Starting phenix.real_space_refine on Sun Aug 24 08:02:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryr_24746/08_2025/7ryr_24746.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryr_24746/08_2025/7ryr_24746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ryr_24746/08_2025/7ryr_24746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryr_24746/08_2025/7ryr_24746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ryr_24746/08_2025/7ryr_24746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryr_24746/08_2025/7ryr_24746.map" } resolution = 3.6 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 8636 2.51 5 N 2080 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13024 Number of models: 1 Model: "" Number of chains: 8 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: "C" 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: "D" 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: "B" 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: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 263 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: 60 Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 263 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: 60 Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 3.34, per 1000 atoms: 0.26 Number of scatterers: 13024 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 2272 8.00 N 2080 7.00 C 8636 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: 1.15 Conformation dependent library (CDL) restraints added in 585.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 76 helices and 8 sheets defined 64.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 removed outlier: 3.895A pdb=" N VAL A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.690A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 4.028A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 113 removed outlier: 4.022A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 131 through 159 removed outlier: 3.637A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 208 removed outlier: 3.687A pdb=" N ALA A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.569A pdb=" N GLU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.951A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 4.192A pdb=" N GLU A 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.569A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 404 through 418 Processing helix chain 'C' and resid 11 through 36 removed outlier: 3.895A pdb=" N VAL C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 55 removed outlier: 3.690A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 4.028A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 113 removed outlier: 4.022A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 131 through 159 removed outlier: 3.637A pdb=" N LEU C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 208 removed outlier: 3.687A pdb=" N ALA C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 224 Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.569A pdb=" N GLU C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 removed outlier: 3.951A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 4.191A pdb=" N GLU C 278 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.570A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'C' and resid 404 through 418 Processing helix chain 'D' and resid 11 through 36 removed outlier: 3.895A pdb=" N VAL D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 55 removed outlier: 3.690A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 4.028A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 113 removed outlier: 4.022A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 131 through 159 removed outlier: 3.638A pdb=" N LEU D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D 159 " --> pdb=" O TRP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.687A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.569A pdb=" N GLU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.951A pdb=" N ARG D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 removed outlier: 4.192A pdb=" N GLU D 278 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.570A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 404 through 418 Processing helix chain 'B' and resid 11 through 36 removed outlier: 3.896A pdb=" N VAL B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 55 removed outlier: 3.689A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 4.028A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 113 removed outlier: 4.022A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 131 through 159 removed outlier: 3.637A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 159 " --> pdb=" O TRP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.688A pdb=" N ALA B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 226 through 246 removed outlier: 3.569A pdb=" N GLU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 removed outlier: 3.951A pdb=" N ARG B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 4.192A pdb=" N GLU B 278 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.569A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 404 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.860A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.491A pdb=" N VAL A 381 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 318 through 322 removed outlier: 6.860A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.491A pdb=" N VAL C 381 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.860A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.492A pdb=" N VAL D 381 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.860A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.492A pdb=" N VAL B 381 " --> pdb=" O ILE B 328 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.51 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: 2014 1.32 - 1.44: 3298 1.44 - 1.56: 7900 1.56 - 1.68: 20 1.68 - 1.81: 48 Bond restraints: 13280 Sorted by residual: 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 7.74e+01 bond pdb=" C10 PGW C 503 " pdb=" C9 PGW C 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 1.509 -0.176 2.00e-02 2.50e+03 7.71e+01 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 7.71e+01 bond pdb=" CA SER C 157 " pdb=" CB SER C 157 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.64e-02 3.72e+03 1.29e+01 ... (remaining 13275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 17187 2.61 - 5.21: 628 5.21 - 7.82: 98 7.82 - 10.42: 15 10.42 - 13.03: 8 Bond angle restraints: 17936 Sorted by residual: angle pdb=" N LEU D 91 " pdb=" CA LEU D 91 " pdb=" C LEU D 91 " ideal model delta sigma weight residual 111.82 104.65 7.17 1.16e+00 7.43e-01 3.83e+01 angle pdb=" N LEU B 91 " pdb=" CA LEU B 91 " pdb=" C LEU B 91 " ideal model delta sigma weight residual 111.82 104.65 7.17 1.16e+00 7.43e-01 3.82e+01 angle pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 111.82 104.67 7.15 1.16e+00 7.43e-01 3.80e+01 angle pdb=" N LEU C 91 " pdb=" CA LEU C 91 " pdb=" C LEU C 91 " ideal model delta sigma weight residual 111.82 104.70 7.12 1.16e+00 7.43e-01 3.77e+01 angle pdb=" CA ASP C 92 " pdb=" C ASP C 92 " pdb=" O ASP C 92 " ideal model delta sigma weight residual 121.56 115.40 6.16 1.09e+00 8.42e-01 3.19e+01 ... (remaining 17931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 7872 35.02 - 70.04: 192 70.04 - 105.06: 20 105.06 - 140.08: 32 140.08 - 175.10: 12 Dihedral angle restraints: 8128 sinusoidal: 3560 harmonic: 4568 Sorted by residual: dihedral pdb=" C01 PGW C 502 " pdb=" C19 PGW C 502 " pdb=" O03 PGW C 502 " pdb=" O04 PGW C 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.10 175.10 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C01 PGW A 502 " pdb=" C19 PGW A 502 " pdb=" O03 PGW A 502 " pdb=" O04 PGW A 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.08 175.08 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C01 PGW D 502 " pdb=" C19 PGW D 502 " pdb=" O03 PGW D 502 " pdb=" O04 PGW D 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.06 175.06 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1857 0.087 - 0.175: 195 0.175 - 0.262: 32 0.262 - 0.350: 4 0.350 - 0.437: 4 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA LYS D 246 " pdb=" N LYS D 246 " pdb=" C LYS D 246 " pdb=" CB LYS D 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA LYS A 246 " pdb=" N LYS A 246 " pdb=" C LYS A 246 " pdb=" CB LYS A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA LYS B 246 " pdb=" N LYS B 246 " pdb=" C LYS B 246 " pdb=" CB LYS B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 2089 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " 0.091 2.00e-02 2.50e+03 9.04e-02 8.17e+01 pdb=" C10 PGW B 503 " -0.091 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " 0.090 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 503 " -0.090 2.00e-02 2.50e+03 9.03e-02 8.16e+01 pdb=" C10 PGW D 503 " 0.091 2.00e-02 2.50e+03 pdb=" C8 PGW D 503 " -0.090 2.00e-02 2.50e+03 pdb=" C9 PGW D 503 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " -0.090 2.00e-02 2.50e+03 9.03e-02 8.16e+01 pdb=" C10 PGW A 503 " 0.091 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " -0.090 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " 0.090 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 847 2.74 - 3.28: 12793 3.28 - 3.82: 19621 3.82 - 4.36: 23486 4.36 - 4.90: 40988 Nonbonded interactions: 97735 Sorted by model distance: nonbonded pdb=" OE1 GLU D 308 " pdb=" OH TYR D 404 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU A 308 " pdb=" OH TYR A 404 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU C 308 " pdb=" OH TYR C 404 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLU B 308 " pdb=" OH TYR B 404 " model vdw 2.198 3.040 nonbonded pdb=" O GLN D 119 " pdb=" OG1 THR D 123 " model vdw 2.245 3.040 ... (remaining 97730 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'B' } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.110 Find NCS groups from input model: 0.100 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 13280 Z= 0.438 Angle : 1.128 13.029 17936 Z= 0.651 Chirality : 0.059 0.437 2092 Planarity : 0.008 0.090 2168 Dihedral : 19.137 175.101 5176 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.60 % Allowed : 1.50 % Favored : 97.90 % Cbeta Deviations : 0.27 % 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 aren not related in a simple way. whole: -1.65 (0.22), residues: 1532 helix: -0.52 (0.17), residues: 988 sheet: -1.63 (0.47), residues: 132 loop : -1.98 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 273 TYR 0.023 0.001 TYR A 26 PHE 0.019 0.002 PHE C 365 TRP 0.007 0.001 TRP B 264 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00732 (13280) covalent geometry : angle 1.12829 (17936) hydrogen bonds : bond 0.20473 ( 672) hydrogen bonds : angle 7.21285 ( 1944) *********************** 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 243 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 235 time to evaluate : 0.487 Fit side-chains REVERT: A 334 MET cc_start: 0.5592 (tmm) cc_final: 0.5243 (tmm) REVERT: C 110 VAL cc_start: 0.8653 (m) cc_final: 0.8427 (p) REVERT: C 289 MET cc_start: 0.8365 (mmm) cc_final: 0.8142 (mmm) REVERT: D 110 VAL cc_start: 0.8688 (m) cc_final: 0.8440 (p) REVERT: D 289 MET cc_start: 0.8328 (mmm) cc_final: 0.8117 (mmm) outliers start: 8 outliers final: 4 residues processed: 243 average time/residue: 0.0938 time to fit residues: 36.1677 Evaluate side-chains 191 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain B residue 92 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN C 196 GLN D 159 GLN D 196 GLN B 410 GLN B 412 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123758 restraints weight = 17467.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114023 restraints weight = 24029.