Starting phenix.real_space_refine on Mon Jun 16 07:06:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e25_47436/06_2025/9e25_47436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e25_47436/06_2025/9e25_47436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e25_47436/06_2025/9e25_47436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e25_47436/06_2025/9e25_47436.map" model { file = "/net/cci-nas-00/data/ceres_data/9e25_47436/06_2025/9e25_47436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e25_47436/06_2025/9e25_47436.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.052 sd= 0.115 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 100 5.16 5 C 11233 2.51 5 N 3381 2.21 5 O 3466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18180 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2910 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 189 Chain: "F" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 11.20, per 1000 atoms: 0.62 Number of scatterers: 18180 At special positions: 0 Unit cell: (121.54, 134.93, 94.76, 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 100 16.00 O 3466 8.00 N 3381 7.00 C 11233 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: 4.94 Conformation dependent library (CDL) restraints added in 2.3 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 13 sheets defined 45.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 98 through 105 Processing helix chain 'A' and resid 106 through 126 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.969A pdb=" N LEU A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.825A pdb=" N ARG A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.994A pdb=" N ASP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.593A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 removed outlier: 3.688A pdb=" N ASN B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 106 through 125 Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.623A pdb=" N LEU B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 286 through 296 Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.143A pdb=" N ASP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 399 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 98 through 105 removed outlier: 3.703A pdb=" N LEU C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 105 " --> pdb=" O GLN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.583A pdb=" N LEU C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 244 through 248 removed outlier: 3.930A pdb=" N LEU C 248 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.564A pdb=" N LEU C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 361 through 372 removed outlier: 3.838A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 98 through 104 removed outlier: 3.538A pdb=" N GLN D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 Processing helix chain 'D' and resid 130 through 146 Processing helix chain 'D' and resid 150 through 157 removed outlier: 4.043A pdb=" N LEU D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.793A pdb=" N ARG D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.894A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.612A pdb=" N ALA D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.645A pdb=" N LEU E 105 " --> pdb=" O GLN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 125 removed outlier: 3.586A pdb=" N GLU E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 150 through 157 removed outlier: 4.520A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 361 through 372 removed outlier: 4.177A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.582A pdb=" N GLY E 400 " --> pdb=" O MET E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 489 through 500 Processing helix chain 'F' and resid 81 through 97 Processing helix chain 'F' and resid 98 through 105 removed outlier: 3.505A pdb=" N LEU F 105 " --> pdb=" O GLN F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 126 Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 245 through 248 removed outlier: 4.186A pdb=" N LEU F 248 " --> pdb=" O LYS F 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 248' Processing helix chain 'F' and resid 249 through 256 removed outlier: 3.724A pdb=" N LEU F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 361 through 372 removed outlier: 3.883A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 442 through 446 Processing helix chain 'F' and resid 480 through 487 Processing helix chain 'F' and resid 489 through 499 removed outlier: 3.529A pdb=" N ALA F 499 " --> pdb=" O GLU F 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 5.795A pdb=" N ARG A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.903A pdb=" N VAL A 304 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU A 323 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR A 306 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY A 356 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N CYS A 307 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL A 358 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET A 378 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLY A 356 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR A 380 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N HIS A 382 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 277 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 381 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 279 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 278 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA A 423 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 280 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ARG A 425 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 420 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE A 436 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N ARG A 432 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N GLU A 456 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR A 434 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 454 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 436 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A 448 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU A 442 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 182 removed outlier: 4.628A pdb=" N VAL B 171 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 320 through 324 removed outlier: 6.596A pdb=" N VAL B 304 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU B 323 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR B 306 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL B 305 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 380 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 278 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA B 423 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER B 280 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG B 425 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 420 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 436 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N ARG B 432 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N GLU B 456 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR B 434 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 454 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 436 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 448 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B 442 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 467 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 182 removed outlier: 4.236A pdb=" N VAL C 171 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.512A pdb=" N VAL C 304 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU C 323 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR C 306 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL C 305 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 353 " --> pdb=" O MET C 378 