Starting phenix.real_space_refine on Thu Sep 18 16:35:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e25_47436/09_2025/9e25_47436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e25_47436/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e25_47436/09_2025/9e25_47436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e25_47436/09_2025/9e25_47436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e25_47436/09_2025/9e25_47436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e25_47436/09_2025/9e25_47436.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 10, 'TYR:plan': 3, 'HIS:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 8, 'GLN:plan1': 7, 'GLU:plan': 7, 'ARG:plan': 5} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 4.57, per 1000 atoms: 0.25 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: 1.47 Conformation dependent library (CDL) restraints added in 869.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.56 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: 3.34 Time building geometry restraints manager: 1.94 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.350 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.640 ------------------------------------------------------------------------------- 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 : 5.22 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (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 ARG 0.006 0.000 ARG F 223 TYR 0.006 0.001 TYR D 402 PHE 0.018 0.001 PHE A 243 TRP 0.008 0.001 TRP E 481 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00325 (18402) covalent geometry : angle 0.46147 (24981) hydrogen bonds : bond 0.12065 ( 958) hydrogen bonds : angle 5.50921 ( 2805) *********************** 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 : 0.694 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: symmetry clash REVERT: A 215 ASP cc_start: 0.8305 (t0) cc_final: 0.7834 (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: 0.8435 (pt0) REVERT: A 475 ILE cc_start: 0.6039 (mt) cc_final: 0.4585 (mt) REVERT: B 162 ASP cc_start: 0.5887 (m-30) cc_final: 0.5656 (m-30) REVERT: B 174 GLU cc_start: 0.7127 (tt0) cc_final: 0.6888 (tt0) REVERT: B 192 LEU cc_start: 0.8062 (tp) cc_final: 0.7735 (tp) REVERT: B 193 MET cc_start: 0.7961 (tpp) cc_final: 0.7667 (tpt) REVERT: B 197 GLN cc_start: 0.6382 (mt0) cc_final: 0.5857 (tp40) REVERT: B 237 THR cc_start: 0.7651 (m) cc_final: 0.7323 (p) REVERT: B 324 GLU cc_start: 0.6316 (tt0) cc_final: 0.5697 (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: 0.7652 (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: 0.6433 (pp) REVERT: C 184 VAL cc_start: 0.8519 (t) cc_final: 0.8309 (m) REVERT: C 319 HIS cc_start: 0.7367 (t-170) cc_final: 0.6750 (t-90) REVERT: C 418 ASP cc_start: 0.6521 (m-30) cc_final: 0.6166 (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: 0.5573 (m-30) REVERT: D 397 ILE cc_start: 0.9188 (mt) cc_final: 0.8861 (mm) REVERT: D 407 LYS cc_start: 0.7883 (tptm) cc_final: 0.7389 (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: 0.5573 (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: 0.8993 (tt0) REVERT: E 222 SER cc_start: 0.8357 (m) cc_final: 0.7995 (p) REVERT: E 283 THR cc_start: 0.7721 (m) cc_final: 0.7488 (m) REVERT: E 306 THR cc_start: 0.8489 (m) cc_final: 0.8031 (p) REVERT: E 338 MET cc_start: 0.7358 (tpp) cc_final: 0.7112 (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: 0.6365 (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: 0.7948 (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: 0.8156 (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: 0.1421 time to fit residues: 157.7527 Evaluate side-chains 542 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 435 HIS B 166 ASN B 169 HIS B 189 ASN B 371 ASN C 169 HIS C 225 ASN C 276 ASN C 314 GLN ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN E 292 ASN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 ASN E 422 GLN F 252 ASN F 314 GLN F 344 ASN F 374 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.104056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082890 restraints weight = 44125.027| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.96 r_work: 0.3165 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18402 Z= 0.170 Angle : 0.688 13.671 24981 Z= 0.358 Chirality : 0.050 0.209 2978 Planarity : 0.006 0.118 3338 Dihedral : 4.302 28.780 2749 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.55 % Allowed : 17.81 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.17), residues: 2520 helix: 1.98 (0.16), residues: 1136 sheet: -0.60 (0.23), residues: 478 loop : 0.04 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 347 TYR 0.023 0.002 TYR D 148 PHE 0.019 0.002 PHE F 480 TRP 0.030 0.003 TRP F 481 HIS 0.006 0.001 HIS E 470 Details of bonding type rmsd covalent geometry : bond 0.00391 (18402) covalent geometry : angle 0.68763 (24981) hydrogen bonds : bond 0.03575 ( 958) hydrogen bonds : angle 4.16429 ( 2805) *********************** 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 681 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 602 