Starting phenix.real_space_refine on Sun Aug 24 22:29:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5h1q_9570/08_2025/5h1q_9570.cif Found real_map, /net/cci-nas-00/data/ceres_data/5h1q_9570/08_2025/5h1q_9570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5h1q_9570/08_2025/5h1q_9570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5h1q_9570/08_2025/5h1q_9570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5h1q_9570/08_2025/5h1q_9570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5h1q_9570/08_2025/5h1q_9570.map" } resolution = 3.3 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 15648 2.51 5 N 3904 2.21 5 O 4136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s 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: 23784 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2973 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 2.50, per 1000 atoms: 0.11 Number of scatterers: 23784 At special positions: 0 Unit cell: (126.69, 126.69, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4136 8.00 N 3904 7.00 C 15648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 742.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5584 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 16 sheets defined 62.1% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 3.803A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.611A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.705A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 178 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 213 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE A 226 " --> pdb=" O TRP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 305 removed outlier: 4.136A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.533A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 3.803A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.612A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 151 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Proline residue: B 169 - end of helix removed outlier: 3.706A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 178 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 213 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE B 226 " --> pdb=" O TRP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.532A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.466A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 3.803A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.612A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.705A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 178 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 213 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.705A pdb=" N ILE C 226 " --> pdb=" O TRP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 305 removed outlier: 4.134A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.543A pdb=" N ILE C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.533A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 3.804A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.612A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Proline residue: D 169 - end of helix removed outlier: 3.705A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 178 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 213 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.705A pdb=" N ILE D 226 " --> pdb=" O TRP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 305 removed outlier: 4.134A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP D 281 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.514A pdb=" N PHE D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE D 341 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.532A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.466A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS E 79 " --> pdb=" O TYR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 3.804A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix Processing helix chain 'E' and resid 136 through 151 removed outlier: 3.611A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Proline residue: E 169 - end of helix removed outlier: 3.706A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E 178 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 213 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE E 226 " --> pdb=" O TRP E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.543A pdb=" N ILE E 341 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.533A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL F 37 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS F 79 " --> pdb=" O TYR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 3.804A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix Processing helix chain 'F' and resid 136 through 151 removed outlier: 3.611A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 151 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 182 removed outlier: 3.522A pdb=" N PHE F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Proline residue: F 169 - end of helix removed outlier: 3.705A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG F 178 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 213 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE F 226 " --> pdb=" O TRP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 275 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS F 295 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 327 through 335 removed outlier: 3.514A pdb=" N PHE F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.545A pdb=" N ILE F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.533A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN F 363 " --> pdb=" O ILE F 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS G 79 " --> pdb=" O TYR G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 3.804A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.611A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Proline residue: G 169 - end of helix removed outlier: 3.705A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG G 178 " --> pdb=" O TRP G 174 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 213 Processing helix chain 'G' and resid 222 through 231 removed outlier: 3.705A pdb=" N ILE G 226 " --> pdb=" O TRP G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS G 275 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP G 281 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.544A pdb=" N ILE G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 365 removed outlier: 3.532A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG G 362 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN G 363 " --> pdb=" O ILE G 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.792A pdb=" N VAL H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 47 removed outlier: 3.609A pdb=" N VAL H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.465A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS H 79 " --> pdb=" O TYR H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 3.804A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix Processing helix chain 'H' and resid 136 through 151 removed outlier: 3.612A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG H 146 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN H 151 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 182 removed outlier: 3.523A pdb=" N PHE H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Proline residue: H 169 - end of helix removed outlier: 3.705A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG H 178 " --> pdb=" O TRP H 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H 179 " --> pdb=" O ASP H 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 213 Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.704A pdb=" N ILE H 226 " --> pdb=" O TRP H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 305 removed outlier: 4.135A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 275 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE H 278 " --> pdb=" O GLU H 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE H 279 " --> pdb=" O LYS H 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP H 281 " --> pdb=" O PHE H 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN H 294 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS H 295 " --> pdb=" O SER H 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 327 through 335 removed outlier: 3.513A pdb=" N PHE H 331 " --> pdb=" O ASP H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 349 removed outlier: 3.545A pdb=" N ILE H 341 " --> pdb=" O ASP H 337 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP H 343 " --> pdb=" O LEU H 339 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.533A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG H 362 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN H 363 " --> pdb=" O ILE H 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AA4, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58 Processing sheet with id=AA6, first strand: chain 'C' and resid 249 through 251 Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 58 Processing sheet with id=AA8, first strand: chain 'D' and resid 249 through 251 Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 58 Processing sheet with id=AB1, first strand: chain 'E' and resid 249 through 251 Processing sheet with id=AB2, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AB3, first strand: chain 'F' and resid 249 through 251 Processing sheet with id=AB4, first strand: chain 'G' and resid 56 through 58 Processing sheet with id=AB5, first strand: chain 'G' and resid 249 through 251 Processing sheet with id=AB6, first strand: chain 'H' and resid 56 through 58 Processing sheet with id=AB7, first strand: chain 'H' and resid 249 through 251 1098 hydrogen bonds defined for protein. 