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR C 380 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL C 355 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N HIS C 382 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 379 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 424 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N ARG C 432 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N GLU C 456 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N THR C 434 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL C 454 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 436 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL C 448 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR C 455 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG C 471 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE C 457 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS C 469 " --> pdb=" O ILE C 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 178 through 181 removed outlier: 4.030A pdb=" N ASP D 162 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 380 through 382 removed outlier: 7.913A pdb=" N LEU D 381 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D 279 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE D 420 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE D 436 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN D 422 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ARG D 432 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N GLU D 456 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR D 434 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL D 454 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE D 436 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL D 448 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU D 442 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.824A pdb=" N VAL D 304 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU D 323 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR D 306 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 305 " --> pdb=" O ILE D 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 178 through 182 removed outlier: 4.622A pdb=" N VAL E 171 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP E 162 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 320 through 324 removed outlier: 6.601A pdb=" N VAL E 304 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU E 323 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR E 306 " --> pdb=" O LEU E 323 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR E 380 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU E 277 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU E 381 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE E 279 " --> pdb=" O LEU E 381 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL E 278 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA E 423 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER E 280 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ARG E 425 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA E 424 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE E 433 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N ARG E 432 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N GLU E 456 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR E 434 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL E 454 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE E 436 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL E 448 " --> pdb=" O VAL E 440 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU E 442 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL E 467 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 178 through 182 removed outlier: 4.366A pdb=" N VAL F 171 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 320 through 324 removed outlier: 6.526A pdb=" N VAL F 304 " --> pdb=" O VAL F 321 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU F 323 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N THR F 306 " --> pdb=" O LEU F 323 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL F 305 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE F 353 " --> pdb=" O MET F 378 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR F 380 " --> pdb=" O ILE F 353 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL F 355 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N HIS F 382 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY F 379 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL F 278 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA F 423 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER F 280 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ARG F 425 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N ARG F 432 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N GLU F 456 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR F 434 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL F 454 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE F 436 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL F 448 " --> pdb=" O VAL F 440 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR F 455 " --> pdb=" O ARG F 471 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG F 471 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE F 457 " --> pdb=" O LYS F 469 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS F 469 " --> pdb=" O ILE F 457 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2805 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: 6.63 Time building geometry restraints manager: 5.76 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: 6502 1.34 - 1.46: 2963 1.46 - 1.58: 8773 1.58 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 18402 Sorted by residual: bond pdb=" C VAL B 417 " pdb=" N ASP B 418 " ideal model delta sigma weight residual 1.332 1.318 0.015 1.40e-02 5.10e+03 1.11e+00 bond pdb=" CA THR A 295 " pdb=" C THR A 295 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.12e-02 7.97e+03 8.09e-01 bond pdb=" CG LEU F 315 " pdb=" CD1 LEU F 315 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.69e-01 bond pdb=" CA THR D 295 " pdb=" C THR D 295 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 7.16e-01 bond pdb=" CG MET E 396 " pdb=" SD MET E 396 " ideal model delta sigma weight residual 1.803 1.782 0.021 2.50e-02 1.60e+03 6.96e-01 ... (remaining 18397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 24457 1.25 - 2.50: 403 2.50 - 3.74: 84 3.74 - 4.99: 31 4.99 - 6.24: 6 Bond angle restraints: 24981 Sorted by residual: angle pdb=" N ASP D 418 " pdb=" CA ASP D 418 " pdb=" C ASP D 418 " ideal model delta sigma weight residual 114.56 111.43 3.13 1.27e+00 6.20e-01 6.09e+00 angle pdb=" CA GLN D 316 " pdb=" CB GLN D 316 " pdb=" CG GLN D 316 " ideal model delta sigma weight residual 114.10 118.31 -4.21 2.00e+00 2.50e-01 4.44e+00 angle pdb=" N PRO F 229 " pdb=" CA PRO F 229 " pdb=" C PRO F 229 " ideal model delta sigma weight residual 110.70 112.97 -2.27 1.22e+00 6.72e-01 3.48e+00 angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" C PRO A 229 " ideal model delta sigma weight residual 110.70 112.96 -2.26 1.22e+00 6.72e-01 3.44e+00 angle pdb=" N PRO C 229 " pdb=" CA PRO C 229 " pdb=" C PRO C 229 " ideal model delta sigma weight residual 110.70 112.94 -2.24 1.22e+00 6.72e-01 3.37e+00 ... (remaining 24976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10294 17.99 - 35.99: 813 35.99 - 53.98: 144 53.98 - 71.97: 28 71.97 - 89.97: 16 Dihedral angle restraints: 11295 sinusoidal: 4096 harmonic: 7199 Sorted by residual: dihedral pdb=" CA LEU B 367 " pdb=" C LEU B 367 " pdb=" N GLN B 368 " pdb=" CA GLN B 368 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ALA B 369 " pdb=" C ALA B 369 " pdb=" N MET B 370 " pdb=" CA MET B 370 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA HIS C 435 " pdb=" C HIS C 435 " pdb=" N ILE C 436 " pdb=" CA ILE C 436 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 