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113401 restraints weight = 22388.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113445 restraints weight = 20871.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113563 restraints weight = 20618.085| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13280 Z= 0.153 Angle : 0.697 12.299 17936 Z= 0.336 Chirality : 0.042 0.155 2092 Planarity : 0.006 0.062 2168 Dihedral : 17.936 138.758 2236 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.08 % Allowed : 7.73 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.22), residues: 1532 helix: 0.01 (0.17), residues: 984 sheet: -1.67 (0.46), residues: 124 loop : -1.72 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 169 TYR 0.015 0.001 TYR A 25 PHE 0.028 0.001 PHE B 40 TRP 0.005 0.001 TRP D 155 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00327 (13280) covalent geometry : angle 0.69734 (17936) hydrogen bonds : bond 0.04346 ( 672) hydrogen bonds : angle 4.42516 ( 1944) *********************** 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 244 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.550 Fit side-chains REVERT: A 221 LEU cc_start: 0.7973 (mp) cc_final: 0.7721 (mp) REVERT: A 289 MET cc_start: 0.8124 (mmm) cc_final: 0.7921 (mmm) REVERT: A 290 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: D 289 MET cc_start: 0.8304 (mmm) cc_final: 0.8088 (mmm) outliers start: 41 outliers final: 25 residues processed: 227 average time/residue: 0.0927 time to fit residues: 33.4568 Evaluate side-chains 198 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 89 optimal weight: 0.0770 chunk 129 optimal weight: 0.4980 chunk 149 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.160017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124480 restraints weight = 17636.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113528 restraints weight = 22747.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112942 restraints weight = 20863.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112918 restraints weight = 18677.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113195 restraints weight = 16927.349| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13280 Z= 0.127 Angle : 0.658 11.841 17936 Z= 0.313 Chirality : 0.041 0.147 2092 Planarity : 0.005 0.065 2168 Dihedral : 15.565 134.042 2232 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.68 % Allowed : 11.56 % 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 aren not related in a simple way. whole: -0.47 (0.23), residues: 1532 helix: 0.43 (0.18), residues: 984 sheet: -1.79 (0.45), residues: 124 loop : -1.40 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 417 TYR 0.011 0.001 TYR D 25 PHE 0.029 0.001 PHE B 40 TRP 0.004 0.001 TRP A 264 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00268 (13280) covalent geometry : angle 0.65836 (17936) hydrogen bonds : bond 0.03473 ( 672) hydrogen bonds : angle 3.92498 ( 1944) *********************** 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 246 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.507 Fit side-chains REVERT: A 290 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: A 389 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8332 (pp) REVERT: C 290 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: C 389 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8479 (pp) REVERT: D 206 LEU cc_start: 0.8339 (pp) cc_final: 0.8086 (mt) REVERT: D 290 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: D 389 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8433 (pp) REVERT: B 290 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: B 389 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8318 (pp) outliers start: 49 outliers final: 28 residues processed: 231 average time/residue: 0.0892 time to fit residues: 33.4273 Evaluate side-chains 217 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.157213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121376 restraints weight = 17418.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112870 restraints weight = 22502.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112019 restraints weight = 20966.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111656 restraints weight = 19395.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111224 restraints weight = 19478.356| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13280 Z= 0.144 Angle : 0.665 11.756 17936 Z= 0.312 Chirality : 0.042 0.138 2092 Planarity : 0.005 0.058 2168 Dihedral : 14.366 134.587 2228 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.13 % Allowed : 14.19 % Favored : 81.68 % 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 aren not related in a simple way. whole: -0.46 (0.23), residues: 1532 helix: 0.44 (0.18), residues: 1020 sheet: -1.78 (0.45), residues: 124 loop : -1.57 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 417 TYR 0.011 0.001 TYR A 175 PHE 0.021 0.001 PHE C 40 TRP 0.006 0.001 TRP D 155 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00330 (13280) covalent geometry : angle 0.66500 (17936) hydrogen bonds : bond 0.03780 ( 672) hydrogen bonds : angle 3.86448 ( 1944) *********************** 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 246 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.494 Fit side-chains REVERT: A 119 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.5942 (pm20) REVERT: A 290 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: A 389 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8418 (pp) REVERT: C 119 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.5966 (pm20) REVERT: C 290 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: C 389 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8470 (pp) REVERT: D 119 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.5836 (pm20) REVERT: D 290 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: D 389 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8446 (pp) REVERT: B 119 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.5708 (pm20) REVERT: B 389 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8405 (pp) outliers start: 55 outliers final: 29 residues processed: 229 average time/residue: 0.0936 time to fit residues: 33.9835 Evaluate side-chains 208 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.0030 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 410 GLN B 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.159211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122338 restraints weight = 17526.