Starting phenix.real_space_refine on Mon May 19 10:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e25_47436/05_2025/9e25_47436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e25_47436/05_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_47436/05_2025/9e25_47436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e25_47436/05_2025/9e25_47436.map" model { file = "/net/cci-nas-00/data/ceres_data/9e25_47436/05_2025/9e25_47436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e25_47436/05_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-5687/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: 4.58 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: 2.11 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: 5.69 Time building geometry restraints manager: 5.29 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.530 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- 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 : 1.876 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: 0.3449 time to fit residues: 378.6075 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 : 1.901 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.102443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081241 restraints weight = 44302.858| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.94 r_work: 0.3106 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 2.113 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: 0.7791 (mt) cc_final: 0.7427 (mm) REVERT: A 315 LEU cc_start: 0.8486 (mp) cc_final: 0.8130 (mp) REVERT: A 339 ARG cc_start: 0.8536 (tpt-90) cc_final: 0.7916 (tpt-90) REVERT: A 345 CYS cc_start: 0.8156 (m) cc_final: 0.7746 (m) REVERT: A 371 ASN cc_start: 0.7736 (t0) cc_final: 0.7449 (t0) REVERT: A 388 GLU cc_start: 0.7876 (tt0) cc_final: 0.7620 (tp30) REVERT: A 411 GLU cc_start: 0.9025 (tp30) cc_final: 0.8505 (pt0) REVERT: A 475 ILE cc_start: 0.6586 (mt) cc_final: 0.6375 (mp) REVERT: B 189 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7205 (t0) REVERT: B 193 MET cc_start: 0.8461 (tpp) cc_final: 0.8079 (tpt) REVERT: B 225 ASN cc_start: 0.8208 (t0) cc_final: 0.7898 (t0) REVERT: B 273 CYS cc_start: 0.8454 (m) cc_final: 0.8052 (p) REVERT: B 339 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7421 (ttm-80) REVERT: B 365 ASP cc_start: 0.8350 (m-30) cc_final: 0.7906 (m-30) REVERT: B 367 LEU cc_start: 0.8208 (mp) cc_final: 0.8004 (mp) REVERT: B 448 VAL cc_start: 0.8421 (t) cc_final: 0.8216 (p) REVERT: B 482 ASP cc_start: 0.8747 (m-30) cc_final: 0.8326 (p0) REVERT: B 497 LEU cc_start: 0.6456 (mp) cc_final: 0.6091 (pp) REVERT: C 174 GLU cc_start: 0.7724 (tt0) cc_final: 0.7407 (tt0) REVERT: C 192 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8259 (tp) REVERT: C 259 ILE cc_start: 0.8649 (mp) cc_final: 0.8444 (mm) REVERT: C 319 HIS cc_start: 0.7798 (t-170) cc_final: 0.7281 (t-90) REVERT: C 355 VAL cc_start: 0.8898 (t) cc_final: 0.8678 (p) REVERT: C 411 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 418 ASP cc_start: 0.7004 (m-30) cc_final: 0.6756 (m-30) REVERT: C 491 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8806 (ttp80) REVERT: D 251 LYS cc_start: 0.9468 (tptp) cc_final: 0.9232 (ttpp) REVERT: D 324 GLU cc_start: 0.8279 (tt0) cc_final: 0.7683 (tm-30) REVERT: D 337 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6801 (m) REVERT: D 390 ILE cc_start: 0.8284 (mt) cc_final: 0.7999 (mt) REVERT: D 410 LYS cc_start: 0.9037 (mttm) cc_final: 0.8777 (mttt) REVERT: E 199 ILE cc_start: 0.8643 (mt) cc_final: 0.8430 (mm) REVERT: E 202 GLN cc_start: 0.9280 (tt0) cc_final: 0.9036 (tt0) REVERT: E 306 THR cc_start: 0.8609 (m) cc_final: 0.8279 (p) REVERT: E 324 GLU cc_start: 0.8333 (tt0) cc_final: 0.8132 (tt0) REVERT: E 338 MET cc_start: 0.8059 (tpp) cc_final: 0.7506 (tpp) REVERT: E 396 MET cc_start: 0.8510 (mmm) cc_final: 0.8210 (mmm) REVERT: F 218 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7845 (mm) REVERT: F 339 ARG cc_start: 0.9045 (tmm-80) cc_final: 0.8591 (ttt90) REVERT: F 341 LEU cc_start: 0.7737 (mt) cc_final: 0.7530 (mt) REVERT: F 345 CYS cc_start: 0.8698 (m) cc_final: 0.8245 (m) REVERT: F 382 HIS cc_start: 0.7717 (t-90) cc_final: 0.7374 (t-90) REVERT: F 395 SER cc_start: 0.8505 (m) cc_final: 0.8216 (t) outliers start: 84 outliers final: 36 residues processed: 624 average time/residue: 0.3348 time to fit residues: 303.1286 Evaluate side-chains 537 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 497 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 491 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 46 optimal weight: 40.0000 chunk 29 optimal weight: 8.9990 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: 6.5788 ------------------------------------------------------------------------------- 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** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.098029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.076513 restraints weight = 44273.051| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.80 r_work: 0.3048 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18402 Z= 0.215 Angle : 0.694 11.134 24981 Z= 0.360 Chirality : 0.049 0.248 2978 Planarity : 0.006 0.060 3338 Dihedral : 4.410 33.588 2749 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.59 % Allowed : 18.85 % Favored : 75.56 % 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: 1.82 (0.16), residues: 1134 sheet: -0.63 (0.21), residues: 524 loop : 0.12 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 481 HIS 0.008 0.001 HIS B 435 PHE 0.021 0.002 PHE D 364 TYR 0.011 0.001 TYR A 486 ARG 0.014 0.001 ARG D 432 