3270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7288 1.34 - 1.46: 6743 1.46 - 1.58: 10305 1.58 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 24472 Sorted by residual: bond pdb=" CB PHE A 242 " pdb=" CG PHE A 242 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.65e+00 bond pdb=" CB PHE B 242 " pdb=" CG PHE B 242 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.62e+00 bond pdb=" CB PHE F 242 " pdb=" CG PHE F 242 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.53e+00 bond pdb=" CB PHE D 242 " pdb=" CG PHE D 242 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.53e+00 bond pdb=" CB PHE E 242 " pdb=" CG PHE E 242 " ideal model delta sigma weight residual 1.502 1.444 0.058 2.30e-02 1.89e+03 6.47e+00 ... (remaining 24467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 32401 2.73 - 5.46: 767 5.46 - 8.19: 128 8.19 - 10.92: 24 10.92 - 13.65: 8 Bond angle restraints: 33328 Sorted by residual: angle pdb=" N LEU C 86 " pdb=" CA LEU C 86 " pdb=" C LEU C 86 " ideal model delta sigma weight residual 107.41 121.06 -13.65 2.02e+00 2.45e-01 4.57e+01 angle pdb=" N LEU F 86 " pdb=" CA LEU F 86 " pdb=" C LEU F 86 " ideal model delta sigma weight residual 107.41 121.03 -13.62 2.02e+00 2.45e-01 4.55e+01 angle pdb=" N LEU D 86 " pdb=" CA LEU D 86 " pdb=" C LEU D 86 " ideal model delta sigma weight residual 107.41 121.03 -13.62 2.02e+00 2.45e-01 4.55e+01 angle pdb=" N LEU B 86 " pdb=" CA LEU B 86 " pdb=" C LEU B 86 " ideal model delta sigma weight residual 107.41 121.02 -13.61 2.02e+00 2.45e-01 4.54e+01 angle pdb=" N LEU H 86 " pdb=" CA LEU H 86 " pdb=" C LEU H 86 " ideal model delta sigma weight residual 107.41 121.02 -13.61 2.02e+00 2.45e-01 4.54e+01 ... (remaining 33323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 13319 16.35 - 32.70: 681 32.70 - 49.04: 152 49.04 - 65.39: 8 65.39 - 81.74: 40 Dihedral angle restraints: 14200 sinusoidal: 5592 harmonic: 8608 Sorted by residual: dihedral pdb=" CA LEU G 86 " pdb=" C LEU G 86 " pdb=" N ASP G 87 " pdb=" CA ASP G 87 " ideal model delta harmonic sigma weight residual 180.00 98.26 81.74 0 5.00e+00 4.00e-02 2.67e+02 dihedral pdb=" CA LEU B 86 " pdb=" C LEU B 86 " pdb=" N ASP B 87 " pdb=" CA ASP B 87 " ideal model delta harmonic sigma weight residual 180.00 98.27 81.73 0 5.00e+00 4.00e-02 2.67e+02 dihedral pdb=" CA LEU A 86 " pdb=" C LEU A 86 " pdb=" N ASP A 87 " pdb=" CA ASP A 87 " ideal model delta harmonic sigma weight residual 180.00 98.29 81.71 0 5.00e+00 4.00e-02 2.67e+02 ... (remaining 14197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2013 0.040 - 0.080: 998 0.080 - 0.121: 489 0.121 - 0.161: 138 0.161 - 0.201: 42 Chirality restraints: 3680 Sorted by residual: chirality pdb=" CB ILE D 218 " pdb=" CA ILE D 218 " pdb=" CG1 ILE D 218 " pdb=" CG2 ILE D 218 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE B 218 " pdb=" CA ILE B 218 " pdb=" CG1 ILE B 218 " pdb=" CG2 ILE B 218 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CB ILE F 218 " pdb=" CA ILE F 218 " pdb=" CG1 ILE F 218 " pdb=" CG2 ILE F 218 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 3677 not shown) Planarity restraints: 4128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 222 " -0.018 2.00e-02 2.50e+03 1.38e-02 4.77e+00 pdb=" CG TRP F 222 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP F 222 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP F 222 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 222 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 222 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 222 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 222 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 222 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 222 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 222 " 0.018 2.00e-02 2.50e+03 1.38e-02 4.76e+00 pdb=" CG TRP C 222 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 222 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 222 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 222 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 222 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 222 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 222 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 222 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 222 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 222 " -0.018 2.00e-02 2.50e+03 1.38e-02 4.75e+00 pdb=" CG TRP A 222 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 222 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 222 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 222 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 222 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 222 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 222 " -0.001 2.00e-02 2.50e+03 ... (remaining 4125 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 232 2.58 - 3.16: 22439 3.16 - 3.74: 35264 3.74 - 4.32: 48194 4.32 - 4.90: 78393 Nonbonded interactions: 184522 Sorted by model distance: nonbonded pdb=" O PRO C 243 " pdb=" ND2 ASN C 270 " model vdw 1.998 3.120 nonbonded pdb=" O PRO B 243 " pdb=" ND2 ASN B 270 " model vdw 1.999 3.120 nonbonded pdb=" O PRO A 243 " pdb=" ND2 ASN A 270 " model vdw 1.999 3.120 nonbonded pdb=" O PRO F 243 " pdb=" ND2 ASN F 270 " model vdw 1.999 3.120 nonbonded pdb=" O PRO D 243 " pdb=" ND2 ASN D 270 " model vdw 1.999 3.120 ... (remaining 184517 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 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 : 0.008 0.059 24488 Z= 0.368 Angle : 1.042 13.654 33360 Z= 0.570 Chirality : 0.059 0.201 3680 Planarity : 0.005 0.041 4128 Dihedral : 11.648 81.742 8568 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.61 % Favored : 86.83 % Rotamer: Outliers : 0.31 % Allowed : 2.49 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -5.07 (0.12), residues: 2856 helix: -3.32 (0.08), residues: 1648 sheet: -2.89 (0.37), residues: 144 loop : -3.22 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 168 TYR 0.020 0.003 TYR F 105 PHE 0.025 0.003 PHE E 64 TRP 0.038 0.003 TRP F 222 HIS 0.005 0.002 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00849 (24472) covalent geometry : angle 1.03869 (33328) SS BOND : bond 0.00231 ( 16) SS BOND : angle 2.99286 ( 32) hydrogen bonds : bond 0.13465 ( 1098) hydrogen bonds : angle 9.86498 ( 3270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1066 time to evaluate : 0.928 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 VAL cc_start: 0.8201 (t) cc_final: 0.7955 (p) REVERT: A 89 GLN cc_start: 0.7397 (tt0) cc_final: 0.7061 (mm110) REVERT: A 99 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7898 (tppp) REVERT: A 103 GLN cc_start: 0.7738 (pt0) cc_final: 0.6698 (pt0) REVERT: A 155 ASP cc_start: 0.8357 (t70) cc_final: 0.7739 (p0) REVERT: A 186 ARG cc_start: 0.8466 (mtt-85) cc_final: 0.7922 (mtp85) REVERT: A 232 GLN cc_start: 0.8164 (mm110) cc_final: 0.7746 (mt0) REVERT: A 237 GLN cc_start: 0.8407 (pm20) cc_final: 0.7931 (pm20) REVERT: A 242 PHE cc_start: 0.7501 (t80) cc_final: 0.7100 (t80) REVERT: A 303 CYS cc_start: 0.7198 (t) cc_final: 0.6934 (m) REVERT: A 304 ASN cc_start: 0.8032 (m-40) cc_final: 0.7453 (t0) REVERT: A 315 TYR cc_start: 0.8060 (m-10) cc_final: 0.7858 (m-10) REVERT: A 329 GLN cc_start: 0.6379 (pt0) cc_final: 0.5812 (pt0) REVERT: A 332 SER cc_start: 0.8295 (t) cc_final: 0.7831 (p) REVERT: A 334 LEU cc_start: 0.7543 (tp) cc_final: 0.7028 (tp) REVERT: A 339 LEU cc_start: 0.8512 (tp) cc_final: 0.8283 (tt) REVERT: A 342 MET cc_start: 0.8138 (mmm) cc_final: 0.7710 (tpp) REVERT: A 347 LEU cc_start: 0.7288 (tt) cc_final: 0.6915 (tt) REVERT: A 349 LEU cc_start: 0.7649 (mp) cc_final: 0.7408 (mp) REVERT: A 351 ASP cc_start: 0.5673 (t0) cc_final: 0.5297 (t0) REVERT: A 368 PHE cc_start: 0.4770 (t80) cc_final: 0.3310 (t80) REVERT: B 69 VAL cc_start: 0.8221 (t) cc_final: 0.7893 (p) REVERT: B 75 TYR cc_start: 0.8503 (t80) cc_final: 0.8269 (t80) REVERT: B 89 GLN cc_start: 0.7358 (tt0) cc_final: 0.7090 (mm110) REVERT: B 99 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7930 (tppp) REVERT: B 154 LYS cc_start: 0.6668 (ttpt) cc_final: 0.6265 (ttpp) REVERT: B 155 ASP cc_start: 0.8227 (t70) cc_final: 0.7857 (p0) REVERT: B 175 ASP cc_start: 0.8544 (t0) cc_final: 0.8200 (t0) REVERT: B 184 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7246 (ttp-110) REVERT: B 186 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7875 (mtp85) REVERT: B 232 GLN cc_start: 0.8192 (mm110) cc_final: 0.7889 (mt0) REVERT: B 303 CYS cc_start: 0.7157 (t) cc_final: 0.6816 (m) REVERT: B 304 ASN cc_start: 0.7956 (m-40) cc_final: 0.7601 (t0) REVERT: B 313 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8322 (ttmt) REVERT: B 329 GLN cc_start: 0.6665 (pt0) cc_final: 0.6187 (pt0) REVERT: B 332 SER cc_start: 0.8191 (t) cc_final: 0.7774 (p) REVERT: B 334 LEU cc_start: 0.7434 (tp) cc_final: 0.7187 (tp) REVERT: B 342 MET cc_start: 0.8157 (mmm) cc_final: 0.7859 (mmm) REVERT: C 69 VAL cc_start: 0.8201 (t) cc_final: 0.7955 (p) REVERT: C 89 GLN cc_start: 0.7407 (tt0) cc_final: 0.7071 (mm110) REVERT: C 99 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7896 (tppp) REVERT: C 103 GLN cc_start: 0.7739 (pt0) cc_final: 0.6697 (pt0) REVERT: C 155 ASP cc_start: 0.8359 (t70) cc_final: 0.7742 (p0) REVERT: C 186 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.7924 (mtp85) REVERT: C 232 GLN cc_start: 0.8150 (mm110) cc_final: 0.7726 (mt0) REVERT: C 237 GLN cc_start: 0.8409 (pm20) cc_final: 0.7932 (pm20) REVERT: C 242 PHE cc_start: 0.7443 (t80) cc_final: 0.7060 (t80) REVERT: C 303 CYS cc_start: 0.7200 (t) cc_final: 0.6936 (m) REVERT: C 304 ASN cc_start: 0.8029 (m-40) cc_final: 0.7452 (t0) REVERT: C 315 TYR cc_start: 0.8056 (m-10) cc_final: 0.7852 (m-10) REVERT: C 329 GLN cc_start: 0.6379 (pt0) cc_final: 0.5825 (pt0) REVERT: C 332 SER cc_start: 0.8297 (t) cc_final: 0.7834 (p) REVERT: C 334 LEU cc_start: 0.7543 (tp) cc_final: 0.7026 (tp) REVERT: C 339 LEU cc_start: 0.8512 (tp) cc_final: 0.8280 (tt) REVERT: C 342 MET cc_start: 0.8139 (mmm) cc_final: 0.7710 (tpp) REVERT: C 347 LEU cc_start: 0.7317 (tt) cc_final: 0.6946 (tt) REVERT: C 349 LEU cc_start: 0.7617 (mp) cc_final: 0.7367 (mp) REVERT: C 351 ASP cc_start: 0.5679 (t0) cc_final: 0.5294 (t0) REVERT: C 368 PHE cc_start: 0.4764 (t80) cc_final: 0.3309 (t80) REVERT: D 69 VAL cc_start: 0.8266 (t) cc_final: 0.7929 (p) REVERT: D 75 TYR cc_start: 0.8566 (t80) cc_final: 0.8316 (t80) REVERT: D 89 GLN cc_start: 0.7351 (tt0) cc_final: 0.6985 (mm110) REVERT: D 99 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7898 (tppp) REVERT: D 154 LYS cc_start: 0.6714 (ttpt) cc_final: 0.6271 (ttpp) REVERT: D 155 ASP cc_start: 0.8326 (t70) cc_final: 0.7827 (p0) REVERT: D 184 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7203 (ttp-110) REVERT: D 186 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.7956 (mtp85) REVERT: D 232 GLN cc_start: 0.8212 (mm110) cc_final: 0.7895 (mt0) REVERT: D 303 CYS cc_start: 0.7228 (t) cc_final: 0.6859 (m) REVERT: D 304 ASN cc_start: 0.7956 (m-40) cc_final: 0.7637 (t0) REVERT: D 329 GLN cc_start: 0.6557 (pt0) cc_final: 0.6098 (pt0) REVERT: D 332 SER cc_start: 0.8192 (t) cc_final: 0.7821 (p) REVERT: D 334 LEU cc_start: 0.7469 (tp) cc_final: 0.7220 (tp) REVERT: D 342 MET cc_start: 0.8206 (mmm) cc_final: 0.7905 (mmm) REVERT: D 362 ARG cc_start: 0.7502 (ttp80) cc_final: 0.7101 (ttp-170) REVERT: D 368 PHE cc_start: 0.4777 (t80) cc_final: 0.4425 (t80) REVERT: E 69 VAL cc_start: 0.8203 (t) cc_final: 0.7956 (p) REVERT: E 89 GLN cc_start: 0.7415 (tt0) cc_final: 0.7079 (mm110) REVERT: E 99 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7899 (tppp) REVERT: E 103 GLN cc_start: 0.7736 (pt0) cc_final: 0.6695 (pt0) REVERT: E 155 ASP cc_start: 0.8360 (t70) cc_final: 0.7738 (p0) REVERT: E 186 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.7883 (mtp85) REVERT: E 232 GLN cc_start: 0.8163 (mm110) cc_final: 0.7743 (mt0) REVERT: E 237 GLN cc_start: 0.8408 (pm20) cc_final: 0.7930 (pm20) REVERT: E 242 PHE cc_start: 0.7501 (t80) cc_final: 0.7098 (t80) REVERT: E 303 CYS cc_start: 0.7196 (t) cc_final: 0.6934 (m) REVERT: E 304 ASN cc_start: 0.8032 (m-40) cc_final: 0.7456 (t0) REVERT: E 315 TYR cc_start: 0.8062 (m-10) cc_final: 0.7856 (m-10) REVERT: E 329 GLN cc_start: 0.6377 (pt0) cc_final: 0.5815 (pt0) REVERT: E 332 SER cc_start: 0.8295 (t) cc_final: 0.7831 (p) REVERT: E 334 LEU cc_start: 0.7544 (tp) cc_final: 0.7026 (tp) REVERT: E 339 LEU cc_start: 0.8514 (tp) cc_final: 0.8299 (tt) REVERT: E 342 MET cc_start: 0.8140 (mmm) cc_final: 0.7731 (tpp) REVERT: E 347 LEU cc_start: 0.7290 (tt) cc_final: 0.6917 (tt) REVERT: E 349 LEU cc_start: 0.7656 (mp) cc_final: 