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111275 restraints weight = 21105.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110379 restraints weight = 20722.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110094 restraints weight = 18820.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110551 restraints weight = 16082.364| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13280 Z= 0.119 Angle : 0.648 11.558 17936 Z= 0.300 Chirality : 0.040 0.142 2092 Planarity : 0.005 0.058 2168 Dihedral : 13.388 133.956 2228 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.13 % Allowed : 16.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.23), residues: 1532 helix: 0.63 (0.18), residues: 1024 sheet: -1.62 (0.45), residues: 124 loop : -1.48 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 417 TYR 0.007 0.001 TYR A 175 PHE 0.020 0.001 PHE A 40 TRP 0.004 0.001 TRP D 176 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00253 (13280) covalent geometry : angle 0.64842 (17936) hydrogen bonds : bond 0.03095 ( 672) hydrogen bonds : angle 3.71457 ( 1944) *********************** 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 231 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.508 Fit side-chains REVERT: A 164 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8752 (t0) REVERT: A 290 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: A 389 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8394 (pp) REVERT: C 290 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: C 389 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8541 (pp) REVERT: D 119 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.5783 (pm20) REVERT: D 290 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: D 389 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8519 (pp) REVERT: B 290 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: B 389 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8392 (pp) outliers start: 55 outliers final: 32 residues processed: 216 average time/residue: 0.0878 time to fit residues: 30.6549 Evaluate side-chains 210 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.158339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120936 restraints weight = 17402.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111140 restraints weight = 22102.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109946 restraints weight = 21160.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110302 restraints weight = 17908.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110451 restraints weight = 16577.440| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13280 Z= 0.126 Angle : 0.649 11.741 17936 Z= 0.299 Chirality : 0.041 0.142 2092 Planarity : 0.005 0.057 2168 Dihedral : 12.783 134.186 2228 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.80 % Allowed : 16.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.23), residues: 1532 helix: 0.77 (0.18), residues: 1028 sheet: -1.59 (0.44), residues: 128 loop : -1.40 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.009 0.001 TYR A 175 PHE 0.025 0.001 PHE B 40 TRP 0.005 0.001 TRP A 155 HIS 0.002 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00278 (13280) covalent geometry : angle 0.64929 (17936) hydrogen bonds : bond 0.03281 ( 672) hydrogen bonds : angle 3.69535 ( 1944) *********************** 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 244 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 0.531 Fit side-chains REVERT: A 119 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.5966 (pm20) REVERT: A 164 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8742 (t0) REVERT: A 289 MET cc_start: 0.8301 (mmm) cc_final: 0.8099 (mmm) REVERT: A 290 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: A 389 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8445 (pp) REVERT: C 119 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.5622 (pm20) REVERT: C 164 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8703 (t0) REVERT: C 290 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: C 389 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8505 (pp) REVERT: D 290 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: D 389 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8480 (pp) REVERT: B 119 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.5726 (pm20) REVERT: B 290 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 389 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8440 (pp) REVERT: B 410 GLN cc_start: 0.8476 (tp40) cc_final: 0.8220 (tp-100) outliers start: 64 outliers final: 33 residues processed: 225 average time/residue: 0.0851 time to fit residues: 31.5459 Evaluate side-chains 215 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 3.9990 chunk 143 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.158345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121812 restraints weight = 17498.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110908 restraints weight = 22262.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110478 restraints weight = 20990.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110436 restraints weight = 17254.