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 958) hydrogen bonds : angle 4.24329 ( 2805) covalent geometry : bond 0.00504 (18402) covalent geometry : angle 0.69422 (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 628 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 531 time to evaluate : 2.125 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: 0.8736 (tt0) cc_final: 0.8442 (tt0) REVERT: A 270 ILE cc_start: 0.9075 (mt) cc_final: 0.8611 (mt) REVERT: A 312 GLU cc_start: 0.8272 (tp30) cc_final: 0.8059 (tp30) REVERT: A 339 ARG cc_start: 0.8855 (tpt-90) cc_final: 0.8385 (tpp80) REVERT: A 351 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7954 (mp0) REVERT: A 364 PHE cc_start: 0.9044 (t80) cc_final: 0.8461 (t80) REVERT: A 365 ASP cc_start: 0.8777 (m-30) cc_final: 0.8158 (m-30) REVERT: A 371 ASN cc_start: 0.8055 (t0) cc_final: 0.7751 (t0) REVERT: A 388 GLU cc_start: 0.8797 (tt0) cc_final: 0.8488 (tp30) REVERT: A 410 LYS cc_start: 0.9193 (mttp) cc_final: 0.8729 (mttp) REVERT: B 193 MET cc_start: 0.8669 (tpp) cc_final: 0.8338 (tpt) REVERT: B 270 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8173 (mt) REVERT: B 339 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: B 343 LYS cc_start: 0.9255 (mtpp) cc_final: 0.9003 (mtmm) REVERT: B 408 THR cc_start: 0.9060 (m) cc_final: 0.8482 (p) REVERT: B 482 ASP cc_start: 0.9030 (m-30) cc_final: 0.8616 (p0) REVERT: B 487 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8138 (t80) REVERT: B 497 LEU cc_start: 0.7040 (mp) cc_final: 0.6558 (pp) REVERT: C 206 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8160 (ttp80) REVERT: C 231 LEU cc_start: 0.9086 (mm) cc_final: 0.8878 (mt) REVERT: C 312 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7876 (mm-30) REVERT: C 338 MET cc_start: 0.8517 (mmm) cc_final: 0.8266 (mmt) REVERT: C 343 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8725 (mtmm) REVERT: C 407 LYS cc_start: 0.8938 (tptm) cc_final: 0.8489 (tppt) REVERT: C 411 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8465 (mt-10) REVERT: D 171 VAL cc_start: 0.9014 (t) cc_final: 0.8777 (t) REVERT: D 243 PHE cc_start: 0.8567 (t80) cc_final: 0.8327 (t80) REVERT: D 333 SER cc_start: 0.9561 (m) cc_final: 0.9333 (p) REVERT: D 481 TRP cc_start: 0.7646 (t-100) cc_final: 0.7135 (t-100) REVERT: E 202 GLN cc_start: 0.9343 (tt0) cc_final: 0.9079 (tt0) REVERT: E 252 ASN cc_start: 0.8125 (m110) cc_final: 0.7894 (m-40) REVERT: E 256 PHE cc_start: 0.8456 (m-10) cc_final: 0.8235 (m-10) REVERT: E 306 THR cc_start: 0.8918 (m) cc_final: 0.8664 (p) REVERT: E 324 GLU cc_start: 0.8731 (tt0) cc_final: 0.8466 (tt0) REVERT: E 338 MET cc_start: 0.8199 (tpp) cc_final: 0.7897 (tpp) REVERT: E 343 LYS cc_start: 0.9326 (ttmt) cc_final: 0.9083 (ttmm) REVERT: E 359 ARG cc_start: 0.9042 (ttm110) cc_final: 0.8452 (ttm110) REVERT: F 181 LEU cc_start: 0.9445 (tp) cc_final: 0.9241 (tp) REVERT: F 242 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8610 (mtmm) REVERT: F 248 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8830 (pp) REVERT: F 289 THR cc_start: 0.9494 (m) cc_final: 0.9087 (p) REVERT: F 339 ARG cc_start: 0.9308 (tmm-80) cc_final: 0.8881 (ttt90) REVERT: F 391 SER cc_start: 0.8677 (m) cc_final: 0.8239 (p) REVERT: F 395 SER cc_start: 0.8793 (m) cc_final: 0.8316 (t) outliers start: 97 outliers final: 52 residues processed: 580 average time/residue: 0.3218 time to fit residues: 268.4281 Evaluate side-chains 504 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 448 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 412 MET 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 407 LYS 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 419 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 196 CYS 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 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: 9.9990 chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 149 optimal weight: 30.0000 chunk 192 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 chunk 65 optimal weight: 40.0000 chunk 22 optimal weight: 0.0570 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 435 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074073 restraints weight = 44733.057| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.84 r_work: 0.2991 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.7941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 18402 Z= 0.198 Angle : 0.663 10.825 24981 Z= 0.340 Chirality : 0.049 0.195 2978 Planarity : 0.005 0.055 3338 Dihedral : 4.352 38.450 2749 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.84 % Allowed : 20.40 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2520 helix: 1.82 (0.16), residues: 1134 sheet: -0.57 (0.21), residues: 548 loop : 0.23 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 481 HIS 0.005 0.001 HIS B 435 PHE 0.021 0.002 PHE D 364 TYR 0.016 0.002 TYR C 402 ARG 0.010 0.001 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 958) hydrogen bonds : angle 4.14918 ( 2805) covalent geometry : bond 0.00472 (18402) covalent geometry : angle 0.66304 (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 526 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 442 time to evaluate : 1.952 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: 0.8916 (tt0) cc_final: 0.8528 (tt0) REVERT: A 244 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8103 (tppt) REVERT: A 270 ILE cc_start: 0.9133 (mt) cc_final: 0.8677 (mt) REVERT: A 339 ARG cc_start: 0.8876 (tpt-90) cc_final: 0.8603 (tpp80) REVERT: A 340 ASP cc_start: 0.9024 (t70) cc_final: 0.8572 (m-30) REVERT: A 351 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8298 (mp0) REVERT: A 365 ASP cc_start: 0.9008 (m-30) cc_final: 0.8732 (m-30) REVERT: A 384 ASN cc_start: 0.8441 (m-40) cc_final: 0.8200 (m-40) REVERT: A 388 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: A 407 LYS cc_start: 0.9548 (tptp) cc_final: 0.9293 (tppt) REVERT: A 411 GLU cc_start: 0.9329 (tp30) cc_final: 0.9092 (mt-10) REVERT: B 193 MET cc_start: 0.8835 (tpp) cc_final: 0.8496 (tpt) REVERT: B 339 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8032 (ttm-80) REVERT: B 343 LYS cc_start: 0.9312 (mtpp) cc_final: 0.8969 (mtpt) REVERT: B 390 ILE cc_start: 0.8748 (mp) cc_final: 0.8521 (mp) REVERT: B 420 ILE cc_start: 0.9039 (mt) cc_final: 0.8773 (mt) REVERT: B 473 THR cc_start: 0.8812 (m) cc_final: 0.8449 (p) REVERT: B 487 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8022 (t80) REVERT: C 246 ASP cc_start: 0.9085 (p0) cc_final: 0.8846 (p0) REVERT: C 339 ARG cc_start: 0.8567 (ttp-170) cc_final: 0.7869 (ttm-80) REVERT: C 343 LYS cc_start: 0.9285 (mtmm) cc_final: 0.9024 (mtmm) REVERT: C 411 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8705 (mt-10) REVERT: C 452 LEU cc_start: 0.9333 (mt) cc_final: 0.9083 (mp) REVERT: D 333 SER cc_start: 0.9581 (m) cc_final: 0.9363 (p) REVERT: D 351 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8010 (mp0) REVERT: E 202 GLN cc_start: 0.9353 (tt0) cc_final: 0.9114 (tt0) REVERT: E 252 ASN cc_start: 0.8366 (m110) cc_final: 0.7280 (m110) REVERT: E 255 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8915 (pt0) REVERT: E 256 PHE cc_start: 0.8777 (m-10) cc_final: 0.8275 (m-10) REVERT: E 343 LYS cc_start: 0.9423 (ttmt) cc_final: 0.9173 (ttmm) REVERT: E 407 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7893 (tttm) REVERT: E 438 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7027 (tm-30) REVERT: E 469 LYS cc_start: 0.8643 (pptt) cc_final: 0.8324 (pptt) REVERT: F 188 ASP cc_start: 0.8628 (t0) cc_final: 0.8268 (p0) REVERT: F 245 LYS cc_start: 0.8736 (mppt) cc_final: 0.8400 (mmtm) REVERT: F 378 MET cc_start: 0.9367 (mtt) cc_final: 0.9115 (mtt) REVERT: F 391 SER cc_start: 0.9094 (m) cc_final: 0.8642 (p) REVERT: F 395 SER cc_start: 0.9270 (m) cc_final: 0.8864 (t) outliers start: 84 outliers final: 48 residues processed: 491 average time/residue: 0.3406 time to fit residues: 240.8212 Evaluate side-chains 435 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 384 time to evaluate : 1.923 ------------------------------------------------------------------------------- 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 345 CYS Chi-restraints excluded: chain A residue 367 LEU 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 178 LYS 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 448 VAL 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 B residue 497 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 325 THR Chi-restraints excluded: chain C residue 330 LEU 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 466 VAL 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 E residue 196 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 277 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 200 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 218 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 399 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 95 optimal weight: 8.9990 chunk 162 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 371 ASN F 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.093046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071092 restraints weight = 45280.107| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.73 r_work: 0.2916 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.9181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18402 Z= 0.239 Angle : 0.670 9.905 24981 Z= 0.345 Chirality : 0.049 0.220 2978 Planarity : 0.005 0.059 3338 Dihedral : 4.425 39.747 2749 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.67 % Allowed : 21.73 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2520 helix: 1.82 (0.16), residues: 1120 sheet: -0.64 (0.21), residues: 560 loop : 0.16 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 481 HIS 0.005 0.001 HIS A 435 PHE 0.029 0.002 PHE A 172 TYR 0.024 0.002 TYR C 486 ARG 0.023 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 958) hydrogen bonds : angle 4.16498 ( 2805) covalent geometry : bond 0.00559 (18402) covalent geometry : angle 0.67048 (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 458 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 377 time to evaluate : 1.938 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: 0.8082 (pm20) cc_final: 0.7429 (pm20) REVERT: A 191 GLN cc_start: 0.9045 (tt0) cc_final: 0.8712 (tt0) REVERT: A 196 CYS cc_start: 0.9395 (m) cc_final: 0.9150 (m) REVERT: A 244 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8515 (tppt) REVERT: A 270 ILE cc_start: 0.9141 (mt) cc_final: 0.8839 (mt) REVERT: A 273 CYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8102 (p) REVERT: A 339 ARG cc_start: 0.8962 (tpt-90) cc_final: 0.8654 (tpp80) REVERT: A 340 ASP cc_start: 0.8972 (t70) cc_final: 0.8705 (m-30) REVERT: A 365 ASP cc_start: 0.9144 (m-30) cc_final: 0.8842 (m-30) REVERT: A 388 GLU cc_start: 0.9103 (tt0) cc_final: 0.8344 (tp30) REVERT: A 407 LYS cc_start: 0.9572 (tptp) cc_final: 0.9227 (tppt) REVERT: A 440 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8511 (t) REVERT: B 180 GLN cc_start: 0.9170 (pt0) cc_final: 0.8926 (pt0) REVERT: B 193 MET cc_start: 0.8848 (tpp) cc_final: 0.8413 (tpp) REVERT: B 343 LYS cc_start: 0.9397 (mtpp) cc_final: 0.9069 (mtmt) REVERT: B 473 THR cc_start: 0.8869 (m) cc_final: 0.8465 (p) REVERT: C 339 ARG cc_start: 0.8840 (ttp-170) cc_final: 0.8163 (ttm-80) REVERT: C 343 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8984 (mtmm) REVERT: C 347 ARG cc_start: 0.9154 (mtm-85) cc_final: 0.8870 (mtp85) REVERT: C 351 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: C 370 MET cc_start: 0.9130 (mtt) cc_final: 0.8708 (mtt) REVERT: C 402 TYR cc_start: 0.8894 (m-80) cc_final: 0.8571 (m-80) REVERT: D 202 GLN cc_start: 0.9356 (tt0) cc_final: 0.8863 (tm-30) REVERT: D 278 VAL cc_start: 0.8322 (t) cc_final: 0.8096 (p) REVERT: E 202 GLN cc_start: 0.9372 (tt0) cc_final: 0.9161 (tt0) REVERT: E 251 LYS cc_start: 0.9159 (ttmm) cc_final: 0.8893 (mmmm) REVERT: E 252 ASN cc_start: 0.8667 (m110) cc_final: 0.7728 (m110) REVERT: E 255 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8916 (pt0) REVERT: E 256 PHE cc_start: 0.8993 (m-10) cc_final: 0.8553 (m-10) REVERT: E 343 LYS cc_start: 0.9495 (ttmt) cc_final: 0.9256 (ttmm) REVERT: E 396 MET cc_start: 0.9431 (ttm) cc_final: 0.9090 (ttm) REVERT: E 438 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6993 (tm-30) REVERT: F 188 ASP cc_start: 0.8638 (t0) cc_final: 0.8368 (t70) REVERT: F 248 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8791 (pp) REVERT: F 256 PHE cc_start: 0.9288 (m-10) cc_final: 0.9000 (m-10) REVERT: F 410 LYS cc_start: 0.8953 (mttm) cc_final: 0.8746 (mttm) REVERT: F 443 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8060 (mp0) outliers start: 81 outliers final: 45 residues processed: 432 average time/residue: 0.3500 time to fit residues: 215.4436 Evaluate side-chains 380 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 298 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 454 VAL 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 C residue 245 LYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 365 ASP 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 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 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 207 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 406 SER 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: 7.9990 chunk 190 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN C 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.092955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.071207 restraints weight = 44937.311| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.71 r_work: 0.2915 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.9569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18402 Z= 0.184 Angle : 0.619 9.790 24981 Z= 0.318 Chirality : 0.047 0.218 2978 Planarity : 0.005 0.054 3338 Dihedral : 4.298 40.519 2749 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.69 % Allowed : 23.98 % Favored : 72.33 % 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: 1.11 (0.17), residues: 2520 helix: 1.90 (0.16), residues: 1134 sheet: -0.59 (0.21), residues: 542 loop : 0.20 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 481 HIS 0.009 0.001 HIS F 319 PHE 0.016 0.002 PHE D 364 TYR 0.021 0.001 TYR C 402 ARG 0.010 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 958) hydrogen bonds : angle 4.03409 ( 2805) covalent geometry : bond 0.00435 (18402) covalent geometry : angle 0.61864 (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 409 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 345 time to evaluate : 2.006 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: A 180 GLN cc_start: 0.7977 (pm20) cc_final: 0.7240 (pm20) REVERT: A 191 GLN cc_start: 0.9035 (tt0) cc_final: 0.8688 (tt0) REVERT: A 196 CYS cc_start: 0.9417 (m) cc_final: 0.9191 (m) REVERT: A 244 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8664 (tppt) REVERT: A 270 ILE cc_start: 0.9102 (mt) cc_final: 0.8797 (mt) REVERT: A 273 CYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 339 ARG cc_start: 0.9014 (tpt-90) cc_final: 0.8712 (tpp80) REVERT: A 340 ASP cc_start: 0.8956 (t70) cc_final: 0.8741 (m-30) REVERT: A 351 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 365 ASP cc_start: 0.9190 (m-30) cc_final: 0.8914 (m-30) REVERT: A 370 MET cc_start: 0.8815 (mtp) cc_final: 0.8419 (mtp) REVERT: A 388 GLU cc_start: 0.9116 (tt0) cc_final: 0.8883 (tt0) REVERT: A 391 SER cc_start: 0.9080 (t) cc_final: 0.8820 (p) REVERT: A 412 MET cc_start: 0.9642 (ttp) cc_final: 0.9422 (ttm) REVERT: B 343 LYS cc_start: 0.9387 (mtpp) cc_final: 0.9077 (mtmt) REVERT: B 408 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.8916 (p) REVERT: C 339 ARG cc_start: 0.8856 (ttp-170) cc_final: 0.8405 (ttm-80) REVERT: C 345 CYS cc_start: 0.9093 (m) cc_final: 0.8778 (m) REVERT: C 347 ARG cc_start: 0.9176 (mtm-85) cc_final: 0.8824 (mtp85) REVERT: C 351 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: C 370 MET cc_start: 0.9112 (mtt) cc_final: 0.8648 (mtt) REVERT: D 202 GLN cc_start: 0.9357 (tt0) cc_final: 0.8876 (tm-30) REVERT: D 351 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8229 (mp0) REVERT: D 394 GLU cc_start: 0.9350 (tm-30) cc_final: 0.9012 (tm-30) REVERT: D 422 GLN cc_start: 0.8602 (tp40) cc_final: 0.7139 (tp40) REVERT: E 202 GLN cc_start: 0.9366 (tt0) cc_final: 0.9129 (tt0) REVERT: E 251 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8963 (mmmm) REVERT: E 252 ASN cc_start: 0.8739 (m110) cc_final: 0.7817 (m110) REVERT: E 255 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8804 (pt0) REVERT: E 256 PHE cc_start: 0.9023 (m-10) cc_final: 0.8615 (m-10) REVERT: E 324 GLU cc_start: 0.8893 (tt0) cc_final: 0.8404 (tp30) REVERT: E 343 LYS cc_start: 0.9502 (ttmt) cc_final: 0.9261 (ttmm) REVERT: E 396 MET cc_start: 0.9451 (ttm) cc_final: 0.9121 (ttm) REVERT: F 188 ASP cc_start: 0.8595 (t0) cc_final: 0.8287 (t70) REVERT: F 248 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8754 (pp) REVERT: F 256 PHE cc_start: 0.9297 (m-10) cc_final: 0.9080 (m-10) REVERT: F 314 GLN cc_start: 0.8979 (mt0) cc_final: 0.8731 (tt0) REVERT: F 407 LYS cc_start: 0.9159 (tppt) cc_final: 0.8925 (tppt) outliers start: 64 outliers final: 43 residues processed: 380 average time/residue: 0.3148 time to fit residues: 175.8980 Evaluate side-chains 364 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 440 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 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 353 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 447 ILE 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 449 THR Chi-restraints excluded: chain C residue 452 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 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 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 407 LYS 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 207 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 307 CYS Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 399 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 229 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 29 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 132 optimal weight: 40.0000 chunk 104 optimal weight: 20.0000 chunk 169 optimal weight: 30.0000 chunk 84 optimal weight: 120.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.069336 restraints weight = 44842.611| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.69 r_work: 0.2878 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 1.0262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18402 Z= 0.213 Angle : 0.656 9.747 24981 Z= 0.337 Chirality : 0.048 0.209 2978 Planarity : 0.005 0.053 3338 Dihedral : 4.394 40.983 2749 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.80 % Allowed : 23.92 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2520 helix: 1.84 (0.16), residues: 1136 sheet: -0.70 (0.21), residues: 528 loop : 0.11 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 481 HIS 0.008 0.001 HIS F 319 PHE 0.024 0.002 PHE D 243 TYR 0.018 0.001 TYR F 486 ARG 0.013 0.001 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 958) hydrogen bonds : angle 4.14821 ( 2805) covalent geometry : bond 0.00502 (18402) covalent geometry : angle 0.65599 (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 395 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 329 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.9111 (tt0) cc_final: 0.8836 (tt0) REVERT: A 273 CYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8386 (p) REVERT: A 339 ARG cc_start: 0.9136 (tpt-90) cc_final: 0.8619 (tpp80) REVERT: A 365 ASP cc_start: 0.9261 (m-30) cc_final: 0.8906 (m-30) REVERT: A 370 MET cc_start: 0.9060 (mtp) cc_final: 0.8565 (mtp) REVERT: A 391 SER cc_start: 0.9125 (t) cc_final: 0.8876 (p) REVERT: B 158 ASP cc_start: 0.9029 (m-30) cc_final: 0.8329 (t0) REVERT: B 193 MET cc_start: 0.9067 (tpt) cc_final: 0.8332 (tpp) REVERT: B 197 GLN cc_start: 0.9046 (pt0) cc_final: 0.8464 (mp10) REVERT: B 202 GLN cc_start: 0.9564 (tt0) cc_final: 0.9361 (tt0) REVERT: B 343 LYS cc_start: 0.9387 (mtpp) cc_final: 0.9120 (mtmt) REVERT: B 408 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.8913 (p) REVERT: B 453 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: C 194 ASN cc_start: 0.9189 (m-40) cc_final: 0.8944 (m110) REVERT: C 339 ARG cc_start: 0.8957 (ttp-170) cc_final: 0.8550 (ttm-80) REVERT: C 345 CYS cc_start: 0.9182 (m) cc_final: 0.8833 (m) REVERT: C 347 ARG cc_start: 0.9188 (mtm-85) cc_final: 0.8772 (mtp85) REVERT: C 351 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: C 370 MET cc_start: 0.9148 (mtt) cc_final: 0.8718 (mtt) REVERT: C 411 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9034 (mt-10) REVERT: C 477 ARG cc_start: 0.9198 (tpp-160) cc_final: 0.8801 (tpp80) REVERT: D 202 GLN cc_start: 0.9386 (tt0) cc_final: 0.8858 (tm-30) REVERT: D 215 ASP cc_start: 0.8184 (t70) cc_final: 0.7426 (t0) REVERT: D 242 LYS cc_start: 0.8911 (mttp) cc_final: 0.8554 (mttt) REVERT: D 244 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8638 (mmtm) REVERT: D 343 LYS cc_start: 0.9299 (mmmm) cc_final: 0.8961 (mtmm) REVERT: D 351 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8175 (mp0) REVERT: D 407 LYS cc_start: 0.9084 (tptt) cc_final: 0.8835 (tppt) REVERT: D 422 GLN cc_start: 0.8627 (tp40) cc_final: 0.7239 (tp40) REVERT: E 202 GLN cc_start: 0.9420 (tt0) cc_final: 0.9201 (tt0) REVERT: E 251 LYS cc_start: 0.9258 (ttmm) cc_final: 0.8887 (mmmm) REVERT: E 252 ASN cc_start: 0.8924 (m110) cc_final: 0.8008 (m-40) REVERT: E 255 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8750 (pt0) REVERT: E 256 PHE cc_start: 0.9157 (m-10) cc_final: 0.8753 (m-10) REVERT: E 324 GLU cc_start: 0.8874 (tt0) cc_final: 0.8393 (tp30) REVERT: E 343 LYS cc_start: 0.9526 (ttmt) cc_final: 0.9286 (ttmm) REVERT: E 396 MET cc_start: 0.9460 (ttm) cc_final: 0.9039 (ttm) REVERT: E 445 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.9101 (t0) REVERT: E 495 GLU cc_start: 0.9324 (tp30) cc_final: 0.8875 (tp30) REVERT: F 188 ASP cc_start: 0.8697 (t0) cc_final: 0.8379 (t70) REVERT: F 258 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8848 (p) REVERT: F 314 GLN cc_start: 0.8997 (mt0) cc_final: 0.8787 (tt0) REVERT: F 407 LYS cc_start: 0.9281 (tppt) cc_final: 0.8991 (tppt) REVERT: F 410 LYS cc_start: 0.9148 (mmtp) cc_final: 0.8921 (mttm) outliers start: 66 outliers final: 41 residues processed: 370 average time/residue: 