0.7415 (mp) REVERT: E 351 ASP cc_start: 0.5668 (t0) cc_final: 0.5274 (t0) REVERT: E 368 PHE cc_start: 0.4756 (t80) cc_final: 0.3314 (t80) REVERT: F 75 TYR cc_start: 0.8501 (t80) cc_final: 0.8255 (t80) REVERT: F 89 GLN cc_start: 0.7230 (tt0) cc_final: 0.7021 (mm110) REVERT: F 99 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7789 (tppp) REVERT: F 154 LYS cc_start: 0.6687 (ttpt) cc_final: 0.6264 (ttpp) REVERT: F 155 ASP cc_start: 0.8216 (t70) cc_final: 0.7771 (p0) REVERT: F 175 ASP cc_start: 0.8556 (t0) cc_final: 0.8190 (t0) REVERT: F 184 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7240 (ttp-110) REVERT: F 186 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7891 (mtp85) REVERT: F 232 GLN cc_start: 0.8186 (mm110) cc_final: 0.7889 (mt0) REVERT: F 303 CYS cc_start: 0.7244 (t) cc_final: 0.6868 (m) REVERT: F 304 ASN cc_start: 0.7978 (m-40) cc_final: 0.7626 (t0) REVERT: F 313 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8354 (ttmt) REVERT: F 329 GLN cc_start: 0.6588 (pt0) cc_final: 0.6102 (pt0) REVERT: F 332 SER cc_start: 0.8174 (t) cc_final: 0.7658 (p) REVERT: F 334 LEU cc_start: 0.7470 (tp) cc_final: 0.7230 (tp) REVERT: F 342 MET cc_start: 0.8120 (mmm) cc_final: 0.7803 (mmm) REVERT: G 69 VAL cc_start: 0.8202 (t) cc_final: 0.7955 (p) REVERT: G 89 GLN cc_start: 0.7400 (tt0) cc_final: 0.7063 (mm110) REVERT: G 99 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7898 (tppp) REVERT: G 103 GLN cc_start: 0.7735 (pt0) cc_final: 0.6693 (pt0) REVERT: G 155 ASP cc_start: 0.8356 (t70) cc_final: 0.7737 (p0) REVERT: G 186 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.7923 (mtp85) REVERT: G 232 GLN cc_start: 0.8162 (mm110) cc_final: 0.7742 (mt0) REVERT: G 237 GLN cc_start: 0.8408 (pm20) cc_final: 0.7935 (pm20) REVERT: G 242 PHE cc_start: 0.7512 (t80) cc_final: 0.7114 (t80) REVERT: G 303 CYS cc_start: 0.7199 (t) cc_final: 0.6934 (m) REVERT: G 304 ASN cc_start: 0.8029 (m-40) cc_final: 0.7451 (t0) REVERT: G 329 GLN cc_start: 0.6377 (pt0) cc_final: 0.5821 (pt0) REVERT: G 332 SER cc_start: 0.8297 (t) cc_final: 0.7833 (p) REVERT: G 334 LEU cc_start: 0.7545 (tp) cc_final: 0.7031 (tp) REVERT: G 339 LEU cc_start: 0.8512 (tp) cc_final: 0.8282 (tt) REVERT: G 342 MET cc_start: 0.8137 (mmm) cc_final: 0.7711 (tpp) REVERT: G 347 LEU cc_start: 0.7310 (tt) cc_final: 0.6939 (tt) REVERT: G 349 LEU cc_start: 0.7645 (mp) cc_final: 0.7404 (mp) REVERT: G 351 ASP cc_start: 0.5666 (t0) cc_final: 0.5363 (t0) REVERT: G 368 PHE cc_start: 0.4768 (t80) cc_final: 0.3312 (t80) REVERT: H 75 TYR cc_start: 0.8499 (t80) cc_final: 0.8267 (t80) REVERT: H 89 GLN cc_start: 0.7227 (tt0) cc_final: 0.7017 (mm110) REVERT: H 99 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7885 (tppp) REVERT: H 154 LYS cc_start: 0.6686 (ttpt) cc_final: 0.6265 (ttpp) REVERT: H 155 ASP cc_start: 0.8226 (t70) cc_final: 0.7850 (p0) REVERT: H 184 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7246 (ttp-110) REVERT: H 186 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.7878 (mtp85) REVERT: H 232 GLN cc_start: 0.8191 (mm110) cc_final: 0.7889 (mt0) REVERT: H 303 CYS cc_start: 0.7153 (t) cc_final: 0.6817 (m) REVERT: H 304 ASN cc_start: 0.7986 (m-40) cc_final: 0.7636 (t0) REVERT: H 329 GLN cc_start: 0.6596 (pt0) cc_final: 0.6110 (pt0) REVERT: H 332 SER cc_start: 0.8184 (t) cc_final: 0.7772 (p) REVERT: H 342 MET cc_start: 0.8136 (mmm) cc_final: 0.7831 (mmm) outliers start: 8 outliers final: 0 residues processed: 1066 average time/residue: 0.2316 time to fit residues: 348.0516 Evaluate side-chains 698 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 199 GLN C 70 ASN C 199 GLN E 70 ASN E 199 GLN G 70 ASN G 199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120458 restraints weight = 28634.667| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.65 r_work: 0.3272 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24488 Z= 0.168 Angle : 0.805 9.460 33360 Z= 0.416 Chirality : 0.046 0.194 3680 Planarity : 0.005 0.044 4128 Dihedral : 7.453 47.348 3168 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.84 % Favored : 91.88 % Rotamer: Outliers : 4.95 % Allowed : 13.67 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.82 (0.15), residues: 2856 helix: -1.20 (0.11), residues: 1712 sheet: -1.32 (0.47), residues: 144 loop : -3.02 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 181 TYR 0.030 0.002 TYR D 105 PHE 0.014 0.002 PHE D 64 TRP 0.026 0.002 TRP G 107 HIS 0.002 0.001 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00360 (24472) covalent geometry : angle 0.80199 (33328) SS BOND : bond 0.00697 ( 16) SS BOND : angle 2.42218 ( 32) hydrogen bonds : bond 0.04768 ( 1098) hydrogen bonds : angle 5.41394 ( 3270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 819 time to evaluate : 0.991 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8366 (ttmm) REVERT: A 102 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8742 (pt) REVERT: A 155 ASP cc_start: 0.8160 (t70) cc_final: 0.7893 (p0) REVERT: A 186 ARG cc_start: 0.8784 (mtt-85) cc_final: 0.8067 (mtp85) REVERT: A 232 GLN cc_start: 0.8672 (mm110) cc_final: 0.8458 (mt0) REVERT: A 310 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8332 (tppp) REVERT: A 329 GLN cc_start: 0.7558 (pt0) cc_final: 0.7255 (tt0) REVERT: A 332 SER cc_start: 0.9229 (t) cc_final: 0.8943 (p) REVERT: A 347 LEU cc_start: 0.9174 (tt) cc_final: 0.8905 (tt) REVERT: A 348 ASN cc_start: 0.8450 (m-40) cc_final: 0.8239 (m110) REVERT: B 33 ARG cc_start: 0.5894 (ttm110) cc_final: 0.5686 (ttm110) REVERT: B 99 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8159 (tppp) REVERT: B 154 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8210 (ttpt) REVERT: B 160 THR cc_start: 0.8420 (p) cc_final: 0.8030 (t) REVERT: B 268 THR cc_start: 0.8999 (m) cc_final: 0.8618 (p) REVERT: B 307 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7944 (mtmm) REVERT: B 309 GLN cc_start: 0.8505 (mt0) cc_final: 0.8190 (mt0) REVERT: B 310 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8268 (tppp) REVERT: B 313 LYS cc_start: 0.9227 (ttmt) cc_final: 0.9003 (ttmt) REVERT: B 314 ASN cc_start: 0.8662 (t0) cc_final: 0.8222 (t0) REVERT: B 315 TYR cc_start: 0.8356 (m-10) cc_final: 0.8156 (m-10) REVERT: B 329 GLN cc_start: 0.7879 (pt0) cc_final: 0.7550 (pt0) REVERT: B 332 SER cc_start: 0.9069 (t) cc_final: 0.8858 (p) REVERT: B 339 LEU cc_start: 0.9025 (tp) cc_final: 0.8744 (tp) REVERT: B 348 ASN cc_start: 0.8627 (m-40) cc_final: 0.8392 (m110) REVERT: C 99 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8354 (ttmm) REVERT: C 102 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8734 (pt) REVERT: C 186 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.8095 (mtp85) REVERT: C 232 GLN cc_start: 0.8687 (mm110) cc_final: 0.8462 (mt0) REVERT: C 310 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8334 (tppp) REVERT: C 329 GLN cc_start: 0.7545 (pt0) cc_final: 0.7238 (tt0) REVERT: C 332 SER cc_start: 0.9231 (t) cc_final: 0.8944 (p) REVERT: C 347 LEU cc_start: 0.9175 (tt) cc_final: 0.8913 (tt) REVERT: C 348 ASN cc_start: 0.8444 (m-40) cc_final: 0.8225 (m110) REVERT: D 99 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8213 (tppp) REVERT: D 102 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8747 (pt) REVERT: D 160 THR cc_start: 0.8436 (p) cc_final: 0.8079 (t) REVERT: D 184 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7663 (ttp-110) REVERT: D 268 THR cc_start: 0.8959 (m) cc_final: 0.8679 (p) REVERT: D 307 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8075 (mtmm) REVERT: D 309 GLN cc_start: 0.8537 (mt0) cc_final: 0.8293 (mt0) REVERT: D 310 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8295 (tppp) REVERT: D 314 ASN cc_start: 0.8639 (t0) cc_final: 0.8330 (t0) REVERT: D 329 GLN cc_start: 0.7857 (pt0) cc_final: 0.7524 (pt0) REVERT: D 332 SER cc_start: 0.9053 (t) cc_final: 0.8809 (p) REVERT: D 339 LEU cc_start: 0.9032 (tp) cc_final: 0.8769 (tp) REVERT: D 368 PHE cc_start: 0.6767 (t80) cc_final: 0.6551 (t80) REVERT: E 99 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8361 (ttmm) REVERT: E 102 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8747 (pt) REVERT: E 186 ARG cc_start: 0.8808 (mtt-85) cc_final: 0.8089 (mtp85) REVERT: E 232 GLN cc_start: 0.8668 (mm110) cc_final: 0.8462 (mt0) REVERT: E 315 TYR cc_start: 0.8493 (m-10) cc_final: 0.8241 (m-80) REVERT: E 329 GLN cc_start: 0.7566 (pt0) cc_final: 0.7268 (tt0) REVERT: E 332 SER cc_start: 0.9231 (t) cc_final: 0.8945 (p) REVERT: E 347 LEU cc_start: 0.9172 (tt) cc_final: 0.8911 (tt) REVERT: E 348 ASN cc_start: 0.8441 (m-40) cc_final: 0.8220 (m110) REVERT: F 33 ARG cc_start: 0.5926 (ttm110) cc_final: 0.5721 (ttm110) REVERT: F 99 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8144 (tppp) REVERT: F 102 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8772 (pt) REVERT: F 160 THR cc_start: 0.8451 (p) cc_final: 0.8054 (t) REVERT: F 268 THR cc_start: 0.9007 (m) cc_final: 0.8626 (p) REVERT: F 307 LYS cc_start: 0.8324 (mtmm) cc_final: 0.8055 (mtmm) REVERT: F 309 GLN cc_start: 0.8473 (mt0) cc_final: 0.8221 (mt0) REVERT: F 310 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8284 (tppp) REVERT: F 313 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8979 (ttmt) REVERT: F 314 ASN cc_start: 0.8656 (t0) cc_final: 0.8205 (t0) REVERT: F 315 TYR cc_start: 0.8384 (m-10) cc_final: 0.8166 (m-10) REVERT: F 329 GLN cc_start: 0.7867 (pt0) cc_final: 0.7547 (pt0) REVERT: F 332 SER cc_start: 0.9086 (t) cc_final: 0.8806 (p) REVERT: F 339 LEU cc_start: 0.9021 (tp) cc_final: 0.8781 (tp) REVERT: F 348 ASN cc_start: 0.8657 (m-40) cc_final: 0.8437 (m110) REVERT: G 99 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8355 (ttmm) REVERT: G 102 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8738 (pt) REVERT: G 186 ARG cc_start: 0.8795 (mtt-85) cc_final: 0.8157 (mtp85) REVERT: G 232 GLN cc_start: 0.8652 (mm110) cc_final: 0.8448 (mt0) REVERT: G 329 GLN cc_start: 0.7553 (pt0) cc_final: 0.7246 (tt0) REVERT: G 332 SER cc_start: 0.9229 (t) cc_final: 0.8945 (p) REVERT: G 347 LEU cc_start: 0.9171 (tt) cc_final: 0.8935 (tt) REVERT: G 348 ASN cc_start: 0.8439 (m-40) cc_final: 0.8114 (m110) REVERT: H 33 ARG cc_start: 0.5906 (ttm110) cc_final: 0.5704 (ttm110) REVERT: H 99 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8148 (tppp) REVERT: H 102 ILE cc_start: 0.8990 (pt) cc_final: 0.8777 (pt) REVERT: H 160 THR cc_start: 0.8404 (p) cc_final: 0.8018 (t) REVERT: H 307 LYS cc_start: 0.8315 (mtmm) cc_final: 0.8042 (mtmm) REVERT: H 309 GLN cc_start: 0.8486 (mt0) cc_final: 0.8170 (mt0) REVERT: H 310 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8263 (tppp) REVERT: H 314 ASN cc_start: 0.8650 (t0) cc_final: 0.8205 (t0) REVERT: H 315 TYR cc_start: 0.8364 (m-10) cc_final: 0.8152 (m-10) REVERT: H 329 GLN cc_start: 0.7895 (pt0) cc_final: 0.7562 (pt0) REVERT: H 332 SER cc_start: 0.9093 (t) cc_final: 0.8883 (p) REVERT: H 339 LEU cc_start: 0.9002 (tp) cc_final: 0.8784 (tp) REVERT: H 348 ASN cc_start: 0.8647 (m-40) cc_final: 0.8424 (m110) outliers start: 127 outliers final: 87 residues processed: 876 average time/residue: 0.2046 time to fit residues: 261.1208 Evaluate side-chains 755 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 662 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 240 