Starting phenix.real_space_refine on Fri Aug 7 02:32:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zrj_74618/08_2026/9zrj_74618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zrj_74618/08_2026/9zrj_74618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zrj_74618/08_2026/9zrj_74618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zrj_74618/08_2026/9zrj_74618.map" model { file = "/net/cci-nas-00/data/ceres_data/9zrj_74618/08_2026/9zrj_74618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zrj_74618/08_2026/9zrj_74618.cif" } resolution = 3.4 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= -0.001 sd= 0.021 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 22 5.16 5 C 11630 2.51 5 N 3106 2.21 5 O 3496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18254 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2947 Classifications: {'peptide': 410} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 398} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 2931 Classifications: {'peptide': 409} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 1, 'PHE:plan': 1, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3020 Classifications: {'peptide': 410} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 11, 'TRANS': 398} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3012 Classifications: {'peptide': 409} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 11, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3044 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3030 Classifications: {'peptide': 410} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 4.28, per 1000 atoms: 0.23 Number of scatterers: 18254 At special positions: 0 Unit cell: (138.46, 135.88, 134.16, 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 22 16.00 O 3496 8.00 N 3106 7.00 C 11630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 839.3 milliseconds 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4630 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 35 sheets defined 23.5% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.941A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 122' Processing helix chain 'A' and resid 184 through 188 removed outlier: 4.314A pdb=" N GLN A 187 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.825A pdb=" N ALA A 226 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.586A pdb=" N LYS A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.688A pdb=" N ASP A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 421 through 428 removed outlier: 4.310A pdb=" N SER A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASN A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 454 Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.614A pdb=" N SER B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 removed outlier: 3.843A pdb=" N VAL B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 removed outlier: 4.372A pdb=" N GLN B 187 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 4.240A pdb=" N ALA B 226 " --> pdb=" O ARG B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 4.083A pdb=" N LYS B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.707A pdb=" N LEU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 324 removed outlier: 3.709A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 399 through 406 Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.463A pdb=" N SER B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 184 through 188 removed outlier: 4.438A pdb=" N GLN C 187 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.898A pdb=" N ALA C 226 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.536A pdb=" N LYS C 272 " --> pdb=" O ASP C 268 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 Processing helix chain 'C' and resid 318 through 324 removed outlier: 3.510A pdb=" N GLY C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 352 Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 423 through 427 removed outlier: 3.988A pdb=" N ASN C 427 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 454 Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 117 through 122 removed outlier: 4.127A pdb=" N VAL D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 122 " --> pdb=" O SER D 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 122' Processing helix chain 'D' and resid 184 through 188 removed outlier: 4.232A pdb=" N GLN D 187 " --> pdb=" O SER D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 226 removed outlier: 4.013A pdb=" N ALA D 226 " --> pdb=" O ARG D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 removed outlier: 3.813A pdb=" N SER D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D 266 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 273 " --> pdb=" O PHE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.608A pdb=" N LEU D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 324 removed outlier: 3.638A pdb=" N LYS D 322 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 352 removed outlier: 3.577A pdb=" N ASP D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE D 352 " --> pdb=" O TYR D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 399 through 406 Processing helix chain 'D' and resid 421 through 426 removed outlier: 3.985A pdb=" N SER D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 453 Processing helix chain 'E' and resid 46 through 59 removed outlier: 3.745A pdb=" N SER E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.997A pdb=" N VAL E 121 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 122' Processing helix chain 'E' and resid 184 through 188 removed outlier: 4.168A pdb=" N GLN E 187 " --> pdb=" O SER E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.768A pdb=" N ASP E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 300 removed outlier: 4.067A pdb=" N LEU E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 324 removed outlier: 3.792A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 350 Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 399 through 406 removed outlier: 3.504A pdb=" N LYS E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 428 Processing helix chain 'E' and resid 446 through 454 Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.890A pdb=" N VAL F 121 " --> pdb=" O ASN F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 173 removed outlier: 4.065A pdb=" N LYS F 172 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU F 173 " --> pdb=" O SER F 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 169 through 173' Processing helix chain 'F' and resid 260 through 271 removed outlier: 3.961A pdb=" N SER F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR F 266 " --> pdb=" O ASN F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 299 removed outlier: 3.866A pdb=" N LEU F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 352 removed outlier: 3.662A pdb=" N VAL F 345 " --> pdb=" O VAL F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 386 Processing helix chain 'F' and resid 399 through 406 Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 446 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 69 removed outlier: 6.009A pdb=" N ILE A 101 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 115 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 150 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS A 144 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 152 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU A 156 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LYS A 138 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 127 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.675A pdb=" N GLY A 199 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE A 214 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE A 256 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 237 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 232 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 338 removed outlier: 5.821A