0.3378 time to fit residues: 181.7762 Evaluate side-chains 355 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 440 VAL 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 283 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 408 THR 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 452 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 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 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 407 LYS Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 445 ASP 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 207 VAL Chi-restraints excluded: chain F residue 258 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 238 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 164 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 46 optimal weight: 40.0000 chunk 71 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 384 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 252 ASN F 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.069696 restraints weight = 45025.360| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.69 r_work: 0.2886 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 1.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18402 Z= 0.197 Angle : 0.639 10.920 24981 Z= 0.328 Chirality : 0.047 0.173 2978 Planarity : 0.005 0.053 3338 Dihedral : 4.319 40.817 2749 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.34 % Allowed : 24.67 % 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: 1.01 (0.17), residues: 2520 helix: 1.90 (0.16), residues: 1136 sheet: -0.76 (0.21), residues: 532 loop : 0.11 (0.21), residues: 852 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 0.023 0.002 PHE B 243 TYR 0.018 0.001 TYR F 486 ARG 0.013 0.001 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 958) hydrogen bonds : angle 4.05079 ( 2805) covalent geometry : bond 0.00466 (18402) covalent geometry : angle 0.63948 (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 384 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 326 time to evaluate : 2.170 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 173 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8827 (pt) REVERT: A 191 GLN cc_start: 0.9177 (tt0) cc_final: 0.8769 (tt0) REVERT: A 273 CYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8459 (p) REVERT: A 339 ARG cc_start: 0.9133 (tpt-90) cc_final: 0.8309 (tpp80) REVERT: A 343 LYS cc_start: 0.9294 (mmmm) cc_final: 0.9057 (mmmm) REVERT: A 365 ASP cc_start: 0.9282 (m-30) cc_final: 0.8634 (m-30) REVERT: A 370 MET cc_start: 0.9102 (mtp) cc_final: 0.8647 (mtp) REVERT: A 388 GLU cc_start: 0.9079 (tt0) cc_final: 0.8862 (tt0) REVERT: A 391 SER cc_start: 0.9183 (t) cc_final: 0.8900 (p) REVERT: A 410 LYS cc_start: 0.9466 (mmtp) cc_final: 0.9256 (mmtp) REVERT: B 158 ASP cc_start: 0.9083 (m-30) cc_final: 0.8582 (t0) REVERT: B 193 MET cc_start: 0.8965 (tpt) cc_final: 0.8319 (tpp) REVERT: B 197 GLN cc_start: 0.9076 (pt0) cc_final: 0.8554 (mp10) REVERT: B 244 LYS cc_start: 0.8586 (tppt) cc_final: 0.8267 (ttpt) REVERT: B 343 LYS cc_start: 0.9285 (mtpp) cc_final: 0.9021 (mtmt) REVERT: B 453 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7837 (m-10) REVERT: C 194 ASN cc_start: 0.9179 (m-40) cc_final: 0.8926 (m110) REVERT: C 245 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8677 (ptpp) REVERT: C 314 GLN cc_start: 0.9057 (tt0) cc_final: 0.8832 (tp40) REVERT: C 339 ARG cc_start: 0.8979 (ttp-170) cc_final: 0.8577 (ttm-80) REVERT: C 345 CYS cc_start: 0.9191 (m) cc_final: 0.8836 (m) REVERT: C 347 ARG cc_start: 0.9189 (mtm-85) cc_final: 0.8840 (mtp85) REVERT: C 351 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: C 370 MET cc_start: 0.9079 (mtt) cc_final: 0.8635 (mtt) REVERT: C 477 ARG cc_start: 0.9203 (tpp-160) cc_final: 0.8796 (tpp80) REVERT: D 202 GLN cc_start: 0.9401 (tt0) cc_final: 0.8866 (tm-30) REVERT: D 215 ASP cc_start: 0.8247 (t70) cc_final: 0.7563 (t0) REVERT: D 251 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8916 (ptmm) REVERT: D 407 LYS cc_start: 0.9084 (tptt) cc_final: 0.8839 (tppt) REVERT: D 422 GLN cc_start: 0.8613 (tp40) cc_final: 0.7238 (tp40) REVERT: E 202 GLN cc_start: 0.9422 (tt0) cc_final: 0.9124 (tt0) REVERT: E 251 LYS cc_start: 0.9282 (ttmm) cc_final: 0.8928 (mmmm) REVERT: E 252 ASN cc_start: 0.8985 (m110) cc_final: 0.8046 (m-40) REVERT: E 255 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8745 (pt0) REVERT: E 256 PHE cc_start: 0.9228 (m-10) cc_final: 0.8810 (m-10) REVERT: E 324 GLU cc_start: 0.8876 (tt0) cc_final: 0.8619 (tt0) REVERT: E 343 LYS cc_start: 0.9525 (ttmt) cc_final: 0.9259 (ttmm) REVERT: E 365 ASP cc_start: 0.9250 (m-30) cc_final: 0.8942 (m-30) REVERT: E 396 MET cc_start: 0.9486 (ttm) cc_final: 0.9063 (ttm) REVERT: E 469 LYS cc_start: 0.8905 (ptmm) cc_final: 0.8560 (ptmm) REVERT: E 495 GLU cc_start: 0.9352 (tp30) cc_final: 0.8906 (tp30) REVERT: F 188 ASP cc_start: 0.8715 (t0) cc_final: 0.8388 (t70) REVERT: F 258 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8839 (p) REVERT: F 314 GLN cc_start: 0.9004 (mt0) cc_final: 0.8800 (tt0) REVERT: F 407 LYS cc_start: 0.9283 (tppt) cc_final: 0.8993 (tppt) outliers start: 58 outliers final: 42 residues processed: 362 average time/residue: 0.3218 time to fit residues: 171.0146 Evaluate side-chains 358 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 310 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 469 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 304 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 453 PHE 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 449 THR Chi-restraints excluded: chain C residue 452 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 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 D residue 457 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 258 SER 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 434 THR Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 129 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.070460 restraints weight = 45068.755| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.70 r_work: 0.2898 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 1.