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 116 optimal weight: 0.0010 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119173 restraints weight = 28834.939| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.69 r_work: 0.3273 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24488 Z= 0.162 Angle : 0.745 8.901 33360 Z= 0.380 Chirality : 0.044 0.162 3680 Planarity : 0.004 0.044 4128 Dihedral : 6.785 39.965 3168 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.35 % Favored : 90.09 % Rotamer: Outliers : 6.54 % Allowed : 16.16 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.05 (0.15), residues: 2856 helix: -0.39 (0.12), residues: 1744 sheet: -1.46 (0.48), residues: 152 loop : -3.10 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 181 TYR 0.019 0.002 TYR G 301 PHE 0.016 0.002 PHE D 242 TRP 0.015 0.001 TRP B 236 HIS 0.002 0.000 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00365 (24472) covalent geometry : angle 0.74151 (33328) SS BOND : bond 0.00470 ( 16) SS BOND : angle 2.32204 ( 32) hydrogen bonds : bond 0.04208 ( 1098) hydrogen bonds : angle 4.68762 ( 3270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 669 time to evaluate : 0.917 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8912 (t0) cc_final: 0.8023 (t0) REVERT: A 74 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: A 99 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8293 (ttmm) REVERT: A 102 ILE cc_start: 0.8920 (pt) cc_final: 0.8678 (pt) REVERT: A 127 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7740 (ttmm) REVERT: A 155 ASP cc_start: 0.8068 (t70) cc_final: 0.7827 (p0) REVERT: A 178 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7852 (ttm170) REVERT: A 184 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7456 (ttp-110) REVERT: A 186 ARG cc_start: 0.8751 (mtt-85) cc_final: 0.8107 (mtp85) REVERT: A 310 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8296 (tppp) REVERT: A 315 TYR cc_start: 0.8428 (m-10) cc_final: 0.8182 (m-10) REVERT: A 327 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8768 (t0) REVERT: A 329 GLN cc_start: 0.7586 (pt0) cc_final: 0.7309 (tt0) REVERT: A 332 SER cc_start: 0.9213 (t) cc_final: 0.8993 (p) REVERT: B 99 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8116 (tppp) REVERT: B 154 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7764 (ttpp) REVERT: B 268 THR cc_start: 0.8840 (m) cc_final: 0.8423 (p) REVERT: B 310 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8192 (tppp) REVERT: B 313 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8819 (ttmt) REVERT: B 329 GLN cc_start: 0.7833 (pt0) cc_final: 0.7368 (tt0) REVERT: B 332 SER cc_start: 0.9102 (t) cc_final: 0.8878 (p) REVERT: B 344 GLN cc_start: 0.8566 (tp40) cc_final: 0.8253 (tp40) REVERT: C 46 LEU cc_start: 0.8293 (mt) cc_final: 0.7972 (mt) REVERT: C 70 ASN cc_start: 0.8925 (t0) cc_final: 0.8030 (t0) REVERT: C 74 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.6839 (mp10) REVERT: C 99 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8287 (ttmm) REVERT: C 102 ILE cc_start: 0.8914 (pt) cc_final: 0.8673 (pt) REVERT: C 127 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7747 (ttmm) REVERT: C 184 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7459 (ttp-110) REVERT: C 186 ARG cc_start: 0.8733 (mtt-85) cc_final: 0.8084 (mtp85) REVERT: C 310 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8290 (tppp) REVERT: C 315 TYR cc_start: 0.8426 (m-10) cc_final: 0.8176 (m-10) REVERT: C 329 GLN cc_start: 0.7577 (pt0) cc_final: 0.7303 (tt0) REVERT: C 332 SER cc_start: 0.9209 (t) cc_final: 0.8993 (p) REVERT: D 99 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8115 (tppp) REVERT: D 102 ILE cc_start: 0.8857 (pt) cc_final: 0.8608 (pt) REVERT: D 160 THR cc_start: 0.8358 (p) cc_final: 0.7955 (t) REVERT: D 184 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7726 (ttp-110) REVERT: D 268 THR cc_start: 0.8909 (m) cc_final: 0.8488 (p) REVERT: D 310 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8271 (tppp) REVERT: D 332 SER cc_start: 0.9125 (t) cc_final: 0.8898 (p) REVERT: D 344 GLN cc_start: 0.8615 (tp40) cc_final: 0.8214 (tp40) REVERT: E 70 ASN cc_start: 0.8908 (t0) cc_final: 0.8032 (t0) REVERT: E 74 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: E 99 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8265 (ttmm) REVERT: E 102 ILE cc_start: 0.8917 (pt) cc_final: 0.8679 (pt) REVERT: E 127 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7755 (ttmm) REVERT: E 178 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7833 (ttm170) REVERT: E 184 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7441 (ttp-110) REVERT: E 186 ARG cc_start: 0.8742 (mtt-85) cc_final: 0.8085 (mtp85) REVERT: E 314 ASN cc_start: 0.8483 (t0) cc_final: 0.8239 (m-40) REVERT: E 329 GLN cc_start: 0.7605 (pt0) cc_final: 0.7325 (tt0) REVERT: E 332 SER cc_start: 0.9166 (t) cc_final: 0.8965 (p) REVERT: F 99 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8113 (tppp) REVERT: F 102 ILE cc_start: 0.8877 (pt) cc_final: 0.8635 (pt) REVERT: F 268 THR cc_start: 0.8839 (m) cc_final: 0.8415 (p) REVERT: F 274 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: F 307 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8044 (mtmm) REVERT: F 310 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8201 (tppp) REVERT: F 313 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8803 (ttmt) REVERT: F 329 GLN cc_start: 0.7803 (pt0) cc_final: 0.7371 (tt0) REVERT: F 339 LEU cc_start: 0.9034 (tp) cc_final: 0.8802 (tp) REVERT: F 344 GLN cc_start: 0.8569 (tp40) cc_final: 0.8257 (tp40) REVERT: G 70 ASN cc_start: 0.8904 (t0) cc_final: 0.8029 (t0) REVERT: G 74 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: G 99 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8262 (ttmm) REVERT: G 102 ILE cc_start: 0.8912 (pt) cc_final: 0.8672 (pt) REVERT: G 127 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7745 (ttmm) REVERT: G 178 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7837 (ttm170) REVERT: G 184 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7443 (ttp-110) REVERT: G 186 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8098 (mtp85) REVERT: G 310 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8289 (tppp) REVERT: G 329 GLN cc_start: 0.7591 (pt0) cc_final: 0.7301 (tt0) REVERT: G 332 SER cc_start: 0.9204 (t) cc_final: 0.8986 (p) REVERT: H 99 LYS cc_start: 0.8427 (ttmt) cc_final: 0.8118 (tppp) REVERT: H 102 ILE cc_start: 0.8857 (pt) cc_final: 0.8639 (pt) REVERT: H 268 THR cc_start: 0.8837 (m) cc_final: 0.8415 (p) REVERT: H 310 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8193 (tppp) REVERT: H 329 GLN cc_start: 0.7811 (pt0) cc_final: 0.7357 (pt0) REVERT: H 332 SER cc_start: 0.9110 (t) cc_final: 0.8886 (p) REVERT: H 339 LEU cc_start: 0.9057 (tp) cc_final: 0.8816 (tp) REVERT: H 344 GLN cc_start: 0.8584 (tp40) cc_final: 0.8272 (tp40) outliers start: 168 outliers final: 87 residues processed: 786 average time/residue: 0.2126 time to fit residues: 242.3513 Evaluate side-chains 736 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 640 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 287 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 279 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 136 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 348 ASN B 348 ASN C 270 ASN C 348 ASN D 329 GLN D 348 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN F 348 ASN G 270 ASN G 348 ASN H 348 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122128 restraints weight = 28406.481| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.72 r_work: 0.3311 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24488 Z= 0.130 Angle : 0.731 8.706 33360 Z= 0.367 Chirality : 0.042 0.180 3680 Planarity : 0.004 0.043 4128 Dihedral : 6.363 33.884 3168 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.38 % Favored : 90.06 % Rotamer: Outliers : 5.92 % Allowed : 19.70 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.45 (0.16), residues: 2856 helix: 0.13 (0.12), residues: 1736 sheet: -1.58 (0.40), residues: 192 loop : -2.92 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 123 TYR 0.024 0.001 TYR G 300 PHE 0.015 0.001 PHE D 242 TRP 0.011 0.001 TRP E 222 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00280 (24472) covalent geometry : angle 0.72944 (33328) SS BOND : bond 0.00214 ( 16) SS BOND : angle 1.79026 ( 32) hydrogen bonds : bond 0.03675 ( 1098) hydrogen bonds : angle 4.22409 ( 3270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 668 time to evaluate : 0.987 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 74 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: A 102 ILE cc_start: 0.8795 (pt) cc_final: 0.8532 (pt) REVERT: A 127 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7626 (ttmm) REVERT: A 155 ASP cc_start: 0.8121 (t70) cc_final: 0.7881 (p0) REVERT: A 182 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8978 (mtpp) REVERT: A 184 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7408 (ttp-110) REVERT: A 186 ARG cc_start: 0.8584 (mtt-85) cc_final: 0.7902 (mtp85) REVERT: A 268 THR cc_start: 0.9003 (m) cc_final: 0.8542 (p) REVERT: A 314 ASN cc_start: 0.8501 (t0) cc_final: 0.8211 (m-40) REVERT: A 327 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8730 (t0) REVERT: A 332 SER cc_start: 0.9121 (t) cc_final: 0.8920 (p) REVERT: B 59 TRP cc_start: 0.8721 (t-100) cc_final: 0.8478 (t-100) REVERT: B 99 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8178 (ttmm) REVERT: B 175 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: B 182 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8923 (mtmm) REVERT: B 186 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.7997 (mtp85) REVERT: B 268 THR cc_start: 0.8830 (m) cc_final: 0.8475 (p) REVERT: B 310 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8197 (tppp) REVERT: B 329 GLN cc_start: 0.7924 (pt0) cc_final: 0.7413 (pt0) REVERT: B 332 SER cc_start: 0.9062 (t) cc_final: 0.8849 (p) REVERT: B 344 GLN cc_start: 0.8534 (tp40) cc_final: 0.8284 (tp40) REVERT: C 74 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: C 102 ILE cc_start: 0.8773 (pt) cc_final: 0.8508 (pt) REVERT: C 127 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7627 (ttmm) REVERT: C 182 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8939 (mtpp) REVERT: C 184 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7408 (ttp-110) REVERT: C 268 THR cc_start: 0.8954 (m) cc_final: 0.8489 (p) REVERT: C 310 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8230 (tppp) REVERT: C 332 SER cc_start: 0.9140 (t) cc_final: 0.8920 (p) REVERT: C 342 MET cc_start: 0.8854 (mmm) cc_final: 0.8594 (mmm) REVERT: D 59 TRP cc_start: 0.8727 (t-100) cc_final: 0.8461 (t-100) REVERT: D 99 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8147 (ttmm) REVERT: D 102 ILE cc_start: 0.8690 (pt) cc_final: 0.8437 (pt) REVERT: D 268 THR cc_start: 0.8937 (m) cc_final: 0.8486 (p) REVERT: D 310 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8214 (tppp) REVERT: D 332 SER cc_start: 0.9084 (t) cc_final: 0.8875 (p) REVERT: D 344 GLN cc_start: 0.8520 (tp40) cc_final: 0.8212 (tp40) REVERT: D 348 ASN cc_start: 0.8614 (m-40) cc_final: 0.8412 (m110) REVERT: E 74 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: E 102 ILE cc_start: 0.8773 (pt) cc_final: 0.8512 (pt) REVERT: E 127 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7622 (ttmm) REVERT: E 182 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8983 (mtpp) REVERT: E 184 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7405 (ttp-110) REVERT: E 268 THR cc_start: 0.8961 (m) cc_final: 0.8496 (p) REVERT: E 329 GLN cc_start: 0.7526 (pt0) cc_final: 0.7309 (tt0) REVERT: E 332 SER cc_start: 0.9128 (t) cc_final: 0.8906 (p) REVERT: F 59 TRP cc_start: 0.8709 (t-100) cc_final: 0.8469 (t-100) REVERT: F 99 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8114 (ttmm) REVERT: F 102 ILE cc_start: 0.8742 (pt) cc_final: 0.8500 (pt) REVERT: F 175 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8530 (m-30) REVERT: F 182 LYS cc_start: 0.9226 (mtmm) cc_final: 0.8938 (mtmm) REVERT: F 186 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8009 (mtp85) REVERT: F 268 THR cc_start: 0.8776 (m) cc_final: 0.8500 (p) REVERT: F 310 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8202 (tppp) REVERT: F 344 GLN cc_start: 0.8535 (tp40) cc_final: 0.8254 (tp40) REVERT: F 361 MET cc_start: 0.9143 (mtp) cc_final: 0.8705 (mtm) REVERT: G 74 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6983 (mt0) REVERT: G 99 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8291 (ttmm) REVERT: G 102 ILE cc_start: 0.8775 (pt) cc_final: 0.8512 (pt) REVERT: G 127 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7628 (ttmm) REVERT: G 178 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7695 (ttm170) REVERT: G 182 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8933 (mtpp) REVERT: G 184 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7405 (ttp-110) REVERT: G 186 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.7913 (mtp85) REVERT: G 268 THR cc_start: 0.8999 (m) cc_final: 0.8541 (p) REVERT: G 332 SER cc_start: 0.9134 (t) cc_final: 0.8911 (p) REVERT: H 59 TRP cc_start: 0.8687 (t-100) cc_final: 0.8427 (t-100) REVERT: H 99 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8122 (ttmm) REVERT: H 102 ILE cc_start: 0.8782 (pt) cc_final: 0.8541 (pt) REVERT: H 186 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8067 (mtp85) REVERT: H 268 THR cc_start: 0.8831 (m) cc_final: 0.8478 (p) REVERT: H 310 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8188 (tppp) REVERT: H 329 GLN cc_start: 0.7934 (pt0) cc_final: 0.7507 (pt0) REVERT: H 332 SER cc_start: 0.9066 (t) cc_final: 0.8853 (p) REVERT: H 344 GLN cc_start: 0.8546 (tp40) cc_final: 0.8280 (tp40) REVERT: H 361 MET cc_start: 0.9227 (mtp) cc_final: 0.8796 (mtm) outliers start: 152 outliers final: 110 residues processed: 765 average time/residue: 0.2113 time to fit residues: 236.5194 Evaluate side-chains 737 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 615 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 265 CYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 265 CYS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 45 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 348 ASN B 329 GLN B 348 ASN C 329 GLN C 348 ASN E 270 ASN E 348 ASN F 329 GLN F 348 ASN G 329 GLN G 348 ASN H 329 GLN H 348 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113371 restraints weight = 28935.496| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.65 r_work: 0.3197 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24488 Z= 0.228 Angle : 0.786 9.271 33360 Z= 0.394 Chirality : 0.046 0.202 3680 Planarity : 0.004 0.072 4128 Dihedral : 6.498 34.209 3168 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.49 % Favored : 89.95 % Rotamer: Outliers : 8.33 % Allowed : 20.40 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.22 (0.16), residues: 2856 helix: 0.38 (0.12), residues: 1736 sheet: -1.77 (0.39), residues: 192 loop : -2.89 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.020 0.002 TYR D 132 PHE 0.021 0.002 PHE F 242 TRP 0.014 0.001 TRP D 59 HIS 0.004 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00535 (24472) covalent geometry : angle 0.78246 (33328) SS BOND : bond 0.00630 ( 16) SS BOND : angle 2.37242 ( 32) hydrogen bonds : bond 0.04355 ( 1098) hydrogen bonds : angle 4.22612 ( 3270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 574 time to evaluate : 0.900 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 74 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: A 182 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8856 (ttmm) REVERT: A 184 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7794 (ttm-80) REVERT: A 280 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 310 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8351 (tppt) REVERT: A 327 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8808 (t0) REVERT: A 332 SER cc_start: 0.9157 (t) cc_final: 0.8950 (p) REVERT: B 99 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8156 (ttmm) REVERT: B 175 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8811 (m-30) REVERT: B 186 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.8352 (mtp180) REVERT: B 268 THR cc_start: 0.8915 (m) cc_final: 0.8389 (p) REVERT: B 310 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8264 (tppp) REVERT: B 321 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.9013 (pt) REVERT: B 329 GLN cc_start: 0.7973 (pt0) cc_final: 0.7519 (pt0) REVERT: B 332 SER cc_start: 0.9111 (t) cc_final: 0.8899 (p) REVERT: B 344 GLN cc_start: 0.8622 (tp40) cc_final: 0.8411 (tp40) REVERT: B 349 LEU cc_start: 0.8728 (mt) cc_final: 0.8451 (mp) REVERT: C 74 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7164 (mt0) REVERT: C 182 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8874 (ttmm) REVERT: C 184 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7805 (ttm-80) REVERT: C 186 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.8084 (mtp85) REVERT: C 280 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7817 (mp) REVERT: C 310 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8075 (tppt) REVERT: C 315 TYR cc_start: 0.8545 (m-10) cc_final: 0.8229 (m-10) REVERT: C 332 SER cc_start: 0.9178 (t) cc_final: 0.8970 (p) REVERT: D 99 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8221 (ttmm) REVERT: D 127 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7819 (ttmm) REVERT: D 160 THR cc_start: 0.8318 (p) cc_final: 0.7894 (t) REVERT: D 310 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8284 (tppp) REVERT: D 329 GLN cc_start: 0.7920 (pt0) cc_final: 0.7506 (pt0) REVERT: D 332 SER cc_start: 0.9089 (t) cc_final: 0.8879 (p) REVERT: D 348 ASN cc_start: 0.8904 (m-40) cc_final: 0.8631 (m110) REVERT: D 349 LEU cc_start: 0.8755 (mt) cc_final: 0.8359 (mp) REVERT: E 74 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: E 127 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7766 (ttmm) REVERT: E 178 ARG cc_start: 0.8241 (ttm170) cc_final: 0.8024 (ttp80) REVERT: E 182 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8940 (mtpp) REVERT: E 184 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7806 (ttm-80) REVERT: E 280 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7822 (mp) REVERT: E 332 SER cc_start: 0.9159 (t) cc_final: 0.8944 (p) REVERT: E 341 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7858 (pp) REVERT: E 342 MET cc_start: 0.8869 (mmm) cc_final: 0.8565 (mmm) REVERT: F 99 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8183 (ttmm) REVERT: F 175 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8675 (m-30) REVERT: F 310 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8267 (tppp) REVERT: F 344 GLN cc_start: 0.8618 (tp40) cc_final: 0.8390 (tp40) REVERT: G 74 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: G 99 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8094 (ttmm) REVERT: G 127 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7776 (ttmm) REVERT: G 182 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.8937 (mtpp) REVERT: G 184 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7793 (ttm-80) REVERT: G 186 ARG cc_start: 0.8621 (mtt-85) cc_final: 0.8101 (mtp85) REVERT: G 280 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7830 (mp) REVERT: G 310 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8026 (tppp) REVERT: G 332 SER cc_start: 0.9176 (t) cc_final: 0.8965 (p) REVERT: H 99 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8155 (ttmm) REVERT: H 186 ARG cc_start: 0.8744 (mtt-85) cc_final: 0.8382 (mtp180) REVERT: H 268 THR cc_start: 0.8905 (m) cc_final: 0.8374 (p) REVERT: H 310 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8253 (tppp) REVERT: H 321 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8993 (pt) REVERT: H 329 GLN cc_start: 0.7945 (pt0) cc_final: 0.7502 (pt0) REVERT: H 332 SER cc_start: 0.9111 (t) cc_final: 0.8902 (p) REVERT: H 344 GLN cc_start: 0.8643 (tp40) cc_final: 0.8404 (tp40) REVERT: H 349 LEU cc_start: 0.8725 (mt) cc_final: 0.8444 (mp) outliers start: 214 outliers final: 155 residues processed: 706 average time/residue: 0.2025 time to fit residues: 210.4106 Evaluate side-chains 697 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 524 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 321 ILE Chi-restraints excluded: chain H residue 337 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 167 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 0.0020 chunk 263 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN C 329 GLN E 329 GLN E 348 ASN F 329 GLN G 329 GLN H 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120662 restraints weight = 28083.957| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.66 r_work: 0.3291 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24488 Z= 0.123 Angle : 0.713 10.423 33360 Z= 0.356 Chirality : 0.041 0.184 3680 Planarity : 0.004 0.046 4128 Dihedral : 6.181 32.829 3168 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.17 % Favored : 90.27 % Rotamer: Outliers : 6.23 % Allowed : 22.94 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.80 (0.16), residues: 2856 helix: 0.77 (0.12), residues: 1752 sheet: -1.67 (0.39), residues: 192 loop : -2.92 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.018 0.001 TYR C 301 PHE 0.026 0.001 PHE D 242 TRP 0.011 0.001 TRP B 107 HIS 0.001 0.000 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00258 (24472) covalent geometry : angle 0.71056 (33328) SS BOND : bond 0.00128 ( 16) SS BOND : angle 1.88739 ( 32) hydrogen bonds : bond 0.03517 ( 1098) hydrogen bonds : angle 3.93186 ( 3270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 561 time to evaluate : 0.979 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8840 (t0) cc_final: 0.8221 (t0) REVERT: A 74 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7084 (mt0) REVERT: A 102 ILE cc_start: 0.8833 (pt) cc_final: 0.8582 (pt) REVERT: A 182 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8830 (ttmm) REVERT: A 184 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7788 (ttm-80) REVERT: A 186 ARG cc_start: 0.8555 (mtt-85) cc_final: 0.8124 (mtp85) REVERT: A 300 TYR cc_start: 0.8598 (t80) cc_final: 0.8166 (t80) REVERT: A 310 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8053 (tppt) REVERT: A 332 SER cc_start: 0.9188 (t) cc_final: 0.8972 (p) REVERT: B 99 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8199 (ttmm) REVERT: B 142 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8305 (mtpt) REVERT: B 175 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8805 (m-30) REVERT: B 186 ARG cc_start: 0.8603 (mtt-85) cc_final: 0.8183 (mtp85) REVERT: B 268 THR cc_start: 0.8918 (m) cc_final: 0.8389 (p) REVERT: B 284 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8006 (mt) REVERT: B 310 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8320 (tppt) REVERT: B 329 GLN cc_start: 0.7896 (pt0) cc_final: 0.7522 (pt0) REVERT: B 332 SER cc_start: 0.9068 (t) cc_final: 0.8864 (p) REVERT: B 344 GLN cc_start: 0.8641 (tp40) cc_final: 0.8364 (tp40) REVERT: B 349 LEU cc_start: 0.8680 (mt) cc_final: 0.8454 (mp) REVERT: C 70 ASN cc_start: 0.8851 (t0) cc_final: 0.8231 (t0) REVERT: C 74 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7082 (mt0) REVERT: C 102 ILE cc_start: 0.8832 (pt) cc_final: 0.8572 (pt) REVERT: C 182 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8851 (ttmm) REVERT: C 184 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7804 (ttm-80) REVERT: C 186 ARG cc_start: 0.8543 (mtt-85) cc_final: 0.8107 (mtp85) REVERT: C 329 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: C 332 SER cc_start: 0.9177 (t) cc_final: 0.8966 (p) REVERT: C 348 ASN cc_start: 0.8795 (m-40) cc_final: 0.8481 (m110) REVERT: D 59 TRP cc_start: 0.8754 (t-100) cc_final: 0.8415 (t-100) REVERT: D 99 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8181 (ttmm) REVERT: D 102 ILE cc_start: 0.8824 (pt) cc_final: 0.8606 (pt) REVERT: D 142 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8247 (mtpt) REVERT: D 186 ARG cc_start: 0.8641 (mtt-85) cc_final: 0.8184 (mtp85) REVERT: D 329 GLN cc_start: 0.7918 (pt0) cc_final: 0.7524 (pt0) REVERT: D 344 GLN cc_start: 0.8643 (tp40) cc_final: 0.8224 (tp40) REVERT: D 348 ASN cc_start: 0.8901 (m-40) cc_final: 0.8564 (m110) REVERT: D 349 LEU cc_start: 0.8693 (mt) cc_final: 0.8357 (mp) REVERT: E 70 ASN cc_start: 0.8849 (t0) cc_final: 0.8232 (t0) REVERT: E 74 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7085 (mt0) REVERT: E 102 ILE cc_start: 0.8836 (pt) cc_final: 0.8582 (pt) REVERT: E 127 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7827 (ttmm) REVERT: E 182 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8901 (mtpp) REVERT: E 186 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.8083 (mtp85) REVERT: E 332 SER cc_start: 0.9153 (t) cc_final: 0.8945 (p) REVERT: F 99 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8201 (ttmm) REVERT: F 102 ILE cc_start: 0.8832 (pt) cc_final: 0.8604 (pt) REVERT: F 142 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8329 (mtpt) REVERT: F 175 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8708 (m-30) REVERT: F 186 ARG cc_start: 0.8574 (mtt-85) cc_final: 0.8187 (mtp85) REVERT: F 268 THR cc_start: 0.8922 (m) cc_final: 0.8451 (p) REVERT: F 284 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8020 (mt) REVERT: F 310 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8343 (tppt) REVERT: F 344 GLN cc_start: 0.8596 (tp40) cc_final: 0.8349 (tp40) REVERT: G 70 ASN cc_start: 0.8843 (t0) cc_final: 0.8224 (t0) REVERT: G 74 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7069 (mt0) REVERT: G 99 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8127 (ttmm) REVERT: G 102 ILE cc_start: 0.8840 (pt) cc_final: 0.8589 (pt) REVERT: G 127 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7840 (ttmm) REVERT: G 182 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8913 (mtpp) REVERT: G 184 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7815 (ttm-80) REVERT: G 186 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.8111 (mtp85) REVERT: G 332 SER cc_start: 0.9173 (t) cc_final: 0.8958 (p) REVERT: G 348 ASN cc_start: 0.8764 (m-40) cc_final: 0.8463 (m110) REVERT: H 99 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8213 (ttmm) REVERT: H 142 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8324 (mtpt) REVERT: H 186 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.8194 (mtp85) REVERT: H 268 THR cc_start: 0.8959 (m) cc_final: 0.8430 (p) REVERT: H 284 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8052 (mt) REVERT: H 310 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8329 (tppt) REVERT: H 329 GLN cc_start: 0.7913 (pt0) cc_final: 0.7542 (pt0) REVERT: H 332 SER cc_start: 0.9104 (t) cc_final: 0.8901 (p) REVERT: H 344 GLN cc_start: 0.8573 (tp40) cc_final: 0.8319 (tp40) REVERT: H 349 LEU cc_start: 0.8647 (mt) cc_final: 0.8415 (mp) outliers start: 160 outliers final: 112 residues processed: 671 average time/residue: 0.2001 time to fit residues: 197.9102 Evaluate side-chains 670 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 544 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 329 GLN Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 32 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN C 329 GLN E 329 GLN F 270 ASN H 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114146 restraints weight = 28788.031| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.68 r_work: 0.3199 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24488 Z= 0.204 Angle : 0.765 10.635 33360 Z= 0.382 Chirality : 0.044 0.203 3680 Planarity : 0.004 0.045 4128 Dihedral : 6.321 32.767 3168 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.87 % Favored : 89.57 % Rotamer: Outliers : 7.17 % Allowed : 22.31 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.72 (0.16), residues: 2856 helix: 0.87 (0.13), residues: 1752 sheet: -1.58 (0.39), residues: 184 loop : -2.97 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 146 TYR 0.017 0.002 TYR C 301 PHE 0.023 0.002 PHE G 242 TRP 0.013 0.001 TRP B 59 HIS 0.004 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00476 (24472) covalent geometry : angle 0.76197 (33328) SS BOND : bond 0.00675 ( 16) SS BOND : angle 2.20269 ( 32) hydrogen bonds : bond 0.04030 ( 1098) hydrogen bonds : angle 3.97519 ( 3270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 538 time to evaluate : 0.913 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8895 (t0) cc_final: 0.8286 (t0) REVERT: A 74 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: A 182 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8873 (ttmm) REVERT: A 184 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7756 (ttm-80) REVERT: A 186 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8183 (mtp85) REVERT: A 215 ASP cc_start: 0.7561 (t0) cc_final: 0.7267 (t0) REVERT: A 310 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8133 (tppt) REVERT: A 332 SER cc_start: 0.9184 (t) cc_final: 0.8981 (p) REVERT: A 348 ASN cc_start: 0.8788 (m-40) cc_final: 0.8445 (m110) REVERT: B 99 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8211 (ttmm) REVERT: B 142 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8370 (mtpt) REVERT: B 186 ARG cc_start: 0.8692 (mtt-85) cc_final: 0.8281 (mtp85) REVERT: B 268 THR cc_start: 0.8966 (m) cc_final: 0.8432 (p) REVERT: B 284 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8079 (mt) REVERT: B 310 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8349 (tppt) REVERT: B 329 GLN cc_start: 0.7956 (pt0) cc_final: 0.7582 (pt0) REVERT: B 344 GLN cc_start: 0.8599 (tp40) cc_final: 0.8361 (tp40) REVERT: B 349 LEU cc_start: 0.8691 (mt) cc_final: 0.8437 (mp) REVERT: C 70 ASN cc_start: 0.8906 (t0) cc_final: 0.8310 (t0) REVERT: C 74 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7187 (mt0) REVERT: C 102 ILE cc_start: 0.8850 (pt) cc_final: 0.8644 (pt) REVERT: C 157 LYS cc_start: 0.7914 (mttm) cc_final: 0.7708 (ptpt) REVERT: C 182 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8840 (ttmm) REVERT: C 184 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7789 (ttm-80) REVERT: C 186 ARG cc_start: 0.8613 (mtt-85) cc_final: 0.8189 (mtp85) REVERT: C 215 ASP cc_start: 0.7557 (t0) cc_final: 0.7267 (t0) REVERT: C 280 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7912 (mp) REVERT: C 284 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7884 (mt) REVERT: C 332 SER cc_start: 0.9192 (t) cc_final: 0.8976 (p) REVERT: C 348 ASN cc_start: 0.8867 (m-40) cc_final: 0.8573 (m110) REVERT: D 82 TYR cc_start: 0.9070 (p90) cc_final: 0.8857 (p90) REVERT: D 99 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8216 (ttmm) REVERT: D 142 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8328 (mtpt) REVERT: D 186 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.8406 (mtp180) REVERT: D 343 ASP cc_start: 0.8569 (m-30) cc_final: 0.8256 (m-30) REVERT: D 344 GLN cc_start: 0.8681 (tp40) cc_final: 0.8273 (tp40) REVERT: D 348 ASN cc_start: 0.8893 (m-40) cc_final: 0.8513 (m110) REVERT: D 349 LEU cc_start: 0.8659 (mt) cc_final: 0.8342 (mp) REVERT: E 70 ASN cc_start: 0.8905 (t0) cc_final: 0.8298 (t0) REVERT: E 74 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: E 102 ILE cc_start: 0.8853 (pt) cc_final: 0.8648 (pt) REVERT: E 127 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7847 (ttmm) REVERT: E 161 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6709 (ptm160) REVERT: E 182 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8875 (mtpp) REVERT: E 186 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8175 (mtp85) REVERT: E 280 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7881 (mp) REVERT: E 284 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7910 (mt) REVERT: E 332 SER cc_start: 0.9180 (t) cc_final: 0.8963 (p) REVERT: F 99 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8172 (ttmm) REVERT: F 142 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8345 (mtpt) REVERT: F 186 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8277 (mtp85) REVERT: F 284 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8122 (mt) REVERT: F 310 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8348 (tppt) REVERT: F 344 GLN cc_start: 0.8651 (tp40) cc_final: 0.8431 (tp40) REVERT: G 70 ASN cc_start: 0.8900 (t0) cc_final: 0.8291 (t0) REVERT: G 74 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7207 (mt0) REVERT: G 99 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8124 (ttmm) REVERT: G 127 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7859 (ttmm) REVERT: G 182 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8913 (mtpp) REVERT: G 186 ARG cc_start: 0.8616 (mtt-85) cc_final: 0.8178 (mtp85) REVERT: G 215 ASP cc_start: 0.7583 (t0) cc_final: 0.7291 (t0) REVERT: G 329 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: G 332 SER cc_start: 0.9185 (t) cc_final: 0.8977 (p) REVERT: G 348 ASN cc_start: 0.8844 (m-40) cc_final: 0.8543 (m110) REVERT: H 99 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8176 (ttmm) REVERT: H 142 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8378 (mtpt) REVERT: H 186 ARG cc_start: 0.8693 (mtt-85) cc_final: 0.8296 (mtp85) REVERT: H 284 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8112 (mt) REVERT: H 329 GLN cc_start: 0.7938 (pt0) cc_final: 0.7565 (pt0) REVERT: H 332 SER cc_start: 0.9087 (t) cc_final: 0.8884 (p) REVERT: H 344 GLN cc_start: 0.8601 (tp40) cc_final: 0.8366 (tp40) REVERT: H 349 LEU cc_start: 0.8705 (mt) cc_final: 0.8447 (mp) outliers start: 184 outliers final: 151 residues processed: 652 average time/residue: 0.1948 time to fit residues: 189.4059 Evaluate side-chains 692 