight residual 1.330 1.424 -0.094 1.38e-02 5.25e+03 4.61e+01 ... (remaining 13151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 17071 2.58 - 5.16: 578 5.16 - 7.73: 119 7.73 - 10.31: 20 10.31 - 12.89: 8 Bond angle restraints: 17796 Sorted by residual: angle pdb=" N TYR C 259 " pdb=" CA TYR C 259 " pdb=" C TYR C 259 " ideal model delta sigma weight residual 111.14 104.24 6.90 1.08e+00 8.57e-01 4.08e+01 angle pdb=" N TYR D 259 " pdb=" CA TYR D 259 " pdb=" C TYR D 259 " ideal model delta sigma weight residual 111.14 104.25 6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" N TYR A 259 " pdb=" CA TYR A 259 " pdb=" C TYR A 259 " ideal model delta sigma weight residual 111.14 104.26 6.88 1.08e+00 8.57e-01 4.06e+01 angle pdb=" N TYR B 259 " pdb=" CA TYR B 259 " pdb=" C TYR B 259 " ideal model delta sigma weight residual 111.14 104.30 6.84 1.08e+00 8.57e-01 4.01e+01 angle pdb=" N LEU A 98 " pdb=" CA LEU A 98 " pdb=" C LEU A 98 " ideal model delta sigma weight residual 113.19 106.71 6.48 1.19e+00 7.06e-01 2.97e+01 ... (remaining 17791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.90: 7800 34.90 - 69.79: 172 69.79 - 104.69: 8 104.69 - 139.58: 24 139.58 - 174.48: 8 Dihedral angle restraints: 8012 sinusoidal: 3444 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 8009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1443 0.048 - 0.096: 462 0.096 - 0.144: 107 0.144 - 0.192: 44 0.192 - 0.240: 28 Chirality restraints: 2084 Sorted by residual: chirality pdb=" CA LEU C 98 " pdb=" N LEU C 98 " pdb=" C LEU C 98 " pdb=" CB LEU C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU A 98 " pdb=" N LEU A 98 " pdb=" C LEU A 98 " pdb=" CB LEU A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LEU B 98 " pdb=" N LEU B 98 " pdb=" C LEU B 98 " pdb=" CB LEU B 98 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2081 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 503 " -0.067 2.00e-02 2.50e+03 6.68e-02 4.47e+01 pdb=" C10 PGW C 503 " 0.067 2.00e-02 2.50e+03 pdb=" C8 PGW C 503 " -0.067 2.00e-02 2.50e+03 pdb=" C9 PGW C 503 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " 0.067 2.00e-02 2.50e+03 6.68e-02 4.46e+01 pdb=" C10 PGW A 503 " -0.067 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " 0.067 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " -0.067 2.00e-02 2.50e+03 6.67e-02 4.45e+01 pdb=" C10 PGW B 503 " 0.067 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " -0.067 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " 0.066 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2428 2.78 - 3.31: 12335 3.31 - 3.84: 19546 3.84 - 4.37: 22523 4.37 - 4.90: 38964 Nonbonded interactions: 95796 Sorted by model distance: nonbonded pdb=" OE1 GLU B 308 " pdb=" OH TYR B 404 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU A 308 " pdb=" OH TYR A 404 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU C 308 " pdb=" OH TYR C 404 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU D 308 " pdb=" OH TYR D 404 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.254 3.040 ... (remaining 95791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.290 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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= 0.482 Angle : 1.122 12.890 17796 Z= 0.655 Chirality : 0.056 0.240 2084 Planarity : 0.008 0.067 2156 Dihedral : 18.240 174.480 5060 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP D 264 HIS 0.007 0.002 HIS D 232 PHE 0.030 0.003 PHE D 340 TYR 0.014 0.002 TYR A 259 ARG 0.010 0.001 ARG D 399 *********************** 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 fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 1.556 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: 0.2770 time to fit residues: 87.0359 Evaluate side-chains 167 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 77 optimal weight: 0.0670 chunk 61 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 138 optimal weight: 2.