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18402 Z= 0.162 Angle : 0.631 10.266 24981 Z= 0.322 Chirality : 0.047 0.172 2978 Planarity : 0.005 0.053 3338 Dihedral : 4.253 40.421 2749 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 25.59 % Favored : 71.41 % 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: 1.07 (0.17), residues: 2520 helix: 1.96 (0.16), residues: 1134 sheet: -0.75 (0.21), residues: 530 loop : 0.15 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 481 HIS 0.006 0.001 HIS F 319 PHE 0.022 0.002 PHE B 243 TYR 0.019 0.001 TYR F 486 ARG 0.012 0.001 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 958) hydrogen bonds : angle 3.99208 ( 2805) covalent geometry : bond 0.00388 (18402) covalent geometry : angle 0.63069 (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: 52 poor density : 324 time to evaluate : 1.922 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 191 GLN cc_start: 0.9126 (tt0) cc_final: 0.8841 (tt0) REVERT: A 273 CYS cc_start: 0.8777 (m) cc_final: 0.8482 (p) REVERT: A 365 ASP cc_start: 0.9288 (m-30) cc_final: 0.8945 (m-30) REVERT: A 370 MET cc_start: 0.9066 (mtp) cc_final: 0.8622 (mtp) REVERT: A 391 SER cc_start: 0.9193 (t) cc_final: 0.8900 (p) REVERT: A 398 THR cc_start: 0.9441 (m) cc_final: 0.9115 (p) REVERT: B 158 ASP cc_start: 0.9108 (m-30) cc_final: 0.8626 (t0) REVERT: B 193 MET cc_start: 0.9012 (tpt) cc_final: 0.8110 (tpp) REVERT: B 197 GLN cc_start: 0.9085 (pt0) cc_final: 0.8611 (mp10) REVERT: B 206 ARG cc_start: 0.7456 (mmm160) cc_final: 0.6969 (tpp-160) REVERT: B 244 LYS cc_start: 0.8524 (tppt) cc_final: 0.8229 (ttpt) REVERT: B 343 LYS cc_start: 0.9295 (mtpp) cc_final: 0.9045 (mtmt) REVERT: B 396 MET cc_start: 0.9311 (mtt) cc_final: 0.8371 (mmt) REVERT: B 453 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7718 (m-10) REVERT: C 194 ASN cc_start: 0.9188 (m-40) cc_final: 0.8934 (m110) REVERT: C 339 ARG cc_start: 0.8940 (ttp-170) cc_final: 0.8533 (ttm-80) REVERT: C 345 CYS cc_start: 0.9157 (m) cc_final: 0.8806 (m) REVERT: C 347 ARG cc_start: 0.9167 (mtm-85) cc_final: 0.8896 (mtp85) REVERT: C 351 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: C 370 MET cc_start: 0.9071 (mtt) cc_final: 0.8644 (mtt) REVERT: C 477 ARG cc_start: 0.9186 (tpp-160) cc_final: 0.8811 (tpp80) REVERT: D 202 GLN cc_start: 0.9396 (tt0) cc_final: 0.8849 (tm-30) REVERT: D 251 LYS cc_start: 0.9184 (ttpp) cc_final: 0.8876 (ptmm) REVERT: D 407 LYS cc_start: 0.9063 (tptt) cc_final: 0.8817 (tppt) REVERT: D 422 GLN cc_start: 0.8614 (tp40) cc_final: 0.7255 (tp40) REVERT: E 202 GLN cc_start: 0.9426 (tt0) cc_final: 0.9128 (tt0) REVERT: E 251 LYS cc_start: 0.9304 (ttmm) cc_final: 0.8964 (mmmm) REVERT: E 252 ASN cc_start: 0.9046 (m110) cc_final: 0.8150 (m-40) REVERT: E 255 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8734 (pt0) REVERT: E 256 PHE cc_start: 0.9256 (m-10) cc_final: 0.8830 (m-10) REVERT: E 324 GLU cc_start: 0.8858 (tt0) cc_final: 0.8583 (tt0) REVERT: E 343 LYS cc_start: 0.9525 (ttmt) cc_final: 0.9251 (ttmm) REVERT: E 365 ASP cc_start: 0.9229 (m-30) cc_final: 0.8926 (m-30) REVERT: E 396 MET cc_start: 0.9482 (ttm) cc_final: 0.9062 (ttm) REVERT: E 469 LYS cc_start: 0.8884 (ptmm) cc_final: 0.8532 (ptmm) REVERT: E 495 GLU cc_start: 0.9366 (tp30) cc_final: 0.8966 (tp30) REVERT: E 498 ASP cc_start: 0.8888 (m-30) cc_final: 0.8433 (m-30) REVERT: F 188 ASP cc_start: 0.8727 (t0) cc_final: 0.8400 (t70) REVERT: F 242 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8451 (mtmm) REVERT: F 314 GLN cc_start: 0.9030 (mt0) cc_final: 0.8774 (tt0) outliers start: 52 outliers final: 35 residues processed: 358 average time/residue: 0.3222 time to fit residues: 168.4976 Evaluate side-chains 346 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 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 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 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 449 THR Chi-restraints excluded: chain C residue 452 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 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 402 TYR Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 242 LYS 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 402 TYR Chi-restraints excluded: chain F residue 434 THR 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: 0.0980 chunk 97 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 40.0000 chunk 158 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 120.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.071115 restraints weight = 45187.715| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.70 r_work: 0.2917 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 1.