11292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1967 0.031 - 0.063: 575 0.063 - 0.094: 191 0.094 - 0.126: 226 0.126 - 0.157: 19 Chirality restraints: 2978 Sorted by residual: chirality pdb=" CA ILE B 436 " pdb=" N ILE B 436 " pdb=" C ILE B 436 " pdb=" CB ILE B 436 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ILE E 436 " pdb=" N ILE E 436 " pdb=" C ILE E 436 " pdb=" CB ILE E 436 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE C 436 " pdb=" N ILE C 436 " pdb=" C ILE C 436 " pdb=" CB ILE C 436 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2975 not shown) Planarity restraints: 3338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 145 " -0.025 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C VAL F 145 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL F 145 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU F 146 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 145 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C VAL E 145 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL E 145 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU E 146 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 228 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 229 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.025 5.00e-02 4.00e+02 ... (remaining 3335 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 237 2.57 - 3.15: 16409 3.15 - 3.74: 28398 3.74 - 4.32: 37513 4.32 - 4.90: 64959 Nonbonded interactions: 147516 Sorted by model distance: nonbonded pdb=" O ASP C 451 " pdb=" OG1 THR C 473 " model vdw 1.991 3.040 nonbonded pdb=" OH TYR A 148 " pdb=" OE1 GLN A 202 " model vdw 2.014 3.040 nonbonded pdb=" O ASP F 451 " pdb=" OG1 THR F 473 " model vdw 2.022 3.040 nonbonded pdb=" OH TYR D 148 " pdb=" OE1 GLN D 202 " model vdw 2.029 3.040 nonbonded pdb=" O ASP E 451 " pdb=" OG1 THR E 473 " model vdw 2.037 3.040 ... (remaining 147511 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 80 through 148 and (name N or name CA or name C or name O \ or name CB )) or resid 149 or (resid 150 through 166 and (name N or name CA or \ name C or name O or name CB )) or (resid 167 through 175 and (name N or name CA \ or name C or name O or name CB )) or resid 176 through 177 or (resid 178 through \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throu \ gh 501)) selection = (chain 'B' and ((resid 80 through 148 and (name N or name CA or name C or name O \ or name CB )) or resid 149 or (resid 150 through 166 and (name N or name CA or \ name C or name O or name CB )) or (resid 167 through 175 and (name N or name CA \ or name C or name O or name CB )) or resid 176 through 177 or (resid 178 through \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throu \ gh 501)) selection = (chain 'C' and ((resid 80 through 148 and (name N or name CA or name C or name O \ or name CB )) or resid 149 or (resid 150 through 166 and (name N or name CA or \ name C or name O or name CB )) or (resid 167 through 175 and (name N or name CA \ or name C or name O or name CB )) or resid 176 through 177 or (resid 178 through \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throu \ gh 501)) selection = (chain 'D' and ((resid 80 through 148 and (name N or name CA or name C or name O \ or name CB )) or resid 149 or (resid 150 through 166 and (name N or name CA or \ name C or name O or name CB )) or (resid 167 through 175 and (name N or name CA \ or name C or name O or name CB )) or resid 176 through 177 or (resid 178 through \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throu \ gh 501)) selection = chain 'E' selection = (chain 'F' and ((resid 80 through 148 and (name N or name CA or name C or name O \ or name CB )) or resid 149 or (resid 150 through 166 and (name N or name CA or \ name C or name O or name CB )) or (resid 167 through 175 and (name N or name CA \ or name C or name O or name CB )) or resid 176 through 177 or (resid 178 through \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throu \ gh 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 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: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.700 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 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 : 0.003 0.033 18402 Z= 0.149 Angle : 0.461 6.241 24981 Z= 0.249 Chirality : 0.044 0.157 2978 Planarity : 0.003 0.049 3338 Dihedral : 13.779 89.967 6651 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.17), residues: 2520 helix: 2.39 (0.16), residues: 1118 sheet: -0.85 (0.23), residues: 458 loop : -0.06 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 481 HIS 0.002 0.001 HIS B 435 PHE 0.018 0.001 PHE A 243 TYR 0.006 0.001 TYR D 402 ARG 0.006 0.000 ARG F 223 Details of bonding type rmsd hydrogen bonds : bond 0.12065 ( 958) hydrogen bonds : angle 5.50921 ( 2805) covalent geometry : bond 0.00325 (18402) covalent geometry : angle 0.46147 (24981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 774 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8305 (t0) cc_final: 0.7835 (t0) REVERT: A 313 LEU cc_start: 0.7307 (mt) cc_final: 0.6376 (mp) REVERT: A 371 ASN cc_start: 0.6959 (t0) cc_final: 0.6747 (t0) REVERT: A 388 GLU cc_start: 0.7684 (tt0) cc_final: 0.7150 (tp30) REVERT: A 411 GLU cc_start: 0.8772 (tp30) cc_final: 0.8419 (pt0) REVERT: A 475 ILE cc_start: 0.6039 (mt) cc_final: 0.4539 (mt) REVERT: B 162 ASP cc_start: 0.5887 (m-30) cc_final: 0.5678 (m-30) REVERT: B 192 LEU cc_start: 0.8062 (tp) cc_final: 0.7729 (tp) REVERT: B 193 MET cc_start: 0.7961 (tpp) cc_final: 0.7626 (tpt) REVERT: B 237 THR cc_start: 0.7651 (m) cc_final: 0.7324 (p) REVERT: B 324 GLU cc_start: 0.6316 (tt0) cc_final: 0.5696 (tt0) REVERT: B 337 THR cc_start: 0.7703 (p) cc_final: 0.7375 (p) REVERT: B 365 ASP cc_start: 0.7994 (m-30) cc_final: 0.7653 (m-30) REVERT: B 408 THR cc_start: 0.8062 (m) cc_final: 0.7661 (p) REVERT: B 482 ASP cc_start: 0.8407 (m-30) cc_final: 0.7775 (p0) REVERT: B 497 LEU cc_start: 0.6878 (mp) cc_final: 0.6432 (pp) REVERT: C 184 VAL cc_start: 0.8519 (t) cc_final: 0.8307 (m) REVERT: C 319 HIS cc_start: 0.7367 (t-170) cc_final: 0.6749 (t-90) REVERT: C 418 ASP cc_start: 0.6521 (m-30) cc_final: 0.6164 (m-30) REVERT: D 206 ARG cc_start: 0.7711 (mtp-110) cc_final: 0.7510 (ttp-110) REVERT: D 251 LYS cc_start: 0.9480 (tptp) cc_final: 0.9170 (tptp) REVERT: D 255 GLU cc_start: 0.8767 (pt0) cc_final: 0.8006 (pt0) REVERT: D 375 ASP cc_start: 0.6110 (m-30) cc_final: 0.5572 (m-30) REVERT: D 397 ILE cc_start: 0.9188 (mt) cc_final: 0.8857 (mm) REVERT: D 407 LYS cc_start: 0.7883 (tptm) cc_final: 0.7390 (tptt) REVERT: D 408 THR cc_start: 0.8444 (m) cc_final: 0.8125 (p) REVERT: D 409 ILE cc_start: 0.7956 (mt) cc_final: 0.7687 (mt) REVERT: D 428 ASP cc_start: 0.6184 (p0) cc_final: 0.5258 (p0) REVERT: E 199 ILE cc_start: 0.8432 (mt) cc_final: 0.8230 (mm) REVERT: E 202 GLN cc_start: 0.9247 (tt0) cc_final: 0.8994 (tt0) REVERT: E 222 SER cc_start: 0.8357 (m) cc_final: 0.7997 (p) REVERT: E 283 THR cc_start: 0.7721 (m) cc_final: 0.7487 (m) REVERT: E 306 THR cc_start: 0.8489 (m) cc_final: 0.8029 (p) REVERT: E 338 MET cc_start: 0.7358 (tpp) cc_final: 0.7110 (tpp) REVERT: E 439 VAL cc_start: 0.6400 (t) cc_final: 0.5922 (t) REVERT: F 172 PHE cc_start: 0.7268 (m-80) cc_final: 0.7012 (m-80) REVERT: F 242 LYS cc_start: 0.7265 (mtpt) cc_final: 0.6364 (mtmm) REVERT: F 289 THR cc_start: 0.8689 (m) cc_final: 0.8423 (t) REVERT: F 298 ILE cc_start: 0.7423 (mt) cc_final: 0.6708 (mt) REVERT: F 316 GLN cc_start: 0.8448 (tp40) cc_final: 0.7947 (tp-100) REVERT: F 341 LEU cc_start: 0.7055 (mt) cc_final: 0.6736 (mt) REVERT: F 345 CYS cc_start: 0.8487 (m) cc_final: 0.8155 (m) REVERT: F 398 THR cc_start: 0.7402 (m) cc_final: 0.7030 (p) outliers start: 1 outliers final: 0 residues processed: 774 average time/residue: 0.3528 time to fit residues: 390.1476 Evaluate side-chains 540 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 435 HIS B 166 ASN B 169 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN C 169 HIS C 