pdb=" N ILE A 331 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 363 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 397 removed outlier: 5.765A pdb=" N TYR A 396 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL A 417 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 393 through 397 removed outlier: 5.765A pdb=" N TYR A 396 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL A 417 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE A 436 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 464 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A 438 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 69 removed outlier: 6.395A pdb=" N ILE B 101 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 115 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 103 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 150 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS B 144 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 152 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 156 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS B 138 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B 127 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 178 through 183 removed outlier: 3.864A pdb=" N GLY B 199 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE B 214 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE B 256 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AB1, first strand: chain 'B' and resid 337 through 338 removed outlier: 6.682A pdb=" N GLU B 361 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL B 334 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN B 359 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 393 through 397 removed outlier: 3.767A pdb=" N TYR B 419 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B 396 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL B 417 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 442 through 443 removed outlier: 6.875A pdb=" N LYS B 462 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL B 439 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B 460 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 137 through 138 removed outlier: 6.126A pdb=" N ILE C 101 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 115 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY C 103 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 152 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 143 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER C 154 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU C 141 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 178 through 183 removed outlier: 3.565A pdb=" N GLY C 199 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE C 214 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE C 256 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU C 230 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 279 through 280 removed outlier: 3.532A pdb=" N ALA C 376 " --> pdb=" O TRP C 280 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 285 Processing sheet with id=AB8, first strand: chain 'C' and resid 330 through 334 removed outlier: 5.547A pdb=" N ILE C 331 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 363 " --> pdb=" O ILE C 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 393 through 397 removed outlier: 6.812A pdb=" N VAL C 394 " --> pdb=" O ASP C 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 393 through 397 removed outlier: 6.812A pdb=" N VAL C 394 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE C 436 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 464 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 136 through 138 removed outlier: 3.622A pdb=" N VAL D 100 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR D 113 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY D 143 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N SER D 154 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU D 141 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 2 through 4 removed outlier: 3.647A pdb=" N ILE D 244 " --> pdb=" O UNK J 3 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE D 256 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY D 199 " --> pdb=" O GLN D 216 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU D 230 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AC5, first strand: chain 'D' and resid 330 through 334 removed outlier: 6.742A pdb=" N GLU D 361 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL D 334 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN D 359 " --> pdb=" O VAL D 334 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 394 through 396 removed outlier: 6.573A pdb=" N VAL D 394 " --> pdb=" O ASP D 418 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 435 through 439 removed outlier: 6.273A pdb=" N ILE D 436 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU D 464 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER D 438 " --> pdb=" O LYS D 462 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 62 through 69 removed outlier: 3.675A pdb=" N VAL E 100 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR E 113 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG E 104 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU E 111 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY E 143 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER E 154 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU E 141 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N GLU E 156 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ALA E 139 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU E 127 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.675A pdb=" N ILE E 244 " --> pdb=" O UNK K 4 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE E 256 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N PHE E 214 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY E 199 " --> pdb=" O GLN E 216 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 230 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 283 through 285 Processing sheet with id=AD2, first strand: chain 'E' and resid 337 through 338 removed outlier: 5.772A pdb=" N ILE E 331 " --> pdb=" O LEU E 363 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU E 363 " --> pdb=" O ILE E 331 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 393 through 396 removed outlier: 5.938A pdb=" N TYR E 396 " --> pdb=" O VAL E 417 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL E 417 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS E 462 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL E 439 " --> pdb=" O THR E 460 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR E 460 " --> pdb=" O VAL E 439 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 62 through 69 removed outlier: 6.227A pdb=" N ILE F 101 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL F 115 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY F 103 " --> pdb=" O TYR F 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 152 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY F 143 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER F 154 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU F 141 " --> pdb=" O SER F 154 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLU F 156 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA F 139 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU F 127 " --> pdb=" O ALA F 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 191 through 195 removed outlier: 3.694A pdb=" N GLY F 239 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE F 256 " --> pdb=" O ALA F 242 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N PHE F 214 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY F 199 " --> pdb=" O GLN F 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 283 through 285 Processing sheet with id=AD7, first strand: chain 'F' and resid 330 through 334 removed outlier: 