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110704 restraints weight = 15655.203| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13280 Z= 0.124 Angle : 0.663 12.288 17936 Z= 0.300 Chirality : 0.041 0.133 2092 Planarity : 0.005 0.060 2168 Dihedral : 12.373 134.019 2228 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.43 % Allowed : 17.57 % Favored : 78.00 % 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 aren not related in a simple way. whole: 0.22 (0.23), residues: 1532 helix: 1.06 (0.18), residues: 984 sheet: -1.48 (0.45), residues: 128 loop : -1.40 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.009 0.001 TYR B 404 PHE 0.017 0.001 PHE A 40 TRP 0.003 0.001 TRP C 176 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00272 (13280) covalent geometry : angle 0.66267 (17936) hydrogen bonds : bond 0.03150 ( 672) hydrogen bonds : angle 3.69491 ( 1944) *********************** 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 235 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.504 Fit side-chains REVERT: A 119 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.5758 (pm20) REVERT: A 164 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8710 (t0) REVERT: A 290 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: A 389 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8440 (pp) REVERT: C 119 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.5614 (pm20) REVERT: C 164 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8687 (t0) REVERT: C 290 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: C 389 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8544 (pp) REVERT: D 119 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.5909 (pm20) REVERT: D 164 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8684 (t0) REVERT: D 290 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: D 389 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 119 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.5903 (pm20) REVERT: B 290 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: B 389 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8468 (pp) REVERT: B 410 GLN cc_start: 0.8489 (tp40) cc_final: 0.8195 (tp-100) outliers start: 59 outliers final: 35 residues processed: 217 average time/residue: 0.0858 time to fit residues: 30.1740 Evaluate side-chains 214 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 97 optimal weight: 0.0770 chunk 103 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 83 optimal weight: 0.0570 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.160192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124108 restraints weight = 17273.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112271 restraints weight = 21115.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111595 restraints weight = 22237.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111734 restraints weight = 19163.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111902 restraints weight = 17384.538| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13280 Z= 0.112 Angle : 0.661 11.915 17936 Z= 0.297 Chirality : 0.040 0.133 2092 Planarity : 0.005 0.062 2168 Dihedral : 11.979 133.830 2228 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.20 % Allowed : 18.09 % Favored : 77.70 % 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 aren not related in a simple way. whole: 0.44 (0.24), residues: 1532 helix: 1.22 (0.18), residues: 984 sheet: -1.23 (0.46), residues: 124 loop : -1.35 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 417 TYR 0.008 0.001 TYR D 390 PHE 0.021 0.001 PHE C 365 TRP 0.004 0.001 TRP A 176 HIS 0.002 0.000 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00229 (13280) covalent geometry : angle 0.66112 (17936) hydrogen bonds : bond 0.02729 ( 672) hydrogen bonds : angle 3.59658 ( 1944) *********************** 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 234 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.500 Fit side-chains REVERT: A 119 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.5770 (pm20) REVERT: A 164 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8693 (t0) REVERT: A 290 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 334 MET cc_start: 0.6269 (tmm) cc_final: 0.6065 (tmm) REVERT: A 389 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 119 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.5809 (pm20) REVERT: C 164 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8660 (t0) REVERT: C 290 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: C 389 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8489 (pp) REVERT: D 164 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8677 (t0) REVERT: D 290 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: D 389 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8434 (pp) REVERT: D 417 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8150 (ttp80) REVERT: B 119 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.5893 (pm20) REVERT: B 290 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: B 389 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 410 GLN cc_start: 0.8516 (tp40) cc_final: 0.8217 (tp-100) outliers start: 56 outliers final: 34 residues processed: 218 average time/residue: 0.0886 time to fit residues: 31.2534 Evaluate side-chains 215 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 119 optimal weight: 0.0370 chunk 29 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.158360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121234 restraints weight = 17536.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109980 restraints weight = 23305.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109300 restraints weight = 20793.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108921 restraints weight = 21712.