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18402 Z= 0.140 Angle : 0.631 9.851 24981 Z= 0.322 Chirality : 0.046 0.172 2978 Planarity : 0.005 0.053 3338 Dihedral : 4.187 39.620 2749 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.31 % Allowed : 26.80 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2520 helix: 2.03 (0.16), residues: 1132 sheet: -0.74 (0.22), residues: 520 loop : 0.17 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 481 HIS 0.006 0.001 HIS F 319 PHE 0.024 0.002 PHE B 243 TYR 0.021 0.001 TYR F 148 ARG 0.010 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 958) hydrogen bonds : angle 3.92214 ( 2805) covalent geometry : bond 0.00336 (18402) covalent geometry : angle 0.63112 (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 362 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 322 time to evaluate : 2.128 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 191 GLN cc_start: 0.9198 (tt0) cc_final: 0.8864 (tt0) REVERT: A 202 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8737 (pp30) REVERT: A 339 ARG cc_start: 0.9113 (tpt-90) cc_final: 0.8390 (tpp80) REVERT: A 343 LYS cc_start: 0.9230 (mmmm) cc_final: 0.9025 (mmmm) REVERT: A 347 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8883 (mtm-85) REVERT: A 365 ASP cc_start: 0.9307 (m-30) cc_final: 0.8649 (m-30) REVERT: A 370 MET cc_start: 0.9046 (mtp) cc_final: 0.8638 (mtp) REVERT: A 391 SER cc_start: 0.9184 (t) cc_final: 0.8892 (p) REVERT: B 158 ASP cc_start: 0.9122 (m-30) cc_final: 0.8621 (t0) REVERT: B 193 MET cc_start: 0.9019 (tpt) cc_final: 0.8386 (tpp) REVERT: B 197 GLN cc_start: 0.9103 (pt0) cc_final: 0.8714 (mp10) REVERT: B 206 ARG cc_start: 0.7475 (mmm160) cc_final: 0.7040 (tpp-160) REVERT: B 244 LYS cc_start: 0.8475 (tppt) cc_final: 0.8196 (ttpt) REVERT: B 343 LYS cc_start: 0.9287 (mtpp) cc_final: 0.9059 (mtmt) REVERT: B 348 MET cc_start: 0.9507 (ttp) cc_final: 0.9252 (ttm) REVERT: B 396 MET cc_start: 0.9261 (mtt) cc_final: 0.8331 (mmt) REVERT: B 453 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: C 193 MET cc_start: 0.9380 (mmm) cc_final: 0.9030 (mmm) REVERT: C 194 ASN cc_start: 0.9194 (m-40) cc_final: 0.8952 (m-40) REVERT: C 250 MET cc_start: 0.9011 (tpp) cc_final: 0.8750 (mmm) REVERT: C 314 GLN cc_start: 0.9039 (tt0) cc_final: 0.8833 (tp40) REVERT: C 339 ARG cc_start: 0.8917 (ttp-170) cc_final: 0.8523 (ttm-80) REVERT: C 345 CYS cc_start: 0.9121 (m) cc_final: 0.8783 (m) REVERT: C 347 ARG cc_start: 0.9140 (mtm-85) cc_final: 0.8732 (mtp85) REVERT: C 351 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: C 370 MET cc_start: 0.9048 (mtt) cc_final: 0.8626 (mtt) REVERT: C 477 ARG cc_start: 0.9158 (tpp-160) cc_final: 0.8837 (tpp80) REVERT: D 215 ASP cc_start: 0.8291 (t70) cc_final: 0.7524 (t0) REVERT: D 251 LYS cc_start: 0.9205 (ttpp) cc_final: 0.8920 (ptmm) REVERT: D 338 MET cc_start: 0.9052 (tpp) cc_final: 0.8498 (mmt) REVERT: D 371 ASN cc_start: 0.8813 (t0) cc_final: 0.8597 (t0) REVERT: D 407 LYS cc_start: 0.9123 (tptt) cc_final: 0.8880 (tppt) REVERT: D 422 GLN cc_start: 0.8560 (tp40) cc_final: 0.7244 (tp40) REVERT: E 202 GLN cc_start: 0.9410 (tt0) cc_final: 0.9114 (tt0) REVERT: E 251 LYS cc_start: 0.9298 (ttmm) cc_final: 0.8973 (mmmm) REVERT: E 252 ASN cc_start: 0.9068 (m110) cc_final: 0.8144 (m-40) REVERT: E 255 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8730 (pt0) REVERT: E 256 PHE cc_start: 0.9275 (m-10) cc_final: 0.8857 (m-10) REVERT: E 324 GLU cc_start: 0.8808 (tt0) cc_final: 0.8548 (tt0) REVERT: E 343 LYS cc_start: 0.9529 (ttmt) cc_final: 0.9253 (ttmm) REVERT: E 365 ASP cc_start: 0.9218 (m-30) cc_final: 0.8891 (m-30) REVERT: E 396 MET cc_start: 0.9445 (ttm) cc_final: 0.9036 (ttm) REVERT: E 469 LYS cc_start: 0.8875 (ptmm) cc_final: 0.8503 (ptmm) REVERT: E 495 GLU cc_start: 0.9332 (tp30) cc_final: 0.8937 (tp30) REVERT: E 498 ASP cc_start: 0.8884 (m-30) cc_final: 0.8439 (m-30) REVERT: F 188 ASP cc_start: 0.8660 (t0) cc_final: 0.8336 (t70) REVERT: F 314 GLN cc_start: 0.8997 (mt0) cc_final: 0.8771 (tt0) outliers start: 40 outliers final: 31 residues processed: 348 average time/residue: 0.3265 time to fit residues: 166.8605 Evaluate side-chains 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 307 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 324 GLU 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 453 PHE Chi-restraints excluded: chain C residue 166 ASN 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 452 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 301 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 269 VAL 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 275 CYS Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 402 TYR 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: 5.9990 chunk 141 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 chunk 220 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN D 202 GLN F 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.070730 restraints weight = 44635.965| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.66 r_work: 0.2922 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 1.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18402 Z= 0.138 Angle : 0.635 10.099 24981 Z= 0.323 Chirality : 0.046 0.172 2978 Planarity : 0.005 0.052 3338 Dihedral : 4.191 39.211 2749 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.31 % Allowed : 26.57 % Favored : 71.12 % 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: 2.01 (0.16), residues: 1134 sheet: -0.65 (0.22), residues: 518 loop : 0.11 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 481 HIS 0.006 0.001 HIS B 382 PHE 0.024 0.002 PHE B 243 TYR 0.021 0.001 TYR F 148 ARG 0.012 0.001 ARG D 491 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 958) hydrogen bonds : angle 3.89805 ( 2805) covalent geometry : bond 0.00332 (18402) covalent geometry : angle 0.63481 (24981) =============================================================================== Job complete usr+sys time: 8505.67 seconds wall clock time: 147 minutes 56.06 seconds (8876.06 seconds total)