5.757A pdb=" N ILE F 331 " --> pdb=" O LEU F 363 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 363 " --> pdb=" O ILE F 331 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL F 367 " --> pdb=" O ARG F 364 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 393 through 396 removed outlier: 3.833A pdb=" N TYR F 419 " --> pdb=" O VAL F 394 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR F 396 " --> pdb=" O VAL F 417 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL F 417 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 438 " --> pdb=" O LYS F 462 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1902 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: 3.47 Time building geometry restraints manager: 2.05 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: 6003 1.34 - 1.46: 4089 1.46 - 1.58: 8396 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 18532 Sorted by residual: bond pdb=" CA ASN C 370 " pdb=" CB ASN C 370 " ideal model delta sigma weight residual 1.536 1.578 -0.042 2.53e-02 1.56e+03 2.73e+00 bond pdb=" CB GLN C 405 " pdb=" CG GLN C 405 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CB ASN C 370 " pdb=" CG ASN C 370 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" CB ASN A 407 " pdb=" CG ASN A 407 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" C LEU C 390 " pdb=" N PRO C 391 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.06e+00 ... (remaining 18527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 24861 1.88 - 3.75: 244 3.75 - 5.63: 36 5.63 - 7.50: 8 7.50 - 9.38: 5 Bond angle restraints: 25154 Sorted by residual: angle pdb=" C ALA E 404 " pdb=" N GLN E 405 " pdb=" CA GLN E 405 " ideal model delta sigma weight residual 122.56 115.04 7.52 1.72e+00 3.38e-01 1.91e+01 angle pdb=" CA LYS B 172 " pdb=" CB LYS B 172 " pdb=" CG LYS B 172 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" C ASN E 222 " pdb=" N ARG E 223 " pdb=" CA ARG E 223 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 angle pdb=" CA GLN E 405 " pdb=" CB GLN E 405 " pdb=" CG GLN E 405 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CB MET F 430 " pdb=" CG MET F 430 " pdb=" SD MET F 430 " ideal model delta sigma weight residual 112.70 122.08 -9.38 3.00e+00 1.11e-01 9.77e+00 ... (remaining 25149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 9528 17.84 - 35.68: 1194 35.68 - 53.52: 266 53.52 - 71.37: 48 71.37 - 89.21: 9 Dihedral angle restraints: 11045 sinusoidal: 3861 harmonic: 7184 Sorted by residual: dihedral pdb=" CA LEU C 390 " pdb=" C LEU C 390 " pdb=" N PRO C 391 " pdb=" CA PRO C 391 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP C 381 " pdb=" CB ASP C 381 " pdb=" CG ASP C 381 " pdb=" OD1 ASP C 381 " ideal model delta sinusoidal sigma weight residual -30.00 -89.19 59.19 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP D 292 " pdb=" CB ASP D 292 " pdb=" CG ASP D 292 " pdb=" OD1 ASP D 292 " ideal model delta sinusoidal sigma weight residual -30.00 -88.95 58.95 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 11042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1864 0.031 - 0.062: 688 0.062 - 0.094: 193 0.094 - 0.125: 244 0.125 - 0.156: 24 Chirality restraints: 3013 Sorted by residual: chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA GLU C 53 " pdb=" N GLU C 53 " pdb=" C GLU C 53 " pdb=" CB GLU C 53 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE A 258 " pdb=" N ILE A 258 " pdb=" C ILE A 258 " pdb=" CB ILE A 258 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 3010 not shown) Planarity restraints: 3215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 49 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C ASP C 49 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP C 49 " -0.014 2.00e-02 2.50e+03 pdb=" N SER C 50 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 396 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO E 397 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 397 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 397 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 396 " 0.031 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 397 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 397 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 397 " 0.027 5.00e-02 4.00e+02 ... (remaining 3212 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1814 2.75 - 3.29: 16831 3.29 - 3.82: 28492 3.82 - 4.36: 30642 4.36 - 4.90: 57517 Nonbonded interactions: 135296 Sorted by model distance: nonbonded pdb=" O GLU F 383 " pdb=" OG SER F 387 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR A 286 " pdb=" O VAL A 395 " model vdw 2.228 3.040 nonbonded pdb=" O ASP E 401 " pdb=" NE2 GLN E 405 " model vdw 2.253 3.120 nonbonded pdb=" O SER D 170 " pdb=" OG SER D 170 " model vdw 2.265 3.040 nonbonded pdb=" OG SER C 118 " pdb=" OD1 ASP C 149 " model vdw 2.283 3.040 ... (remaining 135291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 71 or resid 92 through 104 or (res \ id 105 through 107 and (name N or name CA or name C or name O or name CB )) or r \ esid 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) \ or resid 110 through 121 or (resid 122 through 124 and (name N or name CA or nam \ e C or name O or name CB )) or resid 125 through 127 or (resid 128 and (name N o \ r name CA or name C or name O or name CB )) or resid 129 through 133 or (resid 1 \ 34 through 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 146 or (resid 147 and (name N or name CA or name C or name O or nam \ e CB )) or resid 148 through 186 or (resid 187 and (name N or name CA or name C \ or name O or name CB )) or resid 188 or (resid 189 and (name N or name CA or nam \ e C or name O or name CB )) or resid 190 through 205 or (resid 206 through 208 a \ nd (name N or name CA or name C or name O or name CB )) or resid 209 through 287 \ or (resid 288 through 289 and (name N or name CA or name C or name O or name CB \ )) or resid 290 or (resid 291 through 292 and (name N or name CA or name C or n \ ame O or name CB )) or resid 293 or (resid 294 and (name N or name CA or name C \ or name O or name CB )) or resid 295 or (resid 296 through 297 and (name N or na \ me CA or name C or name O or name CB )) or resid 298 through 304 or (resid 305 t \ hrough 309 and (name N or name CA or name C or name O or name CB )) or resid 310 \ through 328 or (resid 329 and (name N or name CA or name C or name O or name CB \ )) or resid 330 through 331 or (resid 332 and (name N or name CA or name C or n \ ame O or name CB )) or resid 333 through 343 or (resid 344 and (name N or name C \ A or name C or name O or name CB )) or resid 345 through 349 or (resid 350 and ( \ name N or name CA or name C or name O or name CB )) or resid 351 through 355 or \ (resid 356 and (name N or name CA or name C or name O or name CB )) or resid 357 \ through 360 or (resid 361 and (name N or name CA or name C or name O or name CB \ )) or resid 362 through 365 or (resid 366 and (name N or name CA or name C or n \ ame O or name CB )) or resid 367 or (resid 368 and (name N or name CA or name C \ or name O or name CB )) or resid 369 through 371 or (resid 372 and (name N or na \ me CA or name C or name O or name CB )) or resid 373 through 380 or (resid 381 t \ hrough 384 and (name N or name CA or name C or name O or name CB )) or resid 385 \ through 389 or (resid 390 and (name N or name CA or name C or name O or name CB \ )) or resid 391 through 397 or (resid 398 and (name N or name CA or name C or n \ ame O or name CB )) or resid 399 through 402 or (resid 403 through 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 406 or (res \ id 407 through 411 and (name N or name CA or name C or name O or name CB )) or r \ esid 414 through 417 or (resid 418 and (name N or name CA or name C or name O or \ name CB )) or resid 419 through 422 or (resid 423 through 431 and (name N or na \ me CA or name C or name O or name CB )) or resid 432 through 433 or (resid 434 a \ nd (name N or name CA or name C or name O or name CB )) or resid 435 or (resid 4 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 437 through \ 439 or (resid 440 and (name N or name CA or name C or name O or name CB )) or r \ esid 441 through 453 or (resid 454 through 456 and (name N or name CA or name C \ or name O or name CB )) or resid 457 through 463 or (resid 464 through 465 and ( \ name N or name CA or name C or name O or name CB )) or resid 466 through 469 or \ (resid 470 through 472 and (name N or name CA or name C or name O or name CB )) \ or resid 473 or (resid 474 and (name N or name CA or name C or name O or name CB \ or name OXT)))) selection = (chain 'B' and (resid 46 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 69 or (resid 70 through \ 71 and (name N or name CA or name C or name O or name CB )) or resid 92 through \ 104 or (resid 105 through 107 and (name N or name CA or name C or name O or nam \ e CB )) or resid 108 or (resid 109 and (name N or name CA or name C or name O or \ name CB )) or resid 110 through 121 or (resid 122 through 124 and (name N or na \ me CA or name C or name O or name CB )) or resid 125 or (resid 126 and (name N o \ r name CA or name C or name O or name CB )) or resid 127 through 134 or (resid 1 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 136 through \ 155 or (resid 156 and (name N or name CA or name C or name O or name CB )) or r \ esid 157 or (resid 158 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 160 or (resid 161 and (name N or name CA or name C or name \ O or name CB )) or resid 162 through 205 or (resid 206 through 208 and (name N o \ r name CA or name C or name O or name CB )) or resid 209 through 246 or (resid 2 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 248 through \ 271 or (resid 272 and (name N or name CA or name C or name O or name CB )) or ( \ resid 273 through 277 and (name N or name CA or name C or name O or name CB )) o \ r resid 278 through 287 or (resid 288 through 289 and (name N or name CA or name \ C or name O or name CB )) or resid 290 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 296 or (resid 29 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 298 through \ 301 or (resid 302 through 309 and (name N or name CA or name C or name O or name \ CB )) or resid 310 through 331 or (resid 332 and (name N or name CA or name C o \ r name O or name CB )) or resid 333 through 349 or (resid 350 and (name N or nam \ e CA or name C or name O or name CB )) or resid 351 through 355 or (resid 356 an \ d (name N or name CA or name C or name O or name CB )) or resid 357 through 360 \ or (resid 361 and (name N or name CA or name C or name O or name CB )) or resid \ 362 through 365 or (resid 366 and (name N or name CA or name C or name O or name \ CB )) or resid 367 through 371 or (resid 372 and (name N or name CA or name C o \ r name O or name CB )) or resid 373 through 378 or (resid 379 through 384 and (n \ ame N or name CA or name C or name O or name CB )) or resid 385 through 386 or ( \ resid 387 through 390 and (name N or name CA or name C or name O or name CB )) o \ r resid 391 through 399 or (resid 400 and (name N or name CA or name C or name O \ or name CB )) or resid 401 through 402 or (resid 403 through 404 and (name N or \ name CA or name C or name O or name CB )) or resid 405 through 408 or (resid 40 \ 9 through 411 and (name N or name CA or name C or name O or name CB )) or resid \ 414 through 417 or (resid 418 and (name N or name CA or name C or name O or name \ CB )) or resid 419 through 433 or (resid 434 and (name N or name CA or name C o \ r name O or name CB )) or resid 435 through 448 or (resid 449 and (name N or nam \ e CA or name C or name O or name CB )) or resid 450 through 461 or (resid 462 an \ d (name N or name CA or name C or name O or name CB )) or resid 463 or (resid 46 \ 4 through 465 and (name N or name CA or name C or name O or name CB )) or resid \ 466 through 471 or (resid 472 and (name N or name CA or name C or name O or name \ CB )) or resid 473 through 474)) selection = (chain 'C' and (resid 46 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 71 or resid 92 through \ 104 or (resid 105 through 107 and (name N or name CA or name C or name O or name \ CB )) or resid 108 or (resid 109 and (name N or name CA or name C or name O or \ name CB )) or resid 110 through 121 or (resid 122 through 124 and (name N or nam \ e CA or name C or name O or name CB )) or resid 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 or (resid 128 and (name \ N or name CA or name C or name O or name CB )) or resid 129 through 133 or (resi \ d 134 through 135 and (name N or name CA or name C or name O or name CB )) or re \ sid 136 through 146 or (resid 147 and (name N or name CA or name C or name O or \ name CB )) or resid 148 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or resid 157 or (resid 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 through 160 or (resid 161 and (name \ N or name CA or name C or name O or name CB )) or resid 162 through 188 or (resi \ d 189 and (name N or name CA or name C or name O or name CB )) or resid 190 thro \ ugh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) o \ r resid 209 through 246 or (resid 247 and (name N or name CA or name C or name O \ or name CB )) or resid 248 through 271 or (resid 272 and (name N or name CA or \ name C or name O or name CB )) or resid 273 or (resid 274 through 277 and (name \ N or name CA or name C or name O or name CB )) or resid 278 through 287 or (resi \ d 288 through 289 and (name N or name CA or name C or name O or name CB )) or re \ sid 290 through 291 or (resid 292 and (name N or name CA or name C or name O or \ name CB )) or resid 293 through 295 or (resid 296 through 297 and (name N or nam \ e CA or name C or name O or name CB )) or resid 298 through 302 or (resid 303 th \ rough 309 and (name N or name CA or name C or name O or name CB )) or resid 310 \ through 328 or (resid 329 and (name N or name CA or name C or name O or name CB \ )) or resid 330 through 343 or (resid 344 and (name N or name CA or name C or na \ me O or name CB )) or resid 345 through 355 or (resid 356 and (name N or name CA \ or name C or name O or name CB )) or resid 357 through 365 or (resid 366 and (n \ ame N or name CA or name C or name O or name CB )) or resid 367 through 371 or ( \ resid 372 and (name N or name CA or name C or name O or name CB )) or resid 373 \ through 378 or (resid 379 through 384 and (name N or name CA or name C or name O \ or name CB )) or resid 385 through 386 or (resid 387 through 390 and (name N or \ name CA or name C or name O or name CB )) or resid 391 through 397 or (resid 39 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 399 or (resi \ d 400 and (name N or name CA or name C or name O or name CB )) or resid 401 thro \ ugh 402 or (resid 403 through 404 and (name N or name CA or name C or name O or \ name CB )) or resid 405 through 406 or (resid 407 through 411 and (name N or nam \ e CA or name C or name O or name CB )) or resid 414 through 417 or (resid 418 an \ d (name N or name CA or name C or name O or name CB )) or resid 419 through 420 \ or (resid 421 through 431 and (name N or name CA or name C or name O or name CB \ )) or resid 432 through 433 or (resid 434 and (name N or name CA or name C or na \ me O or name CB )) or resid 435 or (resid 436 and (name N or name CA or name C o \ r name O or name CB )) or resid 437 through 439 or (resid 440 and (name N or nam \ e CA or name C or name O or name CB )) or resid 441 through 443 or (resid 444 an \ d (name N or name CA or name C or name O or name CB )) or resid 445 through 448 \ or (resid 449 and (name N or name CA or name C or name O or name CB )) or resid \ 450 through 453 or (resid 454 through 456 and (name N or name CA or name C or na \ me O or name CB )) or resid 457 through 461 or (resid 462 and (name N or name CA \ or name C or name O or name CB )) or resid 463 or (resid 464 through 465 and (n \ ame N or name CA or name C or name O or name CB )) or resid 466 or (resid 467 th \ rough 468 and (name N or name CA or name C or name O or name CB )) or resid 469 \ or (resid 470 through 472 and (name N or name CA or name C or name O or name CB \ )) or resid 473 or (resid 474 and (name N or name CA or name C or name O or name \ CB or name OXT)))) selection = (chain 'D' and (resid 46 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 69 or (resid 70 through \ 92 and (name N or name CA or name C or name O or name CB )) or resid 93 through \ 104 or (resid 105 through 107 and (name N or name CA or name C or name O or nam \ e CB )) or resid 108 through 121 or (resid 122 through 124 and (name N or name C \ A or name C or name O or name CB )) or resid 125 through 127 or (resid 128 and ( \ name N or name CA or name C or name O or name CB )) or resid 129 through 133 or \ (resid 134 through 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 through 160 or (resid 161 and (name N or name CA or name C or name \ O or name CB )) or resid 162 through 186 or (resid 187 and (name N or name CA or \ name C or name O or name CB )) or resid 188 or (resid 189 and (name N or name C \ A or name C or name O or name CB )) or resid 190 through 205 or (resid 206 throu \ gh 208 and (name N or name CA or name C or name O or name CB )) or resid 209 thr \ ough 271 or (resid 272 and (name N or name CA or name C or name O or name CB )) \ or (resid 273 through 277 and (name N or name CA or name C or name O or name CB \ )) or resid 278 through 287 or (resid 288 through 289 and (name N or name CA or \ name C or name O or name CB )) or resid 290 or (resid 291 through 292 and (name \ N or name CA or name C or name O or name CB )) or resid 293 or (resid 294 and (n \ ame N or name CA or name C or name O or name CB )) or resid 295 or (resid 296 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ through 301 or (resid 302 through 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 328 or (resid 329 and (name N or name CA or \ name C or name O or name CB )) or resid 330 through 331 or (resid 332 and (name \ N or name CA or name C or name O or name CB )) or resid 333 through 343 or (resi \ d 344 and (name N or name CA or name C or name O or name CB )) or resid 345 thro \ ugh 349 or (resid 350 and (name N or name CA or name C or name O or name CB )) o \ r resid 351 through 355 or (resid 356 and (name N or name CA or name C or name O \ or name CB )) or resid 357 through 367 or (resid 368 and (name N or name CA or \ name C or name O or name CB )) or resid 369 through 371 or (resid 372 and (name \ N or name CA or name C or name O or name CB )) or resid 373 through 378 or (resi \ d 379 through 384 and (name N or name CA or name C or name O or name CB )) or re \ sid 385 through 386 or (resid 387 through 390 and (name N or name CA or name C o \ r name O or name CB )) or resid 391 through 397 or (resid 398 and (name N or nam \ e CA or name C or name O or name CB )) or resid 399 through 402 or (resid 403 th \ rough 404 and (name N or name CA or name C or name O or name CB )) or resid 405 \ through 406 or (resid 407 through 411 and (name N or name CA or name C or name O \ or name CB )) or resid 414 through 417 or (resid 418 and (name N or name CA or \ name C or name O or name CB )) or resid 419 through 420 or (resid 421 through 43 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 432 through \ 435 or (resid 436 and (name N or name CA or name C or name O or name CB )) or re \ sid 437 through 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 443 or (resid 444 and (name N or name CA or name \ C or name O or name CB )) or resid 445 through 448 or (resid 449 and (name N or \ name CA or name C or name O or name CB )) or resid 450 through 453 or (resid 45 \ 4 through 456 and (name N or name CA or name C or name O or name CB )) or resid \ 457 through 461 or (resid 462 and (name N or name CA or name C or name O or name \ CB )) or resid 463 or (resid 464 through 465 and (name N or name CA or name C o \ r name O or name CB )) or resid 466 through 469 or (resid 470 through 472 and (n \ ame N or name CA or name C or name O or name CB )) or resid 473 or (resid 474 an \ d (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'E' and (resid 46 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 69 or (resid 70 through \ 71 and (name N or name CA or name C or name O or name CB )) or (resid 92 and (n \ ame N or name CA or name C or name O or name CB )) or resid 93 through 105 or (r \ esid 106 through 107 and (name N or name CA or name C or name O or name CB )) or \ resid 108 or (resid 109 and (name N or name CA or name C or name O or name CB ) \ ) or resid 110 through 121 or (resid 122 through 124 and (name N or name CA or n \ ame C or name O or name CB )) or resid 125 through 127 or (resid 128 and (name N \ or name CA or name C or name O or name CB )) or resid 129 through 133 or (resid \ 134 through 135 and (name N or name CA or name C or name O or name CB )) or res \ id 136 through 146 or (resid 147 and (name N or name CA or name C or name O or n \ ame CB )) or resid 148 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or resid 157 through 160 or (resid 161 and (name N or \ name CA or name C or name O or name CB )) or resid 162 through 188 or (resid 189 \ and (name N or name CA or name C or name O or name CB )) or resid 190 through 2 \ 05 or (resid 206 through 208 and (name N or name CA or name C or name O or name \ CB )) or resid 209 through 246 or (resid 247 and (name N or name CA or name C or \ name O or name CB )) or resid 248 through 271 or (resid 272 and (name N or name \ CA or name C or name O or name CB )) or (resid 273 through 277 and (name N or n \ ame CA or name C or name O or name CB )) or resid 278 through 287 or (resid 288 \ through 289 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 0 or (resid 291 through 292 and (name N or name CA or name C or name O or name C \ B )) or resid 293 or (resid 294 and (name N or name CA or name C or name O or na \ me CB )) or resid 295 or (resid 296 through 297 and (name N or name CA or name C \ or name O or name CB )) or resid 298 through 301 or (resid 302 through 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 328 or \ (resid 329 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 0 through 331 or (resid 332 and (name N or name CA or name C or name O or name C \ B )) or resid 333 through 343 or (resid 344 and (name N or name CA or name C or \ name O or name CB )) or resid 345 through 349 or (resid 350 and (name N or name \ CA or name C or name O or name CB )) or resid 351 through 355 or (resid 356 and \ (name N or name CA or name C or name O or name CB )) or resid 357 through 360 or \ (resid 361 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 2 through 365 or (resid 366 and (name N or name CA or name C or name O or name C \ B )) or resid 367 or (resid 368 and (name N or name CA or name C or name O or na \ me CB )) or resid 369 through 378 or (resid 379 through 384 and (name N or name \ CA or name C or name O or name CB )) or resid 385 through 386 or (resid 387 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 th \ rough 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) \ or resid 399 or (resid 400 and (name N or name CA or name C or name O or name C \ B )) or resid 401 through 406 or (resid 407 through 411 and (name N or name CA o \ r name C or name O or name CB )) or resid 414 through 417 or (resid 418 and (nam \ e N or name CA or name C or name O or name CB )) or resid 419 through 420 or (re \ sid 421 through 431 and (name N or name CA or name C or name O or name CB )) or \ resid 432 through 433 or (resid 434 and (name N or name CA or name C or name O o \ r name CB )) or resid 435 or (resid 436 and (name N or name CA or name C or name \ O or name CB )) or resid 437 through 439 or (resid 440 and (name N or name CA o \ r name C or name O or name CB )) or resid 441 through 443 or (resid 444 and (nam \ e N or name CA or name C or name O or name CB )) or resid 445 through 448 or (re \ sid 449 and (name N or name