225 ASN C 252 ASN C 276 ASN C 314 GLN ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN E 292 ASN E 422 GLN F 252 ASN F 314 GLN F 344 ASN F 374 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081249 restraints weight = 44241.944| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.93 r_work: 0.3108 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18402 Z= 0.207 Angle : 0.713 14.737 24981 Z= 0.370 Chirality : 0.050 0.209 2978 Planarity : 0.006 0.088 3338 Dihedral : 4.203 28.722 2749 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.84 % Allowed : 18.33 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2520 helix: 2.02 (0.16), residues: 1136 sheet: -0.80 (0.22), residues: 486 loop : 0.18 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 481 HIS 0.006 0.001 HIS E 470 PHE 0.025 0.002 PHE D 480 TYR 0.018 0.002 TYR D 148 ARG 0.012 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 958) hydrogen bonds : angle 4.31303 ( 2805) covalent geometry : bond 0.00478 (18402) covalent geometry : angle 0.71277 (24981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 590 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.7795 (mt) cc_final: 0.7428 (mm) REVERT: A 315 LEU cc_start: 0.8484 (mp) cc_final: 0.8127 (mp) REVERT: A 339 ARG cc_start: 0.8533 (tpt-90) cc_final: 0.7912 (tpt-90) REVERT: A 345 CYS cc_start: 0.8157 (m) cc_final: 0.7747 (m) REVERT: A 371 ASN cc_start: 0.7736 (t0) cc_final: 0.7448 (t0) REVERT: A 388 GLU cc_start: 0.7881 (tt0) cc_final: 0.7624 (tp30) REVERT: A 411 GLU cc_start: 0.9027 (tp30) cc_final: 0.8504 (pt0) REVERT: A 475 ILE cc_start: 0.6586 (mt) cc_final: 0.6375 (mp) REVERT: B 189 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7204 (t0) REVERT: B 193 MET cc_start: 0.8459 (tpp) cc_final: 0.8077 (tpt) REVERT: B 225 ASN cc_start: 0.8202 (t0) cc_final: 0.7890 (t0) REVERT: B 273 CYS cc_start: 0.8456 (m) cc_final: 0.8049 (p) REVERT: B 339 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7415 (ttm-80) REVERT: B 365 ASP cc_start: 0.8352 (m-30) cc_final: 0.7906 (m-30) REVERT: B 367 LEU cc_start: 0.8207 (mp) cc_final: 0.8001 (mp) REVERT: B 448 VAL cc_start: 0.8419 (t) cc_final: 0.8214 (p) REVERT: B 482 ASP cc_start: 0.8745 (m-30) cc_final: 0.8326 (p0) REVERT: B 497 LEU cc_start: 0.6453 (mp) cc_final: 0.6090 (pp) REVERT: C 174 GLU cc_start: 0.7724 (tt0) cc_final: 0.7406 (tt0) REVERT: C 192 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8260 (tp) REVERT: C 259 ILE cc_start: 0.8649 (mp) cc_final: 0.8443 (mm) REVERT: C 319 HIS cc_start: 0.7797 (t-170) cc_final: 0.7279 (t-90) REVERT: C 355 VAL cc_start: 0.8900 (t) cc_final: 0.8681 (p) REVERT: C 411 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 418 ASP cc_start: 0.7005 (m-30) cc_final: 0.6757 (m-30) REVERT: C 491 ARG cc_start: 0.9036 (ttp80) cc_final: 0.8802 (ttp80) REVERT: D 251 LYS cc_start: 0.9467 (tptp) cc_final: 0.9231 (ttpp) REVERT: D 324 GLU cc_start: 0.8275 (tt0) cc_final: 0.7678 (tm-30) REVERT: D 337 THR cc_start: 0.7058 (OUTLIER) cc_final: 0.6799 (m) REVERT: D 390 ILE cc_start: 0.8289 (mt) cc_final: 0.8003 (mt) REVERT: D 410 LYS cc_start: 0.9037 (mttm) cc_final: 0.8779 (mttt) REVERT: E 199 ILE cc_start: 0.8646 (mt) cc_final: 0.8433 (mm) REVERT: E 202 GLN cc_start: 0.9275 (tt0) cc_final: 0.9031 (tt0) REVERT: E 306 THR cc_start: 0.8607 (m) cc_final: 0.8279 (p) REVERT: E 324 GLU cc_start: 0.8330 (tt0) cc_final: 0.8127 (tt0) REVERT: E 338 MET cc_start: 0.8056 (tpp) cc_final: 0.7504 (tpp) REVERT: E 396 MET cc_start: 0.8511 (mmm) cc_final: 0.8207 (mmm) REVERT: F 218 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7844 (mm) REVERT: F 339 ARG cc_start: 0.9047 (tmm-80) cc_final: 0.8594 (ttt90) REVERT: F 341 LEU cc_start: 0.7739 (mt) cc_final: 0.7532 (mt) REVERT: F 345 CYS cc_start: 0.8694 (m) cc_final: 0.8240 (m) REVERT: F 382 HIS cc_start: 0.7715 (t-90) cc_final: 0.7372 (t-90) REVERT: F 395 SER cc_start: 0.8508 (m) cc_final: 0.8218 (t) outliers start: 84 outliers final: 37 residues processed: 624 average time/residue: 0.3355 time to fit residues: 304.9939 Evaluate side-chains 538 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 497 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 491 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 126 optimal weight: 120.0000 chunk 90 optimal weight: 30.0000 chunk 171 optimal weight: 40.0000 chunk 227 optimal weight: 30.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.078159 restraints weight = 44330.148| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.82 r_work: 0.3065 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 18402 Z= 0.208 Angle : 0.684 11.236 24981 Z= 0.356 Chirality : 0.049 0.229 2978 Planarity : 0.006 0.066 3338 Dihedral : 4.355 33.262 2749 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.30 % Allowed : 19.19 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2520 helix: 1.86 (0.16), residues: 1134 sheet: -0.59 (0.21), residues: 524 loop : 0.14 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 481 HIS 0.010 0.001 HIS B 435 PHE 0.021 0.002 PHE D 364 TYR 0.012 0.001 TYR A 486 ARG 0.029 0.001 ARG D 432 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 958) hydrogen bonds : angle 4.19348 ( 2805) covalent geometry : bond 0.00484 (18402) covalent geometry : angle 0.68416 (24981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 529 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8706 (tt0) cc_final: 0.8424 (tt0) REVERT: A 270 ILE cc_start: 0.9049 (mt) cc_final: 0.8590 (mt) REVERT: A 312 GLU cc_start: 0.8189 (tp30) cc_final: 0.7977 (tp30) REVERT: A 339 ARG cc_start: 0.8848 (tpt-90) cc_final: 0.8467 (tpp80) REVERT: A 364 PHE cc_start: 0.8996 (t80) cc_final: 0.8445 (t80) REVERT: A 365 ASP cc_start: 0.8737 (m-30) cc_final: 0.8290 (m-30) REVERT: A 371 ASN cc_start: 0.8049 (t0) cc_final: 0.7737 (t0) REVERT: A 384 ASN cc_start: 0.8576 (m110) cc_final: 0.7969 (m-40) REVERT: A 388 GLU cc_start: 0.8686 (tt0) cc_final: 0.8245 (tt0) REVERT: A 410 LYS cc_start: 0.9169 (mttp) cc_final: 0.8827 (mtpp) REVERT: B 193 MET cc_start: 0.8662 (tpp) cc_final: 0.8328 (tpt) REVERT: B 270 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 339 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: B 343 LYS cc_start: 0.9223 (mtpp) cc_final: 0.8958 (mtmm) REVERT: B 370 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7385 (mmt) REVERT: B 377 SER cc_start: 0.8689 (t) cc_final: 0.8464 (t) REVERT: B 408 THR cc_start: 0.9027 (m) cc_final: 0.8470 (p) REVERT: B 482 ASP cc_start: 0.8997 (m-30) cc_final: 0.8569 (p0) REVERT: B 487 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8103 (t80) REVERT: B 497 LEU cc_start: 0.6858 (mp) cc_final: 0.6401 (pp) REVERT: C 206 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8162 (ttp80) REVERT: C 231 LEU cc_start: 0.9056 (mm) cc_final: 0.8835 (mt) REVERT: C 312 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7886 (mm-30) REVERT: C 343 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8723 (mtmm) REVERT: C 407 LYS cc_start: 0.8855 (tptm) cc_final: 0.8353 (tppt) REVERT: C 411 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8430 (mt-10) REVERT: D 171 VAL cc_start: 0.8997 (t) cc_final: 0.8758 (t) REVERT: D 243 PHE cc_start: 0.8525 (t80) cc_final: 0.8281 (t80) REVERT: D 333 SER cc_start: 0.9567 (m) cc_final: 0.9336 (p) REVERT: D 481 TRP cc_start: 0.7612 (t-100) cc_final: 0.7271 (t-100) REVERT: E 202 GLN cc_start: 0.9345 (tt0) cc_final: 0.9095 (tt0) REVERT: E 252 ASN cc_start: 0.8092 (m110) cc_final: 0.7059 (m-40) REVERT: E 255 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8787 (mt-10) REVERT: E 256 PHE cc_start: 0.8396 (m-10) cc_final: 0.8089 (m-10) REVERT: E 306 THR cc_start: 0.8889 (m) cc_final: 0.8635 (p) REVERT: E 324 GLU cc_start: 0.8696 (tt0) cc_final: 0.8437 (tt0) REVERT: E 338 MET cc_start: 0.8176 (tpp) cc_final: 0.7882 (tpp) REVERT: E 359 ARG cc_start: 0.9040 (ttm110) cc_final: 0.8443 (ttm110) REVERT: E 481 TRP cc_start: 0.8128 (t-100) cc_final: 0.7727 (t-100) REVERT: F 242 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8591 (mtmm) REVERT: F 248 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8823 (pp) REVERT: F 289 THR cc_start: 0.9475 (m) cc_final: 0.9054 (p) REVERT: F 339 ARG cc_start: 0.9285 (tmm-80) cc_final: 0.8857 (ttt90) REVERT: F 391 SER cc_start: 0.8612 (m) cc_final: 0.8181 (p) REVERT: F 395 SER cc_start: 0.8715 (m) cc_final: 0.8243 (t) REVERT: F 411 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8225 (pt0) outliers start: 92 outliers final: 48 residues processed: 577 average time/residue: 0.3396 time to fit residues: 284.3614 Evaluate side-chains 507 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 453 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 219 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 152 optimal weight: 4.9990 chunk 149 optimal weight: 40.0000 chunk 192 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 207 optimal weight: 0.3980 chunk 65 optimal weight: 50.0000 chunk 22 optimal weight: 40.