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 524 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 337 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 149 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 GLN E 314 ASN F 270 ASN F 329 GLN H 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116034 restraints weight = 28435.964| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.67 r_work: 0.3223 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24488 Z= 0.174 Angle : 0.746 10.603 33360 Z= 0.370 Chirality : 0.044 0.182 3680 Planarity : 0.004 0.047 4128 Dihedral : 6.303 32.050 3168 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.33 % Favored : 89.11 % Rotamer: Outliers : 7.17 % Allowed : 22.98 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -0.61 (0.16), residues: 2856 helix: 1.02 (0.13), residues: 1752 sheet: -1.83 (0.38), residues: 192 loop : -3.00 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 146 TYR 0.017 0.002 TYR C 301 PHE 0.047 0.001 PHE C 242 TRP 0.012 0.001 TRP H 59 HIS 0.005 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00403 (24472) covalent geometry : angle 0.74360 (33328) SS BOND : bond 0.00476 ( 16) SS BOND : angle 2.02468 ( 32) hydrogen bonds : bond 0.03884 ( 1098) hydrogen bonds : angle 3.88308 ( 3270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 505 time to evaluate : 0.878 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8832 (t0) cc_final: 0.8264 (t0) REVERT: A 74 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7120 (mt0) REVERT: A 102 ILE cc_start: 0.8806 (pt) cc_final: 0.8595 (pt) REVERT: A 158 PHE cc_start: 0.7405 (m-80) cc_final: 0.7122 (m-10) REVERT: A 182 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8902 (mtpp) REVERT: A 184 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7703 (ttm-80) REVERT: A 186 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8192 (mtp85) REVERT: A 215 ASP cc_start: 0.7497 (t0) cc_final: 0.7201 (t0) REVERT: A 280 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7910 (mp) REVERT: A 284 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7843 (mt) REVERT: A 310 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8111 (tppt) REVERT: A 332 SER cc_start: 0.9170 (t) cc_final: 0.8962 (p) REVERT: A 348 ASN cc_start: 0.8663 (m-40) cc_final: 0.8221 (m-40) REVERT: B 99 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8181 (ttmm) REVERT: B 142 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8300 (mtpt) REVERT: B 186 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8268 (mtp85) REVERT: B 268 THR cc_start: 0.8893 (m) cc_final: 0.8382 (p) REVERT: B 284 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7789 (mt) REVERT: B 310 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8308 (tppt) REVERT: B 344 GLN cc_start: 0.8623 (tp40) cc_final: 0.8395 (tp40) REVERT: B 349 LEU cc_start: 0.8627 (mt) cc_final: 0.8360 (mp) REVERT: C 74 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7105 (mt0) REVERT: C 102 ILE cc_start: 0.8796 (pt) cc_final: 0.8575 (pt) REVERT: C 161 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.6781 (ptm160) REVERT: C 182 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8886 (mtpp) REVERT: C 184 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7758 (ttm-80) REVERT: C 186 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8220 (mtp85) REVERT: C 332 SER cc_start: 0.9176 (t) cc_final: 0.8970 (p) REVERT: D 99 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8188 (ttmm) REVERT: D 142 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8302 (mtpt) REVERT: D 186 ARG cc_start: 0.8720 (mtt-85) cc_final: 0.8251 (mtp85) REVERT: D 284 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8170 (mt) REVERT: D 344 GLN cc_start: 0.8632 (tp40) cc_final: 0.8204 (tp40) REVERT: D 348 ASN cc_start: 0.8910 (m-40) cc_final: 0.8533 (m110) REVERT: D 349 LEU cc_start: 0.8610 (mt) cc_final: 0.8299 (mp) REVERT: E 70 ASN cc_start: 0.8838 (t0) cc_final: 0.8277 (t0) REVERT: E 74 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7130 (mt0) REVERT: E 82 TYR cc_start: 0.9000 (p90) cc_final: 0.7685 (p90) REVERT: E 102 ILE cc_start: 0.8805 (pt) cc_final: 0.8589 (pt) REVERT: E 127 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7785 (ttmm) REVERT: E 182 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8920 (mtpp) REVERT: E 186 ARG cc_start: 0.8622 (mtt-85) cc_final: 0.8173 (mtp85) REVERT: E 215 ASP cc_start: 0.7497 (t0) cc_final: 0.7217 (t0) REVERT: E 280 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7815 (mp) REVERT: E 284 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7839 (mt) REVERT: E 332 SER cc_start: 0.9165 (t) cc_final: 0.8957 (p) REVERT: F 82 TYR cc_start: 0.9043 (p90) cc_final: 0.8826 (p90) REVERT: F 99 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8139 (ttmm) REVERT: F 142 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8320 (mtpt) REVERT: F 186 ARG cc_start: 0.8635 (mtt-85) cc_final: 0.8255 (mtp85) REVERT: F 284 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7983 (mt) REVERT: F 310 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8323 (tppt) REVERT: G 74 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: G 99 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8113 (ttmm) REVERT: G 102 ILE cc_start: 0.8829 (pt) cc_final: 0.8598 (pt) REVERT: G 127 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7801 (ttmm) REVERT: G 154 LYS cc_start: 0.8616 (pttp) cc_final: 0.7826 (pptt) REVERT: G 182 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8911 (mtpp) REVERT: G 186 ARG cc_start: 0.8632 (mtt-85) cc_final: 0.8196 (mtp85) REVERT: G 215 ASP cc_start: 0.7531 (t0) cc_final: 0.7246 (t0) REVERT: G 280 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7905 (mp) REVERT: G 284 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7824 (mt) REVERT: G 332 SER cc_start: 0.9160 (t) cc_final: 0.8947 (p) REVERT: H 99 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8143 (ttmm) REVERT: H 142 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8250 (mtpt) REVERT: H 186 ARG cc_start: 0.8696 (mtt-85) cc_final: 0.8290 (mtp85) REVERT: H 284 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8070 (mt) REVERT: H 329 GLN cc_start: 0.7851 (pt0) cc_final: 0.7475 (pt0) REVERT: H 332 SER cc_start: 0.9071 (t) cc_final: 0.8868 (p) REVERT: H 344 GLN cc_start: 0.8540 (tp40) cc_final: 0.8312 (tp40) REVERT: H 349 LEU cc_start: 0.8641 (mt) cc_final: 0.8389 (mp) outliers start: 184 outliers final: 153 residues processed: 625 average time/residue: 0.1875 time to fit residues: 175.0033 Evaluate side-chains 670 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 498 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 154 optimal weight: 0.8980 chunk 240 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN C 270 ASN D 329 GLN E 314 ASN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121522 restraints weight = 28126.229| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.70 r_work: 0.3306 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24488 Z= 0.122 Angle : 0.717 9.921 33360 Z= 0.354 Chirality : 0.042 0.181 3680 Planarity : 0.004 0.045 4128 Dihedral : 6.034 32.606 3168 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.66 % Favored : 89.78 % Rotamer: Outliers : 4.98 % Allowed : 25.43 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.35 (0.16), residues: 2856 helix: 1.24 (0.13), residues: 1760 sheet: -1.75 (0.38), residues: 192 loop : -2.96 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 146 TYR 0.018 0.001 TYR C 301 PHE 0.042 0.001 PHE C 242 TRP 0.013 0.001 TRP B 107 HIS 0.002 0.000 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00255 (24472) covalent geometry : angle 0.71546 (33328) SS BOND : bond 0.00264 ( 16) SS BOND : angle 1.68992 ( 32) hydrogen bonds : bond 0.03284 ( 1098) hydrogen bonds : angle 3.68167 ( 3270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 529 time to evaluate : 0.998 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8768 (t0) cc_final: 0.8192 (t0) REVERT: A 74 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7074 (mt0) REVERT: A 102 ILE cc_start: 0.8738 (pt) cc_final: 0.8486 (pt) REVERT: A 158 PHE cc_start: 0.7267 (m-80) cc_final: 0.6983 (m-80) REVERT: A 182 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8880 (mtpp) REVERT: A 184 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7619 (ttm-80) REVERT: A 186 ARG cc_start: 0.8563 (mtt-85) cc_final: 0.7979 (mtp85) REVERT: A 215 ASP cc_start: 0.7498 (t0) cc_final: 0.7235 (t0) REVERT: A 284 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 300 TYR cc_start: 0.8587 (t80) cc_final: 0.8191 (t80) REVERT: A 332 SER cc_start: 0.9170 (t) cc_final: 0.8961 (p) REVERT: B 99 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8064 (tppp) REVERT: B 142 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8220 (mtpt) REVERT: B 182 LYS cc_start: 0.9264 (mtmm) cc_final: 0.8983 (mtpp) REVERT: B 186 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.8210 (mtp85) REVERT: B 268 THR cc_start: 0.8890 (m) cc_final: 0.8376 (p) REVERT: B 284 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7984 (mt) REVERT: B 310 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8310 (tppt) REVERT: B 344 GLN cc_start: 0.8595 (tp40) cc_final: 0.8262 (tp40) REVERT: B 348 ASN cc_start: 0.8843 (m-40) cc_final: 0.8549 (m110) REVERT: C 70 ASN cc_start: 0.8767 (t0) cc_final: 0.8178 (t0) REVERT: C 74 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6976 (mt0) REVERT: C 82 TYR cc_start: 0.8887 (p90) cc_final: 0.8108 (p90) REVERT: C 102 ILE cc_start: 0.8781 (pt) cc_final: 0.8535 (pt) REVERT: C 182 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8884 (mtpp) REVERT: C 184 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7713 (ttm-80) REVERT: C 186 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.8032 (mtp85) REVERT: C 284 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7801 (mt) REVERT: C 300 TYR cc_start: 0.8565 (t80) cc_final: 0.8158 (t80) REVERT: C 332 SER cc_start: 0.9168 (t) cc_final: 0.8957 (p) REVERT: D 99 LYS cc_start: 0.8404 (ttmt) cc_final: 0.8048 (tppp) REVERT: D 102 ILE cc_start: 0.8749 (pt) cc_final: 0.8545 (pt) REVERT: D 142 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8247 (mtpt) REVERT: D 186 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.8212 (mtp85) REVERT: D 284 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8098 (mt) REVERT: D 344 GLN cc_start: 0.8628 (tp40) cc_final: 0.8220 (tp40) REVERT: D 348 ASN cc_start: 0.8881 (m-40) cc_final: 0.8474 (m110) REVERT: D 349 LEU cc_start: 0.8497 (mt) cc_final: 0.8207 (mp) REVERT: E 70 ASN cc_start: 0.8775 (t0) cc_final: 0.8205 (t0) REVERT: E 74 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7094 (mt0) REVERT: E 82 TYR cc_start: 0.8911 (p90) cc_final: 0.7887 (p90) REVERT: E 102 ILE cc_start: 0.8788 (pt) cc_final: 0.8539 (pt) REVERT: E 127 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7830 (ttmm) REVERT: E 182 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8941 (mtpp) REVERT: E 186 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.8175 (mtp85) REVERT: E 215 ASP cc_start: 0.7499 (t0) cc_final: 0.7248 (t0) REVERT: E 284 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7782 (mt) REVERT: E 