CA or name C or name O or name CB )) or resid 450 th \ rough 453 or (resid 454 through 456 and (name N or name CA or name C or name O o \ r name CB )) or resid 457 through 463 or (resid 464 through 465 and (name N or n \ ame CA or name C or name O or name CB )) or resid 466 through 469 or (resid 470 \ through 472 and (name N or name CA or name C or name O or name CB )) or resid 47 \ 3 or (resid 474 and (name N or name CA or name C or name O or name CB or name OX \ T)))) selection = (chain 'F' and (resid 46 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 69 or (resid 70 through \ 71 and (name N or name CA or name C or name O or name CB )) or resid 92 through \ 104 or (resid 105 through 107 and (name N or name CA or name C or name O or nam \ e CB )) or resid 108 through 122 or (resid 123 through 124 and (name N or name C \ A or name C or name O or name CB )) or resid 125 or (resid 126 and (name N or na \ me CA or name C or name O or name CB )) or resid 127 or (resid 128 and (name N o \ r name CA or name C or name O or name CB )) or resid 129 through 133 or (resid 1 \ 34 through 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 155 or (resid 156 and (name N or name CA or name C or name O or nam \ e CB )) or resid 157 or (resid 158 and (name N or name CA or name C or name O or \ name CB )) or resid 159 through 160 or (resid 161 and (name N or name CA or nam \ e C or name O or name CB )) or resid 162 through 186 or (resid 187 and (name N o \ r name CA or name C or name O or name CB )) or resid 188 through 205 or (resid 2 \ 06 through 208 and (name N or name CA or name C or name O or name CB )) or resid \ 209 through 246 or (resid 247 and (name N or name CA or name C or name O or nam \ e CB )) or resid 248 through 271 or (resid 272 and (name N or name CA or name C \ or name O or name CB )) or resid 273 or (resid 274 through 277 and (name N or na \ me CA or name C or name O or name CB )) or resid 278 through 290 or (resid 291 t \ hrough 292 and (name N or name CA or name C or name O or name CB )) or resid 293 \ through 295 or (resid 296 through 297 and (name N or name CA or name C or name \ O or name CB )) or resid 298 through 302 or (resid 303 through 309 and (name N o \ r name CA or name C or name O or name CB )) or resid 310 through 328 or (resid 3 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 330 through \ 343 or (resid 344 and (name N or name CA or name C or name O or name CB )) or r \ esid 345 through 349 or (resid 350 and (name N or name CA or name C or name O or \ name CB )) or resid 351 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 365 or (resid 366 and (name N o \ r name CA or name C or name O or name CB )) or resid 367 or (resid 368 and (name \ N or name CA or name C or name O or name CB )) or resid 369 through 371 or (res \ id 372 and (name N or name CA or name C or name O or name CB )) or resid 373 thr \ ough 378 or (resid 379 through 384 and (name N or name CA or name C or name O or \ name CB )) or resid 385 through 386 or (resid 387 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 through 397 or (resid 398 a \ nd (name N or name CA or name C or name O or name CB )) or resid 399 or (resid 4 \ 00 and (name N or name CA or name C or name O or name CB )) or resid 401 through \ 402 or (resid 403 through 404 and (name N or name CA or name C or name O or nam \ e CB )) or resid 405 through 406 or (resid 407 through 411 and (name N or name C \ A or name C or name O or name CB )) or resid 414 through 422 or (resid 423 throu \ gh 431 and (name N or name CA or name C or name O or name CB )) or resid 432 thr \ ough 433 or (resid 434 and (name N or name CA or name C or name O or name CB )) \ or resid 435 or (resid 436 and (name N or name CA or name C or name O or name CB \ )) or resid 437 through 439 or (resid 440 and (name N or name CA or name C or n \ ame O or name CB )) or resid 441 through 443 or (resid 444 and (name N or name C \ A or name C or name O or name CB )) or resid 445 through 453 or (resid 454 throu \ gh 456 and (name N or name CA or name C or name O or name CB )) or resid 457 thr \ ough 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) \ or resid 463 through 464 or (resid 465 and (name N or name CA or name C or name \ O or name CB )) or resid 466 or (resid 467 through 468 and (name N or name CA or \ name C or name O or name CB )) or resid 469 through 470 or (resid 471 through 4 \ 72 and (name N or name CA or name C or name O or name CB )) or resid 473 or (res \ id 474 and (name N or name CA or name C or name O or name CB or name OXT)))) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 4.840 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.300 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.002 0.042 18532 Z= 0.097 Angle : 0.497 9.379 25154 Z= 0.263 Chirality : 0.046 0.156 3013 Planarity : 0.003 0.050 3215 Dihedral : 16.391 89.207 6415 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.27 % Allowed : 34.20 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2433 helix: 0.98 (0.26), residues: 458 sheet: 0.55 (0.21), residues: 628 loop : -0.78 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 291 TYR 0.012 0.001 TYR E 396 PHE 0.028 0.001 PHE B 270 TRP 0.029 0.001 TRP A 95 HIS 0.002 0.000 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (18532) covalent geometry : angle 0.49691 / 0.26 (25154) hydrogen bonds : bond 0.14140 / 9.15 ( 705) hydrogen bonds : angle 6.13492 / 4.24 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 198 average time/residue: 0.1140 time to fit residues: 35.4560 Evaluate side-chains 182 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain E residue 424 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN B 222 ASN B 366 ASN C 222 ASN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.162513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104837 restraints weight = 25140.165| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.25 r_work: 0.3083 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 18532 Z= 0.352 Angle : 0.711 9.863 25154 Z= 0.386 Chirality : 0.055 0.212 3013 Planarity : 0.004 0.058 3215 Dihedral : 4.855 46.920 2628 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 7.71 % Allowed : 29.29 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2433 helix: 0.52 (0.25), residues: 460 sheet: 0.20 (0.21), residues: 601 loop : -1.08 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 211 TYR 0.019 0.002 TYR B 348 PHE 0.029 0.003 PHE B 155 TRP 0.020 0.002 TRP C 411 HIS 0.008 0.002 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00868 / 0.35 (18532) covalent geometry : angle 0.71142 / 0.39 (25154) hydrogen bonds : bond 0.05569 / 3.78 ( 705) hydrogen bonds : angle 5.84078 / 4.02 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 189 time to evaluate : 0.705 Fit side-chains REVERT: A 95 TRP cc_start: 0.6629 (p90) cc_final: 0.6348 (p90) REVERT: A 291 ARG cc_start: 0.8692 (tpp80) cc_final: 0.8465 (tpp80) REVERT: B 68 THR cc_start: 0.6412 (OUTLIER) cc_final: 0.6134 (p) REVERT: B 275 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7524 (tptp) REVERT: B 395 VAL cc_start: 0.8818 (t) cc_final: 0.8605 (m) REVERT: C 209 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7462 (tm-30) REVERT: D 343 GLN cc_start: 0.8210 (mp10) cc_final: 0.7932 (mp10) REVERT: E 339 MET cc_start: 0.8211 (mtp) cc_final: 0.7910 (mtp) outliers start: 143 outliers final: 93 residues processed: 307 average time/residue: 0.1263 time to fit residues: 61.4004 Evaluate side-chains 271 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 177 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 269 PHE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 468 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 58 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN B 366 ASN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.167730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.109264 restraints weight = 24897.168| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.16 