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109273 restraints weight = 19044.800| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13280 Z= 0.124 Angle : 0.665 12.594 17936 Z= 0.302 Chirality : 0.041 0.130 2092 Planarity : 0.005 0.062 2168 Dihedral : 11.910 134.072 2228 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.83 % Allowed : 18.17 % Favored : 78.00 % 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 aren not related in a simple way. whole: 0.45 (0.24), residues: 1532 helix: 1.23 (0.18), residues: 984 sheet: -1.21 (0.46), residues: 124 loop : -1.35 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 417 TYR 0.010 0.001 TYR A 404 PHE 0.021 0.001 PHE C 365 TRP 0.004 0.001 TRP A 155 HIS 0.002 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00274 (13280) covalent geometry : angle 0.66510 (17936) hydrogen bonds : bond 0.03079 ( 672) hydrogen bonds : angle 3.64934 ( 1944) *********************** 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 215 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.507 Fit side-chains REVERT: A 119 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.5607 (pm20) REVERT: A 290 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 389 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8395 (pp) REVERT: C 119 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.5676 (pm20) REVERT: C 290 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: C 389 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8488 (pp) REVERT: D 119 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6012 (pm20) REVERT: D 290 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: D 389 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8445 (pp) REVERT: D 417 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8205 (ttp80) REVERT: B 119 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.5929 (pm20) REVERT: B 290 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 389 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8495 (pp) REVERT: B 410 GLN cc_start: 0.8597 (tp40) cc_final: 0.8308 (tp-100) outliers start: 51 outliers final: 36 residues processed: 199 average time/residue: 0.0900 time to fit residues: 29.0284 Evaluate side-chains 207 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 50 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 32 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.159802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123472 restraints weight = 17519.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111337 restraints weight = 22001.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110796 restraints weight = 21949.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110863 restraints weight = 19923.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111128 restraints weight = 17670.151| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13280 Z= 0.116 Angle : 0.669 12.623 17936 Z= 0.303 Chirality : 0.040 0.140 2092 Planarity : 0.005 0.064 2168 Dihedral : 11.619 133.750 2228 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.60 % Allowed : 18.39 % Favored : 78.00 % 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 aren not related in a simple way. whole: 0.56 (0.24), residues: 1532 helix: 1.30 (0.18), residues: 984 sheet: -1.17 (0.47), residues: 124 loop : -1.29 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 417 TYR 0.008 0.001 TYR D 390 PHE 0.020 0.001 PHE B 365 TRP 0.004 0.001 TRP A 176 HIS 0.001 0.000 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00243 (13280) covalent geometry : angle 0.66910 (17936) hydrogen bonds : bond 0.02724 ( 672) hydrogen bonds : angle 3.59176 ( 1944) ********************** 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 213 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.562 Fit side-chains REVERT: A 119 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.5672 (pm20) REVERT: A 290 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 389 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 119 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.5907 (pm20) REVERT: C 290 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: C 389 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8387 (pp) REVERT: D 389 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8443 (pp) REVERT: D 417 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8217 (ttp80) REVERT: B 119 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.5885 (pm20) REVERT: B 290 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: B 389 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8427 (pp) REVERT: B 410 GLN cc_start: 0.8568 (tp40) cc_final: 0.8276 (tp-100) outliers start: 48 outliers final: 35 residues processed: 198 average time/residue: 0.0861 time to fit residues: 28.0469 Evaluate side-chains 209 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 28 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.159458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124518 restraints weight = 17402.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114122 restraints weight = 24049.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111589 restraints weight = 25608.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111989 restraints weight = 24240.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112430 restraints weight = 19090.292| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13280 Z= 0.117 Angle : 0.667 12.523 17936 Z= 0.302 Chirality : 0.040 0.141 2092 Planarity : 0.005 0.064 2168 Dihedral : 11.465 133.841 2228 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.60 % Allowed : 18.17 % Favored : 78.23 % 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 aren not related in a simple way. whole: 0.60 (0.24), residues: 1532 helix: 1.35 (0.18), residues: 984 sheet: -1.16 (0.47), residues: 124 loop : -1.33 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 417 TYR 0.011 0.001 TYR A 404 PHE 0.021 0.001 PHE C 365 TRP 0.004 0.001 TRP B 15 HIS 0.001 0.000 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00250 (13280) covalent geometry : angle 0.66673 (17936) hydrogen bonds : bond 0.02824 ( 672) hydrogen bonds : angle 3.60669 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2344.00 seconds wall clock time: 41 minutes 20.70 seconds (2480.70 seconds total)