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 253 GLN B 131 ASN B 364 GLN C 131 ASN D 131 ASN D 253 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13156 Z= 0.178 Angle : 0.704 8.590 17796 Z= 0.333 Chirality : 0.042 0.177 2084 Planarity : 0.005 0.049 2156 Dihedral : 16.800 151.716 2112 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.45 % Allowed : 10.66 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1532 helix: 0.25 (0.18), residues: 944 sheet: -1.81 (0.35), residues: 132 loop : -1.40 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.005 0.001 HIS D 232 PHE 0.021 0.002 PHE D 365 TYR 0.013 0.001 TYR D 357 ARG 0.004 0.001 ARG D 136 *********************** 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 204 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 198 time to evaluate : 1.607 Fit side-chains REVERT: A 103 PRO cc_start: 0.6840 (Cg_endo) cc_final: 0.6638 (Cg_exo) REVERT: A 261 ASP cc_start: 0.7628 (t70) cc_final: 0.7260 (t0) REVERT: B 261 ASP cc_start: 0.7714 (t70) cc_final: 0.7338 (t0) REVERT: B 277 LYS cc_start: 0.7960 (mttm) cc_final: 0.7651 (pttt) REVERT: C 261 ASP cc_start: 0.7774 (t70) cc_final: 0.7458 (t0) REVERT: D 210 MET cc_start: 0.6612 (mpp) cc_final: 0.6084 (mpp) REVERT: D 342 ASN cc_start: 0.8568 (t0) cc_final: 0.8365 (t0) outliers start: 6 outliers final: 3 residues processed: 201 average time/residue: 0.2623 time to fit residues: 74.3243 Evaluate side-chains 164 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 HIS C 99 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13156 Z= 0.348 Angle : 0.733 8.058 17796 Z= 0.349 Chirality : 0.045 0.161 2084 Planarity : 0.005 0.050 2156 Dihedral : 15.688 133.012 2112 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.50 % Allowed : 14.04 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1532 helix: 0.02 (0.17), residues: 976 sheet: -1.97 (0.35), residues: 124 loop : -1.47 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 15 HIS 0.005 0.002 HIS C 149 PHE 0.017 0.002 PHE D 365 TYR 0.017 0.001 TYR D 175 ARG 0.006 0.001 ARG A 330 *********************** 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 194 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.447 Fit side-chains REVERT: A 261 ASP cc_start: 0.7661 (t70) cc_final: 0.7259 (t0) REVERT: A 277 LYS cc_start: 0.8216 (pttt) cc_final: 0.7265 (mttm) REVERT: B 261 ASP cc_start: 0.7743 (t70) cc_final: 0.7360 (t0) REVERT: C 261 ASP cc_start: 0.7758 (t70) cc_final: 0.7443 (t0) REVERT: D 206 LEU cc_start: 0.8355 (tp) cc_final: 0.8124 (tp) REVERT: D 397 PHE cc_start: 0.6989 (t80) cc_final: 0.6675 (t80) outliers start: 20 outliers final: 11 residues processed: 190 average time/residue: 0.2610 time to fit residues: 71.2357 Evaluate side-chains 167 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 210 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 0.0010 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN D 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13156 Z= 0.182 Angle : 0.663 7.963 17796 Z= 0.308 Chirality : 0.042 0.167 2084 Planarity : 0.005 0.055 2156 Dihedral : 13.674 133.769 2112 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.20 % Allowed : 17.04 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1532 helix: 0.40 (0.17), residues: 980 sheet: -1.85 (0.35), residues: 124 loop : -1.35 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 15 HIS 0.002 0.001 HIS C 232 PHE 0.019 0.001 PHE D 365 TYR 0.010 0.001 TYR B 357 ARG 0.005 0.000 ARG A 399 *********************** 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 184 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.468 Fit side-chains REVERT: A 261 ASP cc_start: 0.7686 (t70) cc_final: 0.7297 (t0) REVERT: A 397 PHE cc_start: 0.6876 (t80) cc_final: 0.6648 (t80) REVERT: B 261 ASP cc_start: 0.7712 (t70) cc_final: 0.7323 (t0) REVERT: C 261 ASP cc_start: 0.7705 (t70) cc_final: 0.7332 (t0) REVERT: D 397 PHE cc_start: 0.6977 (t80) cc_final: 0.6726 (t80) outliers start: 16 outliers final: 7 residues processed: 180 average time/residue: 0.2742 time to fit residues: 69.7315 Evaluate side-chains 158 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 89 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 109 optimal weight: 0.0470 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13156 Z= 0.194 Angle : 0.658 8.860 17796 Z= 0.306 Chirality : 0.041 0.150 2084 Planarity : 0.005 0.056 2156 Dihedral : 12.556 133.498 2112 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.20 % Allowed : 16.82 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1532 helix: 0.66 (0.18), residues: 956 sheet: -1.62 (0.36), residues: 124 loop : -1.28 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 15 HIS 0.002 0.001 HIS D 232 PHE 0.018 0.001 PHE D 365 TYR 0.010 0.001 TYR B 175 ARG 0.005 0.000 ARG B 399 *********************** 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 190 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.395 Fit side-chains REVERT: A 261 ASP cc_start: 0.7697 (t70) cc_final: 0.7329 (t0) REVERT: A 397 PHE cc_start: 0.6920 (t80) cc_final: 0.6687 (t80) REVERT: B 210 MET cc_start: 0.6659 (mtt) cc_final: 0.6054 (mpp) REVERT: B 261 ASP cc_start: 0.7748 (t70) cc_final: 0.7383 (t0) REVERT: C 261 ASP cc_start: 0.7723 (t70) cc_final: 0.7507 (t0) REVERT: D 210 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6124 (mpp) REVERT: D 397 PHE cc_start: 0.7036 (t80) cc_final: 0.6800 (t80) outliers start: 16 outliers final: 8 residues processed: 185 average time/residue: 0.2665 time to fit residues: 70.0767 Evaluate side-chains 160 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain C residue 89 LEU 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 210 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN D 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13156 Z= 0.206 Angle : 0.651 7.787 17796 Z= 0.304 Chirality : 0.042 0.150 2084 Planarity : 0.005 0.059 2156 Dihedral : 11.737 133.411 2112 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.58 % Allowed : 17.94 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1532 helix: 0.73 (0.18), residues: 956 sheet: -1.29 (0.39), residues: 124 loop : -1.26 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 15 HIS 0.002 0.001 HIS B 232 PHE 0.016 0.001 PHE D 365 TYR 0.011 0.001 TYR C 175 ARG 0.005 0.000 ARG B 399 *********************** 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 188 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7699 (t70) cc_final: 0.7328 (t0) REVERT: B 261 ASP cc_start: 0.7711 (t70) cc_final: 0.7346 (t0) REVERT: C 261 ASP cc_start: 0.7728 (t70) cc_final: 0.7495 (t0) REVERT: D 210 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6122 (mpp) REVERT: D 397 PHE cc_start: 0.7201 (t80) cc_final: 0.6969 (t80) outliers start: 21 outliers final: 12 residues processed: 178 average time/residue: 0.2529 time to fit residues: 64.6945 Evaluate side-chains 171 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 140 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13156 Z= 0.172 Angle : 0.649 8.770 17796 Z= 0.300 Chirality : 0.041 0.149 2084 Planarity : 0.005 0.063 2156 Dihedral : 11.185 133.371 2112 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.35 % Allowed : 19.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1532 helix: 0.87 (0.18), residues: 956 sheet: -1.12 (0.40), residues: 124 loop : -1.14 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.002 0.001 HIS D 232 PHE 0.017 0.001 PHE A 397 TYR 0.009 0.001 TYR D 357 ARG 0.007 0.000 ARG A 399 *********************** 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 188 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.505 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7671 (t70) cc_final: 0.7336 (t0) REVERT: A 397 PHE cc_start: 0.7019 (t80) cc_final: 0.6692 (t80) REVERT: B 261 ASP cc_start: 0.7699 (t70) cc_final: 0.7383 (t0) REVERT: C 261 ASP cc_start: 0.7783 (t70) cc_final: 0.7438 (t0) REVERT: D 210 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6253 (mpp) outliers start: 18 outliers final: 12 residues processed: 180 average time/residue: 0.2792 time to fit residues: 70.8803 Evaluate side-chains 159 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 381 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 251 GLU 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 210 MET Chi-restraints excluded: chain D residue 338 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 58 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 133 optimal weight: 0.0370 chunk 140 optimal weight: 6.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13156 Z= 0.192 Angle : 0.652 7.979 17796 Z= 0.302 Chirality : 0.041 0.156 2084 Planarity : 0.005 0.057 2156 Dihedral : 11.074 133.634 2112 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.35 % Allowed : 19.74 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1532 helix: 0.88 (0.18), residues: 956 sheet: -1.06 (0.41), residues: 124 loop : -1.10 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 15 HIS 0.002 0.001 HIS D 232 PHE 0.017 0.001 PHE D 397 TYR 0.010 0.001 TYR A 175 ARG 0.008 0.000 ARG A 399 *********************** 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 182 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7663 (t70) cc_final: 0.7318 (t0) REVERT: A 397 PHE cc_start: 0.6992 (t80) cc_final: 0.6679 (t80) REVERT: B 261 ASP cc_start: 0.7671 (t70) cc_final: 0.7334 (t0) REVERT: C 261 ASP cc_start: 0.7781 (t70) cc_final: 0.7439 (t0) REVERT: D 210 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6031 (mpp) outliers start: 18 outliers final: 16 residues processed: 172 average time/residue: 0.2563 time to fit residues: 63.4443 Evaluate side-chains 167 