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS A 435 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS C 435 HIS D 450 GLN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.098787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.076881 restraints weight = 44481.524| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.81 r_work: 0.3045 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 18402 Z= 0.160 Angle : 0.626 11.040 24981 Z= 0.321 Chirality : 0.048 0.197 2978 Planarity : 0.005 0.054 3338 Dihedral : 4.229 36.546 2749 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.50 % Allowed : 20.52 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2520 helix: 1.89 (0.16), residues: 1134 sheet: -0.55 (0.21), residues: 534 loop : 0.27 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 481 HIS 0.004 0.001 HIS B 169 PHE 0.020 0.002 PHE D 364 TYR 0.017 0.002 TYR C 486 ARG 0.016 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 958) hydrogen bonds : angle 4.08224 ( 2805) covalent geometry : bond 0.00380 (18402) covalent geometry : angle 0.62599 (24981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 464 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.8865 (tt0) cc_final: 0.8521 (tt0) REVERT: A 244 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8009 (tppt) REVERT: A 270 ILE cc_start: 0.9035 (mt) cc_final: 0.8593 (mt) REVERT: A 339 ARG cc_start: 0.8914 (tpt-90) cc_final: 0.8536 (tpp80) REVERT: A 340 ASP cc_start: 0.9042 (t70) cc_final: 0.8576 (m-30) REVERT: A 351 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8083 (mp0) REVERT: A 364 PHE cc_start: 0.9174 (t80) cc_final: 0.8732 (t80) REVERT: A 365 ASP cc_start: 0.8806 (m-30) cc_final: 0.8394 (m-30) REVERT: A 388 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8602 (tp30) REVERT: A 411 GLU cc_start: 0.9280 (tp30) cc_final: 0.8952 (mt-10) REVERT: B 193 MET cc_start: 0.8702 (tpp) cc_final: 0.8302 (tpt) REVERT: B 197 GLN cc_start: 0.8258 (pt0) cc_final: 0.7932 (pt0) REVERT: B 206 ARG cc_start: 0.7671 (mmm160) cc_final: 0.7431 (mmm160) REVERT: B 339 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: B 420 ILE cc_start: 0.8836 (mt) cc_final: 0.8565 (mt) REVERT: B 487 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8036 (t80) REVERT: C 246 ASP cc_start: 0.9028 (p0) cc_final: 0.8744 (p0) REVERT: C 407 LYS cc_start: 0.9055 (tptm) cc_final: 0.8509 (tppt) REVERT: C 411 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8517 (mt-10) REVERT: D 182 THR cc_start: 0.8846 (p) cc_final: 0.8635 (p) REVERT: D 333 SER cc_start: 0.9581 (m) cc_final: 0.9357 (p) REVERT: D 351 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7922 (mp0) REVERT: D 390 ILE cc_start: 0.9165 (mt) cc_final: 0.8927 (mt) REVERT: D 481 TRP cc_start: 0.7787 (t-100) cc_final: 0.7396 (t-100) REVERT: E 202 GLN cc_start: 0.9333 (tt0) cc_final: 0.9067 (tt0) REVERT: E 252 ASN cc_start: 0.8238 (m110) cc_final: 0.7036 (m110) REVERT: E 255 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8838 (pt0) REVERT: E 256 PHE cc_start: 0.8633 (m-10) cc_final: 0.8145 (m-10) REVERT: E 343 LYS cc_start: 0.9253 (ttmm) cc_final: 0.9039 (ttmm) REVERT: E 357 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7363 (tm-30) REVERT: E 359 ARG cc_start: 0.8710 (ttm110) cc_final: 0.8276 (ttm110) REVERT: E 438 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6957 (tm-30) REVERT: F 188 ASP cc_start: 0.8583 (t0) cc_final: 0.8222 (p0) REVERT: F 242 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8388 (mtmm) REVERT: F 289 THR cc_start: 0.9550 (m) cc_final: 0.9182 (p) REVERT: F 378 MET cc_start: 0.9252 (mtt) cc_final: 0.8933 (mtt) REVERT: F 391 SER cc_start: 0.8867 (m) cc_final: 0.8405 (p) REVERT: F 395 SER cc_start: 0.9130 (m) cc_final: 0.8728 (t) REVERT: F 407 LYS cc_start: 0.8737 (tptm) cc_final: 0.8468 (tptp) outliers start: 78 outliers final: 44 residues processed: 505 average time/residue: 0.3292 time to fit residues: 242.8885 Evaluate side-chains 447 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 400 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 95 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 435 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.072757 restraints weight = 44971.441| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.79 r_work: 0.2952 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.8693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18402 Z= 0.213 Angle : 0.662 10.152 24981 Z= 0.341 Chirality : 0.049 0.198 2978 Planarity : 0.005 0.053 3338 Dihedral : 4.360 39.472 2749 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.27 % Allowed : 22.36 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2520 helix: 1.87 (0.16), residues: 1122 sheet: -0.61 (0.21), residues: 562 loop : 0.20 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 481 HIS 0.006 0.001 HIS A 435 PHE 0.024 0.002 PHE F 243 TYR 0.011 0.001 TYR F 455 ARG 0.023 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 958) hydrogen bonds : angle 4.12374 ( 2805) covalent geometry : bond 0.00497 (18402) covalent geometry : angle 0.66175 (24981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 403 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: A 191 GLN cc_start: 0.8984 (tt0) cc_final: 0.8614 (tt0) REVERT: A 244 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8431 (tppt) REVERT: A 270 ILE cc_start: 0.9170 (mt) cc_final: 0.8632 (mt) REVERT: A 273 CYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7848 (p) REVERT: A 339 ARG cc_start: 0.8907 (tpt-90) cc_final: 0.8559 (tpp80) REVERT: A 340 ASP cc_start: 0.8993 (t70) cc_final: 0.8656 (m-30) REVERT: A 365 ASP cc_start: 0.9108 (m-30) cc_final: 0.8765 (m-30) REVERT: A 388 GLU cc_start: 0.9037 (tt0) cc_final: 0.8752 (tt0) REVERT: A 407 LYS cc_start: 0.9583 (tptp) cc_final: 0.9287 (tppt) REVERT: A 479 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7559 (ptm160) REVERT: B 193 MET cc_start: 0.8846 (tpp) cc_final: 0.8537 (tpt) REVERT: B 206 ARG cc_start: 0.7663 (mmm160) cc_final: 0.7392 (mmm160) REVERT: B 343 LYS cc_start: 0.9405 (mtpp) cc_final: 0.9073 (mtmt) REVERT: B 359 ARG cc_start: 0.9397 (mtm-85) cc_final: 0.8973 (mtm-85) REVERT: B 473 THR cc_start: 0.8757 (m) cc_final: 0.8447 (p) REVERT: C 339 ARG cc_start: 0.8670 (ttp-170) cc_final: 0.8128 (ttm-80) REVERT: C 347 ARG cc_start: 0.9142 (mtm-85) cc_final: 0.8796 (mtp85) REVERT: C 370 MET cc_start: 0.9071 (mtt) cc_final: 0.8566 (mtt) REVERT: C 396 MET cc_start: 0.8946 (mtt) cc_final: 0.8677 (mtt) REVERT: C 402 TYR cc_start: 0.8971 (m-80) cc_final: 0.8554 (m-80) REVERT: C 411 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8922 (mt-10) REVERT: D 304 VAL cc_start: 0.9481 (t) cc_final: 0.9250 (p) REVERT: D 333 SER cc_start: 0.9591 (m) cc_final: 0.9387 (p) REVERT: D 481 TRP cc_start: 0.8033 (t-100) cc_final: 0.7713 (t-100) REVERT: E 251 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8706 (mmmm) REVERT: E 252 ASN cc_start: 0.8573 (m110) cc_final: 0.7411 (m-40) REVERT: E 255 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8802 (pt0) REVERT: E 256 PHE