r_work: 0.3180 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18532 Z= 0.107 Angle : 0.505 9.632 25154 Z= 0.268 Chirality : 0.046 0.164 3013 Planarity : 0.003 0.055 3215 Dihedral : 3.994 30.337 2624 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.34 % Allowed : 33.50 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2433 helix: 0.81 (0.25), residues: 468 sheet: 0.44 (0.21), residues: 610 loop : -0.95 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 326 TYR 0.009 0.001 TYR A 113 PHE 0.020 0.001 PHE B 269 TRP 0.011 0.001 TRP A 95 HIS 0.002 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (18532) covalent geometry : angle 0.50476 / 0.27 (25154) hydrogen bonds : bond 0.03391 / 2.30 ( 705) hydrogen bonds : angle 5.14014 / 3.53 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.6576 (p90) cc_final: 0.6246 (p90) REVERT: B 275 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7542 (tptp) REVERT: B 378 ARG cc_start: 0.8297 (tpp80) cc_final: 0.8045 (tpp80) REVERT: B 395 VAL cc_start: 0.8747 (t) cc_final: 0.8544 (m) REVERT: C 209 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7460 (tm-30) REVERT: E 339 MET cc_start: 0.8223 (mtp) cc_final: 0.7851 (mtp) REVERT: F 407 ASN cc_start: 0.8316 (p0) cc_final: 0.8064 (p0) outliers start: 62 outliers final: 41 residues processed: 240 average time/residue: 0.1259 time to fit residues: 47.9415 Evaluate side-chains 218 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 177 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 212 optimal weight: 0.2980 chunk 120 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN B 366 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.166139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105388 restraints weight = 25091.839| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.88 r_work: 0.3170 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18532 Z= 0.152 Angle : 0.530 9.950 25154 Z= 0.283 Chirality : 0.048 0.168 3013 Planarity : 0.003 0.054 3215 Dihedral : 4.086 30.802 2624 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.66 % Allowed : 31.12 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2433 helix: 0.81 (0.25), residues: 469 sheet: 0.43 (0.21), residues: 609 loop : -0.99 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 326 TYR 0.018 0.001 TYR A 396 PHE 0.020 0.002 PHE B 269 TRP 0.013 0.001 TRP B 280 HIS 0.004 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (18532) covalent geometry : angle 0.53000 / 0.28 (25154) hydrogen bonds : bond 0.03676 / 2.50 ( 705) hydrogen bonds : angle 5.16022 / 3.54 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 186 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.6560 (p90) cc_final: 0.6157 (p90) REVERT: A 339 MET cc_start: 0.7431 (mmt) cc_final: 0.7167 (mmm) REVERT: B 275 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7519 (tptp) REVERT: C 209 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7455 (tm-30) REVERT: C 389 MET cc_start: 0.6595 (mmp) cc_final: 0.6378 (mmp) REVERT: D 449 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8327 (mt-10) REVERT: E 339 MET cc_start: 0.8333 (mtp) cc_final: 0.8085 (mtp) REVERT: F 407 ASN cc_start: 0.8299 (p0) cc_final: 0.8063 (p0) outliers start: 105 outliers final: 80 residues processed: 272 average time/residue: 0.1152 time to fit residues: 50.5906 Evaluate side-chains 255 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 175 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 349 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 161 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 81 optimal weight: 0.0040 chunk 33 optimal weight: 0.0470 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 0.0050 chunk 145 optimal weight: 2.9990 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN B 251 ASN B 366 ASN C 222 ASN D 66 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.171105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.114910 restraints weight = 24849.856| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.21 r_work: 0.3239 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18532 Z= 0.081 Angle : 0.473 10.924 25154 Z= 0.245 Chirality : 0.046 0.155 3013 Planarity : 0.003 0.055 3215 Dihedral : 3.592 30.798 2624 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.18 % Allowed : 33.39 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2433 helix: 1.03 (0.26), residues: 468 sheet: 0.56 (0.21), residues: 617 loop : -0.82 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 378 TYR 0.007 0.001 TYR F 451 PHE 0.017 0.001 PHE B 269 TRP 0.023 0.001 TRP F 411 HIS 0.002 0.000 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.08 (18532) covalent geometry : angle 0.47347 / 0.24 (25154) hydrogen bonds : bond 0.02572 / 1.76 ( 705) hydrogen bonds : angle 4.69426 / 3.23 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 201 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.6546 (p90) cc_final: 0.6220 (p90) REVERT: A 339 MET cc_start: 0.7464 (mmt) cc_final: 0.7234 (mmm) REVERT: A 448 ARG cc_start: 0.7367 (tpp80) cc_final: 0.7047 (tpp80) REVERT: B 378 ARG cc_start: 0.8303 (tpp80) cc_final: 0.8077 (tpp80) REVERT: C 389 MET cc_start: 0.6492 (mmp) cc_final: 0.6238 (mmp) REVERT: D 343 GLN cc_start: 0.8407 (mp10) cc_final: 0.8052 (mp10) REVERT: E 339 MET cc_start: 0.8193 (mtp) cc_final: 0.7932 (mtp) REVERT: E 405 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: F 407 ASN cc_start: 0.8310 (p0) cc_final: 0.8062 (p0) outliers start: 59 outliers final: 32 residues processed: 249 average time/residue: 0.1231 time to fit residues: 49.1443 Evaluate side-chains 211 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 96 optimal weight: 0.7980 chunk 108 optimal weight: 0.0970 chunk 222 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 132 optimal weight: 0.0570 chunk 240 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN B 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110017 restraints weight = 24745.514| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.90 r_work: 0.3244 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18532 Z= 0.086 Angle : 0.474 8.974 25154 Z= 0.248 Chirality : 0.046 0.158 3013 Planarity : 0.003 0.053 3215 Dihedral : 3.517 30.126 2624 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.80 % Allowed : 33.98 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.17), residues: 2433 helix: 1.08 (0.26), residues: 469 sheet: 0.65 (0.21), residues: 621 loop : -0.78 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 326 TYR 0.022 0.001 TYR A 396 PHE 0.015 0.001 PHE B 269 TRP 0.029 0.001 TRP F 411 HIS 0.002 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (18532) covalent geometry : angle 0.47382 / 0.25 (25154) hydrogen bonds : bond 0.02675 / 1.84 ( 705) hydrogen bonds : angle 4.63744 / 3.19 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.6469 (p90) cc_final: 0.6203 (p90) REVERT: A 339 MET cc_start: 0.7480 (mmt) cc_final: 0.7230 (mmm) REVERT: B 378 ARG cc_start: 0.8331 (tpp80) cc_final: 0.8031 (tpp80) REVERT: B 462 LYS cc_start: 0.6817 (tppt) cc_final: 0.6599 (tppt) REVERT: D 343 GLN cc_start: 0.8396 (mp10) cc_final: 0.8116 (mp10) REVERT: E 339 MET cc_start: 0.8200 (mtp) cc_final: 0.7936 (mtp) REVERT: E 405 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: F 407 ASN cc_start: 0.8376 (p0) cc_final: 0.8098 (p0) outliers start: 52 outliers final: 38 residues processed: 230 average time/residue: 0.1234 time to fit residues: 45.0602 Evaluate side-chains 216 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 117 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 66 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 174 optimal weight: 0.0030 chunk 205 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 overall best weight: 1.0072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.169309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111383 restraints weight = 24806.793| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.24 r_work: 0.3194 