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 213 LEU 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 381 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 210 MET 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 128 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13156 Z= 0.244 Angle : 0.676 7.920 17796 Z= 0.317 Chirality : 0.043 0.178 2084 Planarity : 0.005 0.056 2156 Dihedral : 11.197 133.295 2112 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.10 % Allowed : 19.14 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1532 helix: 0.78 (0.18), residues: 956 sheet: -1.08 (0.41), residues: 124 loop : -1.14 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.002 0.001 HIS D 232 PHE 0.025 0.001 PHE D 397 TYR 0.012 0.001 TYR C 175 ARG 0.008 0.000 ARG A 399 *********************** 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 188 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7676 (t70) cc_final: 0.7315 (t0) REVERT: A 308 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: A 397 PHE cc_start: 0.7030 (t80) cc_final: 0.6778 (t80) REVERT: B 261 ASP cc_start: 0.7668 (t70) cc_final: 0.7312 (t0) REVERT: B 310 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7440 (mt) REVERT: C 261 ASP cc_start: 0.7765 (t70) cc_final: 0.7396 (t0) REVERT: D 210 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6021 (mpp) outliers start: 28 outliers final: 19 residues processed: 173 average time/residue: 0.2711 time to fit residues: 66.9324 Evaluate side-chains 176 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 308 GLU 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 310 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 100 optimal weight: 0.0020 chunk 151 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13156 Z= 0.190 Angle : 0.665 8.465 17796 Z= 0.307 Chirality : 0.042 0.165 2084 Planarity : 0.005 0.066 2156 Dihedral : 11.020 133.433 2112 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.65 % Allowed : 19.29 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1532 helix: 0.89 (0.18), residues: 956 sheet: -1.04 (0.42), residues: 124 loop : -1.12 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 15 HIS 0.002 0.001 HIS B 232 PHE 0.014 0.001 PHE D 365 TYR 0.010 0.001 TYR B 175 ARG 0.009 0.000 ARG A 399 ********************** 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 178 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.5944 (mtm) REVERT: A 261 ASP cc_start: 0.7646 (t70) cc_final: 0.7315 (t0) REVERT: A 308 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: A 397 PHE cc_start: 0.6948 (t80) cc_final: 0.6679 (t80) REVERT: B 261 ASP cc_start: 0.7636 (t70) cc_final: 0.7325 (t0) REVERT: B 310 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7407 (mt) REVERT: C 210 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.5983 (mtm) REVERT: C 261 ASP cc_start: 0.7713 (t70) cc_final: 0.7405 (t0) REVERT: C 345 SER cc_start: 0.8335 (p) cc_final: 0.8112 (p) REVERT: D 210 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6090 (mpp) REVERT: D 399 ARG cc_start: 0.6980 (mtm110) cc_final: 0.6772 (ttm-80) outliers start: 22 outliers final: 13 residues processed: 164 average time/residue: 0.2573 time to fit residues: 60.0003 Evaluate side-chains 170 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 308 GLU 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 B residue 381 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 210 MET 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 36 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 106 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.210412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.190550 restraints weight = 14498.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.187646 restraints weight = 20550.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.185655 restraints weight = 22784.654| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13156 Z= 0.182 Angle : 0.656 7.931 17796 Z= 0.302 Chirality : 0.041 0.167 2084 Planarity : 0.005 0.063 2156 Dihedral : 10.926 133.415 2112 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.58 % Allowed : 19.29 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1532 helix: 0.94 (0.18), residues: 956 sheet: -0.97 (0.42), residues: 124 loop : -1.08 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 15 HIS 0.002 0.001 HIS B 232 PHE 0.015 0.001 PHE D 397 TYR 0.009 0.001 TYR C 175 ARG 0.009 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2263.43 seconds wall clock time: 41 minutes 49.53 seconds (2509.53 seconds total)