cc_start: 0.8887 (m-10) cc_final: 0.8471 (m-10) REVERT: E 343 LYS cc_start: 0.9449 (ttmm) cc_final: 0.9225 (ttmm) REVERT: E 357 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7843 (tm-30) REVERT: E 396 MET cc_start: 0.9259 (mtm) cc_final: 0.9045 (ttm) REVERT: F 188 ASP cc_start: 0.8633 (t0) cc_final: 0.8341 (t70) REVERT: F 248 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8764 (pp) REVERT: F 395 SER cc_start: 0.9326 (m) cc_final: 0.9115 (t) REVERT: F 473 THR cc_start: 0.8254 (p) cc_final: 0.8032 (p) outliers start: 74 outliers final: 43 residues processed: 447 average time/residue: 0.3471 time to fit residues: 224.6077 Evaluate side-chains 398 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 352 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 42 optimal weight: 120.0000 chunk 44 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 109 optimal weight: 0.0050 chunk 190 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN C 292 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 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 = 0.3540 r_free = 0.3540 target = 0.095458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073530 restraints weight = 44493.126| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.77 r_work: 0.2971 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.8982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18402 Z= 0.143 Angle : 0.616 9.966 24981 Z= 0.314 Chirality : 0.047 0.230 2978 Planarity : 0.005 0.052 3338 Dihedral : 4.202 39.515 2749 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.29 % Allowed : 24.73 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.17), residues: 2520 helix: 2.00 (0.16), residues: 1124 sheet: -0.52 (0.21), residues: 558 loop : 0.23 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 481 HIS 0.005 0.001 HIS F 319 PHE 0.021 0.002 PHE E 297 TYR 0.021 0.001 TYR B 486 ARG 0.016 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 958) hydrogen bonds : angle 3.92761 ( 2805) covalent geometry : bond 0.00340 (18402) covalent geometry : angle 0.61602 (24981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 397 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.9028 (tt0) cc_final: 0.8657 (tt0) REVERT: A 244 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8558 (tppt) REVERT: A 270 ILE cc_start: 0.9055 (mt) cc_final: 0.8522 (mt) REVERT: A 273 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7758 (p) REVERT: A 339 ARG cc_start: 0.8896 (tpt-90) cc_final: 0.8633 (tpp80) REVERT: A 340 ASP cc_start: 0.8988 (t70) cc_final: 0.8670 (m-30) REVERT: A 351 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 365 ASP cc_start: 0.9082 (m-30) cc_final: 0.8786 (m-30) REVERT: A 479 ARG cc_start: 0.7682 (ttp-110) cc_final: 0.7413 (ptm160) REVERT: B 180 GLN cc_start: 0.8994 (pt0) cc_final: 0.8691 (pt0) REVERT: B 184 VAL cc_start: 0.9239 (t) cc_final: 0.9016 (p) REVERT: B 193 MET cc_start: 0.8787 (tpp) cc_final: 0.8380 (tpp) REVERT: B 244 LYS cc_start: 0.8273 (tppt) cc_final: 0.8060 (tptm) REVERT: B 339 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7751 (ttm-80) REVERT: B 343 LYS cc_start: 0.9354 (mtpp) cc_final: 0.9050 (mtmt) REVERT: B 359 ARG cc_start: 0.9391 (mtm-85) cc_final: 0.8973 (mtm-85) REVERT: B 473 THR cc_start: 0.8759 (m) cc_final: 0.8419 (p) REVERT: C 339 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.7984 (ttm-80) REVERT: C 347 ARG cc_start: 0.9109 (mtm-85) cc_final: 0.8807 (mtp85) REVERT: C 351 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: C 370 MET cc_start: 0.9006 (mtt) cc_final: 0.8503 (mtt) REVERT: C 396 MET cc_start: 0.9019 (mtt) cc_final: 0.8723 (mtt) REVERT: C 407 LYS cc_start: 0.9223 (tptm) cc_final: 0.8556 (tppt) REVERT: C 411 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8789 (mt-10) REVERT: C 465 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8822 (mmmt) REVERT: C 491 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8738 (ttp80) REVERT: D 351 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8184 (mp0) REVERT: D 481 TRP cc_start: 0.7985 (t-100) cc_final: 0.7596 (t-100) REVERT: E 251 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8822 (mmmm) REVERT: E 252 ASN cc_start: 0.8606 (m110) cc_final: 0.7468 (m-40) REVERT: E 255 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8804 (pt0) REVERT: E 256 PHE cc_start: 0.8929 (m-10) cc_final: 0.8492 (m-10) REVERT: E 343 LYS cc_start: 0.9445 (ttmm) cc_final: 0.9221 (ttmm) REVERT: E 357 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7642 (tm-30) REVERT: E 438 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6814 (tm-30) REVERT: F 188 ASP cc_start: 0.8630 (t0) cc_final: 0.8330 (t70) REVERT: F 248 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8721 (pp) REVERT: F 410 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8708 (mtmm) outliers start: 57 outliers final: 33 residues processed: 432 average time/residue: 0.3886 time to fit residues: 242.4089 Evaluate side-chains 406 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 370 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 229 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 113 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 132 optimal weight: 40.0000 chunk 104 optimal weight: 5.9990 chunk 169 optimal weight: 40.0000 chunk 84 optimal weight: 120.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN C 292 ASN C 384 ASN C 435 HIS E 368 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.093147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.071414 restraints weight = 44754.111| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.71 r_work: 0.2918 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.9719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18402 Z= 0.193 Angle : 0.651 10.328 24981 Z= 0.332 Chirality : 0.048 0.191 2978 Planarity : 0.005 0.052 3338 Dihedral : 4.288 40.142 2749 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.69 % Allowed : 23.92 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2520 helix: 1.93 (0.16), residues: 1136 sheet: -0.62 (0.21), residues: 556 loop : 0.25 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 481 HIS 0.008 0.001 HIS F 319 PHE 0.027 0.002 PHE F 256 TYR 0.019 0.001 TYR C 402 ARG 0.017 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 958) hydrogen bonds : angle 3.98152 ( 2805) covalent geometry : bond 0.00460 (18402) covalent geometry : angle 0.65082 (24981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 367 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8310 (pm20) cc_final: 0.7893 (pm20) REVERT: A 191 GLN cc_start: 0.9028 (tt0) cc_final: 0.8674 (tt0) REVERT: A 196 CYS cc_start: 0.9424 (m) cc_final: 0.9218 (m) REVERT: A 244 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8628 (tppt) REVERT: A 270 ILE cc_start: 0.9120 (mt) cc_final: 0.8522 (mp) REVERT: A 273 CYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 339 ARG cc_start: 0.8960 (tpt-90) cc_final: 0.8689 (tpp80) REVERT: A 340 ASP cc_start: 0.8956 (t70) cc_final: 0.8755 (m-30) REVERT: A 365 ASP cc_start: 0.9216 (m-30) cc_final: 0.8917 (m-30) REVERT: A 391 SER cc_start: 0.9143 (t) cc_final: 0.8925 (p) REVERT: A 396 MET cc_start: 0.7811 (ttt) cc_final: 0.7370 (ttt) REVERT: A 407 LYS cc_start: 0.9571 (tppt) cc_final: 0.9257 (tppt) REVERT: B 180 GLN cc_start: 0.9076 (pt0) cc_final: 0.8709 (pt0) REVERT: B 244 LYS cc_start: 0.8440 (tppt) cc_final: 0.8147 (tptm) REVERT: B 433 ILE cc_start: 0.9505 (mm) cc_final: 0.9287 (mm) REVERT: B 453 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: B 473 THR cc_start: 0.8863 (m) cc_final: 0.8481 (p) REVERT: C 339 ARG cc_start: 0.8771 (ttp-170) cc_final: 0.8291 (ttm-80) REVERT: C 347 ARG cc_start: 0.9169 (mtm-85) cc_final: 0.8882 (mtp85) REVERT: C 351 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: C 407 LYS cc_start: 0.9291 (tptm) cc_final: 0.8688 (tppt) REVERT: C 411 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8906 (mt-10) REVERT: C 491 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8728 (ttp80) REVERT: D 202 GLN cc_start: 0.9352 (tt0) cc_final: 0.8877 (tm-30) REVERT: D 274 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8951 (mmm-85) REVERT: D 343 LYS cc_start: 0.9322 (mmmm) cc_final: 0.8951 (mtmm) REVERT: D 351 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8389 (mt-10) REVERT: D 481 TRP cc_start: 0.8170 (t-100) cc_final: 0.7525 (t-100) REVERT: D 491 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7900 (ttp80) REVERT: E 251 LYS cc_start: 0.9193 (ttmm) cc_final: 0.8716 (mmmm) REVERT: E 252 ASN cc_start: 0.8787 (m110) cc_final: 0.7775 (m-40) REVERT: E 255 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8765 (pt0) REVERT: E 256 PHE cc_start: 0.9052 (m-10) cc_final: 0.8622 (m-10) REVERT: E 343 LYS cc_start: 0.9479 (ttmm) cc_final: 0.9264 (ttmm) REVERT: E 357 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7694 (tm-30) REVERT: E 396 MET cc_start: 0.9435 (mtm) cc_final: 0.9232 (mtp) REVERT: E 438 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6918 (tm-30) REVERT: F 188 ASP cc_start: 0.8668 (t0) cc_final: 0.8338 (t70) REVERT: F 242 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8484 (mtmm) REVERT: F 248 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8789 (pp) REVERT: F 394 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8390 (mt-10) REVERT: F 398 THR cc_start: 0.9298 (m) cc_final: 0.8922 (p) REVERT: F 410 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8771 (mtmm) outliers start: 64 outliers final: 36 residues processed: 403 average time/residue: 0.3541 time to fit residues: 204.0376 Evaluate side-chains 358 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 238 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 164 optimal weight: 50.0000 chunk 13 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN ** C 319 HIS ** 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 = 0.3500 r_free = 0.3500 target = 0.093001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.071953 restraints weight = 44690.569| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.69 r_work: 0.2933 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 1.0003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18402 Z= 0.157 Angle : 0.640 9.998 24981 Z= 0.324 Chirality : 0.047 0.189 2978 Planarity : 0.005 0.052 3338 Dihedral : 4.178 39.638 2749 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.40 % Allowed : 24.61 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2520 helix: 1.98 (0.16), residues: 1136 sheet: -0.56 (0.21), residues: 542 loop : 0.24 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 481 HIS 0.007 0.001 HIS F 319 PHE 0.025 0.002 PHE F 256 TYR 0.018 0.001 TYR C 402 ARG 0.014 0.001 ARG E 359 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 958) hydrogen bonds : angle 3.90782 ( 2805) covalent geometry : bond 0.00378 (18402) covalent geometry : angle 0.64028 (24981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 348 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8399 (pm20) cc_final: 0.7921 (pm20) REVERT: A 191 GLN cc_start: 0.9074 (tt0) cc_final: 0.8777 (tt0) REVERT: A 270 ILE cc_start: 0.9064 (mt) cc_final: 0.8485 (mp) REVERT: A 273 CYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8234 (p) REVERT: A 343 LYS cc_start: 0.9259 (mtmt) cc_final: 0.8913 (mttt) REVERT: A 365 ASP cc_start: 0.9226 (m-30) cc_final: 0.8854 (m-30) REVERT: A 396 MET cc_start: 0.7786 (ttt) cc_final: 0.7435 (ttt) REVERT: B 180 GLN cc_start: 0.9072 (pt0) cc_final: 0.8742 (pt0) REVERT: B 193 MET cc_start: 0.8983 (tpt) cc_final: 0.8056 (tpp) REVERT: B 197 GLN cc_start: 0.8840 (pt0) cc_final: 0.8215 (mp10) REVERT: B 247 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8206 (mmtt) REVERT: B 453 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: B 473 THR cc_start: 0.8928 (m) cc_final: 0.8534 (p) REVERT: C 324 GLU cc_start: 0.8931 (tt0) cc_final: 0.8662 (tt0) REVERT: C 339 ARG cc_start: 0.8794 (ttp-170) cc_final: 0.8412 (ttm-80) REVERT: C 347 ARG cc_start: 0.9155 (mtm-85) cc_final: 0.8781 (mtp85) REVERT: C 351 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: C 407 LYS cc_start: 0.9260 (tptm) cc_final: 0.8707 (tppt) REVERT: C 411 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8927 (mt-10) REVERT: C 491 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8663 (ttp80) REVERT: D 202 GLN cc_start: 0.9357 (tt0) cc_final: 0.8884 (tm-30) REVERT: D 351 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8204 (mp0) REVERT: D 481 TRP cc_start: 0.8189 (t-100) cc_final: 0.7488 (t-100) REVERT: E 251 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8872 (mmmm) REVERT: E 252 ASN cc_start: 0.8825 (m110) cc_final: 0.7838 (m-40) REVERT: E 255 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8759 (pt0) REVERT: E 256 PHE cc_start: 0.9064 (m-10) cc_final: 0.8620 (m-10) REVERT: E 324 GLU cc_start: 0.8912 (tt0) cc_final: 0.8482 (tp30) REVERT: E 357 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7550 (tm-30) REVERT: E 388 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8406 (pt0) REVERT: E 396 MET cc_start: 0.9392 (mtm) cc_final: 0.9034 (mtp) REVERT: F 188 ASP cc_start: 0.8651 (t0) cc_final: 0.8312 (t70) REVERT: F 242 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8505 (mtmm) REVERT: F 314 GLN cc_start: 0.8977 (tt0) cc_final: 0.8682 (tp40) REVERT: F 343 LYS cc_start: 0.9513 (ttmm) cc_final: 0.9288 (mmmm) REVERT: F 398 THR cc_start: 0.9323 (m) cc_final: 0.8998 (p) REVERT: F 410 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8842 (mtmm) outliers start: 59 outliers final: 37 residues processed: 386 average time/residue: 0.3315 time to fit residues: 186.8373 Evaluate side-chains 352 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 129 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 173 optimal weight: 50.0000 chunk 186 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN F 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.071372 restraints weight = 45053.054| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.72 r_work: 0.2924 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 1.0259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18402 Z= 0.171 Angle : 0.666 11.248 24981 Z= 0.337 Chirality : 0.047 0.173 2978 Planarity : 0.005 0.055 3338 Dihedral : 4.224 39.554 2749 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.82 % Allowed : 25.59 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2520 helix: 1.98 (0.16), residues: 1138 sheet: -0.64 (0.21), residues: 536 loop : 0.22 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 481 HIS 0.008 0.001 HIS F 319 PHE 0.027 0.002 PHE F 256 TYR 0.014 0.001 TYR C 402 ARG 0.014 0.001 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 958) hydrogen bonds : angle 3.93800 ( 2805) covalent geometry : bond 0.00411 (18402) covalent geometry : angle 0.66559 (24981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 327 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8455 (pm20) cc_final: 0.8023 (pm20) REVERT: A 191 GLN cc_start: 0.9143 (tt0) cc_final: 0.8721 (tt0) REVERT: A 244 LYS cc_start: 0.8986 (tppt) cc_final: 0.8282 (tppt) REVERT: A 273 CYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8307 (p) REVERT: A 343 LYS cc_start: 0.9257 (mtmt) cc_final: 0.8925 (mttt) REVERT: A 365 ASP cc_start: 0.9274 (m-30) cc_final: 0.8948 (m-30) REVERT: A 396 MET cc_start: 0.7652 (ttt) cc_final: 0.7300 (ttt) REVERT: A 407 LYS cc_start: 0.9556 (tppt) cc_final: 0.9116 (tppt) REVERT: B 193 MET cc_start: 0.8951 (tpt) cc_final: 0.8026 (tpp) REVERT: B 197 GLN cc_start: 0.8946 (pt0) cc_final: 0.8402 (mp10) REVERT: B 338 MET cc_start: 0.9339 (mmt) cc_final: 0.8830 (mmt) REVERT: B 453 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: B 473 THR cc_start: 0.8978 (m) cc_final: 0.8593 (p) REVERT: C 324 GLU cc_start: 0.8903 (tt0) cc_final: 0.8624 (tt0) REVERT: C 339 ARG cc_start: 0.8868 (ttp-170) cc_final: 0.8545 (ttt-90) REVERT: C 347 ARG cc_start: 0.9146 (mtm-85) cc_final: 0.8854 (mtp85) REVERT: C 351 