307 LYS cc_start: 0.8132 (tmmt) cc_final: 0.7738 (tmmt) REVERT: E 332 SER cc_start: 0.9161 (t) cc_final: 0.8950 (p) REVERT: F 99 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8122 (ttmm) REVERT: F 102 ILE cc_start: 0.8789 (pt) cc_final: 0.8568 (pt) REVERT: F 142 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8208 (mtpt) REVERT: F 186 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.8236 (mtp85) REVERT: F 268 THR cc_start: 0.8928 (m) cc_final: 0.8444 (p) REVERT: F 284 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7975 (mt) REVERT: F 310 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8220 (tppt) REVERT: G 70 ASN cc_start: 0.8753 (t0) cc_final: 0.8157 (t0) REVERT: G 74 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.6979 (mt0) REVERT: G 82 TYR cc_start: 0.8897 (p90) cc_final: 0.7883 (p90) REVERT: G 99 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8115 (ttmm) REVERT: G 102 ILE cc_start: 0.8785 (pt) cc_final: 0.8512 (pt) REVERT: G 127 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7848 (ttmm) REVERT: G 154 LYS cc_start: 0.8621 (pttp) cc_final: 0.7894 (pptt) REVERT: G 182 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8886 (mtpp) REVERT: G 186 ARG cc_start: 0.8571 (mtt-85) cc_final: 0.8010 (mtp85) REVERT: G 215 ASP cc_start: 0.7524 (t0) cc_final: 0.7265 (t0) REVERT: G 284 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7791 (mt) REVERT: G 307 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7723 (tmmt) REVERT: G 332 SER cc_start: 0.9151 (t) cc_final: 0.8934 (p) REVERT: H 99 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8102 (tppp) REVERT: H 142 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8220 (mtpt) REVERT: H 186 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.8226 (mtp85) REVERT: H 268 THR cc_start: 0.8942 (m) cc_final: 0.8459 (p) REVERT: H 284 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8007 (mt) REVERT: H 329 GLN cc_start: 0.7820 (pt0) cc_final: 0.7402 (pt0) REVERT: H 344 GLN cc_start: 0.8572 (tp40) cc_final: 0.8239 (tp40) REVERT: H 348 ASN cc_start: 0.8762 (m-40) cc_final: 0.8476 (m110) outliers start: 128 outliers final: 107 residues processed: 611 average time/residue: 0.1953 time to fit residues: 177.8921 Evaluate side-chains 633 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 510 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 29 ARG Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 301 TYR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 96 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 155 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 241 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 329 GLN D 329 GLN E 314 ASN F 314 ASN F 329 GLN G 314 ASN H 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.158226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123096 restraints weight = 28093.655| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.68 r_work: 0.3326 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24488 Z= 0.119 Angle : 0.715 12.213 33360 Z= 0.348 Chirality : 0.041 0.177 3680 Planarity : 0.004 0.043 4128 Dihedral : 5.920 32.010 3168 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.49 % Favored : 89.95 % Rotamer: Outliers : 4.56 % Allowed : 25.58 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.23 (0.16), residues: 2856 helix: 1.36 (0.13), residues: 1760 sheet: -1.77 (0.38), residues: 192 loop : -2.95 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 146 TYR 0.026 0.001 TYR F 300 PHE 0.042 0.001 PHE C 242 TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00251 (24472) covalent geometry : angle 0.71394 (33328) SS BOND : bond 0.00280 ( 16) SS BOND : angle 1.65719 ( 32) hydrogen bonds : bond 0.03113 ( 1098) hydrogen bonds : angle 3.57606 ( 3270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 537 time to evaluate : 0.917 Fit side-chains TARDY: cannot create tardy model for: "ASP A 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 28 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP D 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP F 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP G 28 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP H 28 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8676 (t0) cc_final: 0.8138 (t0) REVERT: A 74 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7184 (mt0) REVERT: A 82 TYR cc_start: 0.8863 (p90) cc_final: 0.8215 (p90) REVERT: A 102 ILE cc_start: 0.8791 (pt) cc_final: 0.8511 (pt) REVERT: A 182 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8925 (mtpp) REVERT: A 186 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.8059 (mtp85) REVERT: A 284 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 300 TYR cc_start: 0.8605 (t80) cc_final: 0.8207 (t80) REVERT: A 332 SER cc_start: 0.9172 (t) cc_final: 0.8966 (p) REVERT: B 33 ARG cc_start: 0.5665 (ttm-80) cc_final: 0.5400 (ttm110) REVERT: B 99 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8122 (tppp) REVERT: B 182 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8963 (mtpp) REVERT: B 183 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7841 (pttm) REVERT: B 186 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.8234 (mtp85) REVERT: B 268 THR cc_start: 0.8903 (m) cc_final: 0.8405 (p) REVERT: B 284 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8090 (mt) REVERT: B 300 TYR cc_start: 0.8527 (t80) cc_final: 0.8307 (t80) REVERT: B 310 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8234 (tppt) REVERT: B 344 GLN cc_start: 0.8677 (tp40) cc_final: 0.8338 (tp40) REVERT: B 348 ASN cc_start: 0.8909 (m-40) cc_final: 0.8626 (m110) REVERT: C 70 ASN cc_start: 0.8668 (t0) cc_final: 0.8161 (t0) REVERT: C 74 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7168 (mt0) REVERT: C 82 TYR cc_start: 0.8853 (p90) cc_final: 0.8331 (p90) REVERT: C 102 ILE cc_start: 0.8794 (pt) cc_final: 0.8504 (pt) REVERT: C 182 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8842 (mtpp) REVERT: C 184 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7675 (ttm-80) REVERT: C 186 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.7642 (mmt90) REVERT: C 284 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7929 (mt) REVERT: C 300 TYR cc_start: 0.8573 (t80) cc_final: 0.8169 (t80) REVERT: D 99 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8128 (tppp) REVERT: D 102 ILE cc_start: 0.8820 (pt) cc_final: 0.8587 (pt) REVERT: D 142 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8270 (mtpt) REVERT: D 186 ARG cc_start: 0.8499 (mtt-85) cc_final: 0.8214 (mtp85) REVERT: D 300 TYR cc_start: 0.8564 (t80) cc_final: 0.8326 (t80) REVERT: D 344 GLN cc_start: 0.8705 (tp40) cc_final: 0.8294 (tp40) REVERT: D 348 ASN cc_start: 0.8944 (m-40) cc_final: 0.8566 (m110) REVERT: D 349 LEU cc_start: 0.8488 (mt) cc_final: 0.8223 (mp) REVERT: E 74 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7209 (mt0) REVERT: E 82 TYR cc_start: 0.8890 (p90) cc_final: 0.8039 (p90) REVERT: E 102 ILE cc_start: 0.8806 (pt) cc_final: 0.8525 (pt) REVERT: E 127 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7946 (ttmm) REVERT: E 182 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8905 (mtpp) REVERT: E 186 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.8012 (mtp85) REVERT: E 210 LEU cc_start: 0.8764 (tt) cc_final: 0.8478 (tp) REVERT: E 284 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7932 (mt) REVERT: E 307 LYS cc_start: 0.8084 (tmmt) cc_final: 0.7765 (tmmt) REVERT: E 332 SER cc_start: 0.9171 (t) cc_final: 0.8959 (p) REVERT: F 99 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8176 (ttmm) REVERT: F 102 ILE cc_start: 0.8843 (pt) cc_final: 0.8613 (pt) REVERT: F 142 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8250 (mtpt) REVERT: F 268 THR cc_start: 0.8852 (m) cc_final: 0.8372 (p) REVERT: F 284 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7918 (mt) REVERT: F 310 LYS cc_start: 0.8455 (ttpt) cc_final: 0.8253 (tppt) REVERT: G 70 ASN cc_start: 0.8655 (t0) cc_final: 0.8139 (t0) REVERT: G 74 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7188 (mt0) REVERT: G 82 TYR cc_start: 0.8874 (p90) cc_final: 0.8110 (p90) REVERT: G 99 LYS cc_start: 0.8261 (ttmt) cc_final: 0.8015 (ttmm) REVERT: G 102 ILE cc_start: 0.8818 (pt) cc_final: 0.8522 (pt) REVERT: G 127 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7960 (ttmm) REVERT: G 154 LYS cc_start: 0.8604 (pttp) cc_final: 0.7826 (pptt) REVERT: G 155 ASP cc_start: 0.7612 (t0) cc_final: 0.7289 (t0) REVERT: G 182 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8908 (mtpp) REVERT: G 186 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.8091 (mtp85) REVERT: G 210 LEU cc_start: 0.8753 (tt) cc_final: 0.8464 (tp) REVERT: G 284 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7938 (mt) REVERT: G 307 LYS cc_start: 0.8066 (tmmt) cc_final: 0.7707 (tmmt) REVERT: G 332 SER cc_start: 0.9159 (t) cc_final: 0.8941 (p) REVERT: H 99 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8169 (tppp) REVERT: H 102 ILE cc_start: 0.8827 (pt) cc_final: 0.8603 (pt) REVERT: H 142 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8307 (mtpt) REVERT: H 186 ARG cc_start: 0.8435 (mtt-85) cc_final: 0.8210 (mtp85) REVERT: H 268 THR cc_start: 0.8949 (m) cc_final: 0.8436 (p) REVERT: H 284 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8122 (mt) REVERT: H 343 ASP cc_start: 0.8473 (m-30) cc_final: 0.8149 (m-30) REVERT: H 344 GLN cc_start: 0.8700 (tp40) cc_final: 0.8381 (tp40) REVERT: H 348 ASN cc_start: 0.8944 (m-40) cc_final: 0.8703 (m110) outliers start: 117 outliers final: 96 residues processed: 608 average time/residue: 0.1971 time to fit residues: 178.3503 Evaluate side-chains 621 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 510 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 337 ASP Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 301 TYR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 210 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 285 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN B 329 GLN D 329 GLN F 314 ASN F 329 GLN G 314 ASN H 314 ASN H 329 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123267 restraints weight = 27960.582| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.69 r_work: 0.3358 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24488 Z= 0.120 Angle : 0.713 11.634 33360 Z= 0.346 Chirality : 0.041 0.177 3680 Planarity : 0.004 0.044 4128 Dihedral : 5.889 32.161 3168 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.56 % Favored : 90.02 % Rotamer: Outliers : 5.10 % Allowed : 25.74 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.17 (0.16), residues: 2856 helix: 1.42 (0.13), residues: 1760 sheet: -1.74 (0.38), residues: 192 loop : -2.95 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 168 TYR 0.018 0.001 TYR H 300 PHE 0.047 0.001 PHE H 242 TRP 0.010 0.001 TRP C 107 HIS 0.001 0.000 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00260 (24472) covalent geometry : angle 0.71101 (33328) SS BOND : bond 0.00305 ( 16) SS BOND : angle 1.66769 ( 32) hydrogen bonds : bond 0.03095 ( 1098) hydrogen bonds : angle 3.54674 ( 3270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5818.48 seconds wall clock time: 100 minutes 33.95 seconds (6033.95 seconds total)