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18532 Z= 0.106 Angle : 0.495 9.633 25154 Z= 0.260 Chirality : 0.046 0.164 3013 Planarity : 0.003 0.052 3215 Dihedral : 3.626 29.760 2624 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.61 % Allowed : 33.33 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.17), residues: 2433 helix: 1.08 (0.26), residues: 469 sheet: 0.63 (0.21), residues: 616 loop : -0.77 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 326 TYR 0.009 0.001 TYR B 348 PHE 0.015 0.001 PHE B 269 TRP 0.030 0.001 TRP F 411 HIS 0.002 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (18532) covalent geometry : angle 0.49541 / 0.26 (25154) hydrogen bonds : bond 0.02965 / 2.04 ( 705) hydrogen bonds : angle 4.72604 / 3.25 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 182 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.6557 (p90) cc_final: 0.6209 (p90) REVERT: B 378 ARG cc_start: 0.8331 (tpp80) cc_final: 0.8008 (tpp80) REVERT: D 326 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.6949 (ttp80) REVERT: D 343 GLN cc_start: 0.8402 (mp10) cc_final: 0.8005 (mp10) REVERT: E 339 MET cc_start: 0.8316 (mtp) cc_final: 0.7993 (mtp) REVERT: E 405 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6764 (pm20) outliers start: 67 outliers final: 52 residues processed: 239 average time/residue: 0.1124 time to fit residues: 43.0840 Evaluate side-chains 226 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 147 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN B 366 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109636 restraints weight = 25300.107| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.17 r_work: 0.3167 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18532 Z= 0.167 Angle : 0.558 9.997 25154 Z= 0.296 Chirality : 0.048 0.169 3013 Planarity : 0.003 0.051 3215 Dihedral : 4.022 30.657 2624 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.26 % Allowed : 32.90 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2433 helix: 0.97 (0.26), residues: 469 sheet: 0.51 (0.21), residues: 607 loop : -0.88 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 326 TYR 0.015 0.001 TYR B 348 PHE 0.018 0.002 PHE D 155 TRP 0.025 0.002 TRP F 411 HIS 0.004 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (18532) covalent geometry : angle 0.55793 / 0.30 (25154) hydrogen bonds : bond 0.03656 / 2.49 ( 705) hydrogen bonds : angle 5.04675 / 3.47 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 182 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.6540 (p90) cc_final: 0.6145 (p90) REVERT: A 339 MET cc_start: 0.7534 (mmt) cc_final: 0.7305 (mmm) REVERT: D 343 GLN cc_start: 0.8407 (mp10) cc_final: 0.7932 (mp10) REVERT: E 339 MET cc_start: 0.8362 (mtp) cc_final: 0.7981 (mtp) REVERT: E 405 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6742 (pm20) outliers start: 79 outliers final: 62 residues processed: 249 average time/residue: 0.1176 time to fit residues: 46.9582 Evaluate side-chains 238 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 175 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 419 TYR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 21 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN B 366 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107147 restraints weight = 24999.998| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.22 r_work: 0.3159 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18532 Z= 0.144 Angle : 0.542 10.765 25154 Z= 0.286 Chirality : 0.048 0.170 3013 Planarity : 0.003 0.053 3215 Dihedral : 3.967 31.318 2624 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.05 % Allowed : 33.01 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2433 helix: 0.90 (0.25), residues: 470 sheet: 0.49 (0.21), residues: 605 loop : -0.90 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 326 TYR 0.012 0.001 TYR C 315 PHE 0.016 0.002 PHE D 155 TRP 0.021 0.001 TRP F 411 HIS 0.003 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (18532) covalent geometry : angle 0.54150 / 0.29 (25154) hydrogen bonds : bond 0.03375 / 2.31 ( 705) hydrogen bonds : angle 4.98581 / 3.43 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 175 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.6608 (p90) cc_final: 0.6221 (p90) REVERT: A 339 MET cc_start: 0.7559 (mmt) cc_final: 0.7341 (mmm) REVERT: D 343 GLN cc_start: 0.8434 (mp10) cc_final: 0.7954 (mp10) REVERT: E 339 MET cc_start: 0.8355 (mtp) cc_final: 0.7971 (mtp) REVERT: E 405 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: F 406 LEU cc_start: 0.8431 (tp) cc_final: 0.8191 (tt) outliers start: 75 outliers final: 67 residues processed: 242 average time/residue: 0.1225 time to fit residues: 48.1056 Evaluate side-chains 239 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 181 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN B 251 ASN B 366 ASN D 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116515 restraints weight = 24772.778| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.24 r_work: 0.3224 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18532 Z= 0.099 Angle : 0.506 11.558 25154 Z= 0.265 Chirality : 0.046 0.159 3013 Planarity : 0.003 0.053 3215 Dihedral : 3.705 31.788 2624 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.56 % Allowed : 33.50 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2433 helix: 1.00 (0.26), residues: 471 sheet: 0.57 (0.21), residues: 610 loop : -0.80 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 326 TYR 0.010 0.001 TYR C 315 PHE 0.014 0.001 PHE B 342 TRP 0.029 0.001 TRP F 411 HIS 0.002 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (18532) covalent geometry : angle 0.50593 / 0.26 (25154) hydrogen bonds : bond 0.02799 / 1.92 ( 705) hydrogen bonds : angle 4.76979 / 3.28 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 181 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 95 TRP cc_start: 0.6658 (p90) cc_final: 0.6260 (p90) REVERT: A 291 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8663 (tpp80) REVERT: B 172 LYS cc_start: 0.7988 (tptm) cc_final: 0.7752 (tptp) REVERT: C 360 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7661 (m) REVERT: D 343 GLN cc_start: 0.8406 (mp10) cc_final: 0.7940 (mp10) REVERT: D 405 GLN cc_start: 0.8209 (pt0) cc_final: 0.7875 (pt0) REVERT: D 449 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7967 (pt0) REVERT: E 339 MET cc_start: 0.8322 (mtp) cc_final: 0.7927 (mtp) REVERT: E 405 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: F 406 LEU cc_start: 0.8439 (tp) cc_final: 0.8222 (tt) outliers start: 66 outliers final: 56 residues processed: 239 average time/residue: 0.1239 time to fit residues: 48.1442 Evaluate side-chains 234 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 183 optimal weight: 0.0370 chunk 120 optimal weight: 9.9990 chunk 200 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 238 optimal weight: 20.0000 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 GLN B 251 ASN B 366 ASN D 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112710 restraints weight = 24804.545| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.22 r_work: 0.3210 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 18532 Z= 0.141 Angle : 0.705 59.194 25154 Z= 0.411 Chirality : 0.047 0.429 3013 Planarity : 0.003 0.053 3215 Dihedral : 3.802 43.655 2624 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.40 % Allowed : 33.66 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2433 helix: 0.99 (0.26), residues: 471 sheet: 0.58 (0.21), residues: 610 loop : -0.80 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 326 TYR 0.008 0.001 TYR F 451 PHE 0.027 0.001 PHE B 270 TRP 0.025 0.001 TRP F 411 HIS 0.002 0.001 HIS E 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (18532) covalent geometry : angle 0.70456 / 0.41 (25154) hydrogen bonds : bond 0.02814 / 1.93 ( 705) hydrogen bonds : angle 4.76983 / 3.28 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4300.70 seconds wall clock time: 74 minutes 26.14 seconds (4466.14 seconds total)