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: C 407 LYS cc_start: 0.9296 (tptm) cc_final: 0.8753 (tppt) REVERT: C 411 GLU cc_start: 0.9403 (mt-10) cc_final: 0.8967 (mt-10) REVERT: C 477 ARG cc_start: 0.9160 (tpp-160) cc_final: 0.8793 (tpp80) REVERT: C 491 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8657 (ttp80) REVERT: D 202 GLN cc_start: 0.9367 (tt0) cc_final: 0.8784 (tm-30) REVERT: D 251 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8851 (ptmm) REVERT: D 338 MET cc_start: 0.8984 (tpp) cc_final: 0.8428 (mmt) REVERT: D 351 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8255 (mp0) REVERT: D 391 SER cc_start: 0.9300 (t) cc_final: 0.8888 (p) REVERT: D 481 TRP cc_start: 0.8300 (t-100) cc_final: 0.7529 (t-100) REVERT: E 251 LYS cc_start: 0.9228 (ttmm) cc_final: 0.8825 (mmmm) REVERT: E 252 ASN cc_start: 0.8909 (m110) cc_final: 0.7938 (m-40) REVERT: E 255 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8752 (pt0) REVERT: E 256 PHE cc_start: 0.9105 (m-10) cc_final: 0.8675 (m-10) REVERT: E 324 GLU cc_start: 0.8904 (tt0) cc_final: 0.8526 (tp30) REVERT: E 357 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7606 (tm-30) REVERT: E 388 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8413 (pt0) REVERT: E 396 MET cc_start: 0.9420 (mtm) cc_final: 0.9199 (mtp) REVERT: E 469 LYS cc_start: 0.8867 (ptmm) cc_final: 0.8488 (ptmm) REVERT: E 498 ASP cc_start: 0.8808 (m-30) cc_final: 0.8393 (m-30) REVERT: F 188 ASP cc_start: 0.8657 (t0) cc_final: 0.8320 (t70) REVERT: F 242 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8484 (mtmm) REVERT: F 343 LYS cc_start: 0.9499 (ttmm) cc_final: 0.9278 (mmmm) REVERT: F 398 THR cc_start: 0.9379 (m) cc_final: 0.9093 (p) outliers start: 49 outliers final: 36 residues processed: 357 average time/residue: 0.3465 time to fit residues: 179.8984 Evaluate side-chains 348 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 116 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 169 optimal weight: 50.0000 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 40.0000 chunk 158 optimal weight: 30.0000 chunk 74 optimal weight: 8.9990 chunk 42 optimal weight: 110.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 368 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS C 202 GLN E 202 GLN F 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.069164 restraints weight = 45449.281| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.68 r_work: 0.2887 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 1.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18402 Z= 0.231 Angle : 0.710 12.642 24981 Z= 0.361 Chirality : 0.049 0.206 2978 Planarity : 0.005 0.061 3338 Dihedral : 4.368 40.755 2749 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.65 % Allowed : 26.34 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2520 helix: 1.87 (0.16), residues: 1138 sheet: -0.76 (0.21), residues: 532 loop : 0.12 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 481 HIS 0.008 0.001 HIS F 319 PHE 0.028 0.002 PHE F 256 TYR 0.025 0.002 TYR F 148 ARG 0.014 0.001 ARG E 359 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 958) hydrogen bonds : angle 4.08143 ( 2805) covalent geometry : bond 0.00550 (18402) covalent geometry : angle 0.71030 (24981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 318 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8508 (pm20) cc_final: 0.8105 (pm20) REVERT: A 191 GLN cc_start: 0.9135 (tt0) cc_final: 0.8844 (tt0) REVERT: A 244 LYS cc_start: 0.9057 (tppt) cc_final: 0.8318 (tppt) REVERT: A 273 CYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8404 (p) REVERT: A 343 LYS cc_start: 0.9307 (mtmt) cc_final: 0.8938 (mttt) REVERT: A 365 ASP cc_start: 0.9236 (m-30) cc_final: 0.8918 (m-30) REVERT: A 370 MET cc_start: 0.8984 (mtp) cc_final: 0.8632 (mtp) REVERT: B 180 GLN cc_start: 0.8952 (pt0) cc_final: 0.8718 (pt0) REVERT: B 192 LEU cc_start: 0.9116 (tp) cc_final: 0.8912 (tp) REVERT: B 193 MET cc_start: 0.9028 (tpt) cc_final: 0.8334 (tpp) REVERT: B 197 GLN cc_start: 0.8995 (pt0) cc_final: 0.8498 (mp10) REVERT: B 453 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7879 (m-10) REVERT: C 194 ASN cc_start: 0.9201 (m-40) cc_final: 0.8954 (m110) REVERT: C 250 MET cc_start: 0.8956 (tpp) cc_final: 0.8714 (mmm) REVERT: C 324 GLU cc_start: 0.8971 (tt0) cc_final: 0.8704 (tt0) REVERT: C 339 ARG cc_start: 0.8940 (ttp-170) cc_final: 0.8648 (ttt-90) REVERT: C 345 CYS cc_start: 0.9234 (m) cc_final: 0.8876 (m) REVERT: C 347 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8837 (mtp85) REVERT: C 351 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: C 477 ARG cc_start: 0.9208 (tpp-160) cc_final: 0.8840 (tpp80) REVERT: C 491 ARG cc_start: 0.8876 (ttp80) cc_final: 0.8661 (ttp80) REVERT: D 202 GLN cc_start: 0.9381 (tt0) cc_final: 0.8871 (tm-30) REVERT: D 251 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8872 (ptmm) REVERT: D 274 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8925 (mmm-85) REVERT: D 351 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8446 (mp0) REVERT: D 481 TRP cc_start: 0.8436 (t-100) cc_final: 0.7766 (t-100) REVERT: D 491 ARG cc_start: 0.8688 (ppt170) cc_final: 0.8311 (pmt-80) REVERT: E 251 LYS cc_start: 0.9298 (ttmm) cc_final: 0.8942 (mmmm) REVERT: E 252 ASN cc_start: 0.9028 (m110) cc_final: 0.8143 (m-40) REVERT: E 255 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8734 (pt0) REVERT: E 256 PHE cc_start: 0.9243 (m-10) cc_final: 0.8821 (m-10) REVERT: E 324 GLU cc_start: 0.8889 (tt0) cc_final: 0.8502 (tp30) REVERT: E 357 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 388 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8417 (pt0) REVERT: E 445 ASP cc_start: 0.9412 (m-30) cc_final: 0.9191 (t0) REVERT: E 469 LYS cc_start: 0.8885 (ptmm) cc_final: 0.8517 (ptmm) REVERT: E 498 ASP cc_start: 0.8883 (m-30) cc_final: 0.8451 (m-30) REVERT: F 188 ASP cc_start: 0.8720 (t0) cc_final: 0.8387 (t70) REVERT: F 242 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8429 (mtmm) REVERT: F 258 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8737 (p) REVERT: F 343 LYS cc_start: 0.9505 (ttmm) cc_final: 0.9272 (mmmm) REVERT: F 396 MET cc_start: 0.8895 (ttm) cc_final: 0.8623 (mtp) REVERT: F 398 THR cc_start: 0.9500 (m) cc_final: 0.9205 (p) outliers start: 46 outliers final: 32 residues processed: 349 average time/residue: 0.3825 time to fit residues: 194.1287 Evaluate side-chains 339 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 301 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 51 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 189 optimal weight: 0.0270 chunk 93 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 164 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 chunk 220 optimal weight: 5.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 169 HIS ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN F 463 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.070963 restraints weight = 44787.618| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.65 r_work: 0.2915 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 1.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18402 Z= 0.156 Angle : 0.680 11.312 24981 Z= 0.343 Chirality : 0.047 0.179 2978 Planarity : 0.005 0.057 3338 Dihedral : 4.283 40.366 2749 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.71 % Allowed : 26.22 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2520 helix: 1.89 (0.16), residues: 1138 sheet: -0.74 (0.22), residues: 518 loop : 0.09 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 481 HIS 0.008 0.001 HIS F 319 PHE 0.028 0.002 PHE F 256 TYR 0.022 0.001 TYR F 148 ARG 0.013 0.001 ARG E 359 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 958) hydrogen bonds : angle 3.96725 ( 2805) covalent geometry : bond 0.00381 (18402) covalent geometry : angle 0.67955 (24981) =============================================================================== Job complete usr+sys time: 8888.49 seconds wall clock time: 155 minutes 2.51 seconds (9302.51 seconds total)