time to evaluate : 0.691 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: A 173 ILE cc_start: 0.7623 (mt) cc_final: 0.7234 (tp) REVERT: A 248 LEU cc_start: 0.6440 (mt) cc_final: 0.6214 (tp) REVERT: A 250 MET cc_start: 0.5508 (mmm) cc_final: 0.5204 (mmm) REVERT: A 339 ARG cc_start: 0.8489 (tpt-90) cc_final: 0.7811 (tpp80) REVERT: A 345 CYS cc_start: 0.8245 (m) cc_final: 0.7802 (m) REVERT: A 371 ASN cc_start: 0.7673 (t0) cc_final: 0.7350 (t0) REVERT: A 411 GLU cc_start: 0.9005 (tp30) cc_final: 0.8680 (pt0) REVERT: B 174 GLU cc_start: 0.7922 (tt0) cc_final: 0.7636 (tt0) REVERT: B 189 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7207 (t0) REVERT: B 193 MET cc_start: 0.8178 (tpp) cc_final: 0.7854 (tpt) REVERT: B 197 GLN cc_start: 0.6677 (mt0) cc_final: 0.6301 (tp40) REVERT: B 273 CYS cc_start: 0.8221 (m) cc_final: 0.7941 (p) REVERT: B 337 THR cc_start: 0.8028 (p) cc_final: 0.7799 (p) REVERT: B 339 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7291 (ttm-80) REVERT: B 365 ASP cc_start: 0.8378 (m-30) cc_final: 0.7990 (m-30) REVERT: B 367 LEU cc_start: 0.8156 (mp) cc_final: 0.7942 (mp) REVERT: B 482 ASP cc_start: 0.8791 (m-30) cc_final: 0.8294 (p0) REVERT: B 497 LEU cc_start: 0.6130 (mp) cc_final: 0.5807 (pp) REVERT: C 152 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8004 (tm-30) REVERT: C 319 HIS cc_start: 0.7708 (t-170) cc_final: 0.7102 (t-90) REVERT: C 418 ASP cc_start: 0.6875 (m-30) cc_final: 0.6616 (m-30) REVERT: C 491 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8920 (ttp80) REVERT: D 251 LYS cc_start: 0.9479 (tptp) cc_final: 0.9235 (ttpp) REVERT: D 324 GLU cc_start: 0.8204 (tt0) cc_final: 0.7612 (tm-30) REVERT: D 337 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6847 (m) REVERT: D 390 ILE cc_start: 0.8164 (mt) cc_final: 0.7881 (mt) REVERT: D 410 LYS cc_start: 0.9051 (mttm) cc_final: 0.8810 (mttt) REVERT: D 428 ASP cc_start: 0.6578 (p0) cc_final: 0.6328 (p0) REVERT: D 491 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7759 (ttp80) REVERT: D 492 GLU cc_start: 0.8258 (tp30) cc_final: 0.7752 (tp30) REVERT: E 202 GLN cc_start: 0.9209 (tt0) cc_final: 0.8968 (tt0) REVERT: E 279 ILE cc_start: 0.8634 (mp) cc_final: 0.8337 (mt) REVERT: E 306 THR cc_start: 0.8540 (m) cc_final: 0.8210 (p) REVERT: E 338 MET cc_start: 0.8120 (tpp) cc_final: 0.7887 (tpp) REVERT: E 380 THR cc_start: 0.7806 (p) cc_final: 0.7571 (t) REVERT: E 396 MET cc_start: 0.8437 (mmm) cc_final: 0.8197 (mmm) REVERT: F 322 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7529 (mtm-85) REVERT: F 339 ARG cc_start: 0.9035 (tmm-80) cc_final: 0.8597 (ttt90) REVERT: F 345 CYS cc_start: 0.8672 (m) cc_final: 0.8218 (m) outliers start: 79 outliers final: 31 residues processed: 631 average time/residue: 0.1372 time to fit residues: 126.6663 Evaluate side-chains 542 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 509 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 283 THR 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 238 LEU Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 246 ASP 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 E residue 196 CYS Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 188 ASP 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 469 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 237 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS C 252 ASN C 319 HIS ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 ASN F 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.100569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078917 restraints weight = 44350.578| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.87 r_work: 0.3105 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18402 Z= 0.175 Angle : 0.660 11.808 24981 Z= 0.342 Chirality : 0.048 0.179 2978 Planarity : 0.005 0.058 3338 Dihedral : 4.207 33.187 2749 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.48 % Allowed : 18.73 % Favored : 75.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.17), residues: 2520 helix: 1.83 (0.16), residues: 1136 sheet: -0.42 (0.23), residues: 494 loop : 0.14 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 432 TYR 0.014 0.001 TYR F 455 PHE 0.020 0.002 PHE A 364 TRP 0.012 0.001 TRP F 481 HIS 0.009 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00400 (18402) covalent geometry : angle 0.65964 (24981) hydrogen bonds : bond 0.03425 ( 958) hydrogen bonds : angle 4.11520 ( 2805) *********************** 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 638 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 543 time to evaluate : 0.598 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: A 172 PHE cc_start: 0.8301 (m-80) cc_final: 0.7996 (m-10) REVERT: A 191 GLN cc_start: 0.8620 (tt0) cc_final: 0.8332 (tt0) REVERT: A 244 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8229 (tppt) REVERT: A 248 LEU cc_start: 0.7079 (mt) cc_final: 0.6822 (tp) REVERT: A 270 ILE cc_start: 0.8999 (mt) cc_final: 0.8546 (mt) REVERT: A 339 ARG cc_start: 0.8619 (tpt-90) cc_final: 0.8159 (tpp80) REVERT: A 343 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8543 (ttmt) REVERT: A 364 PHE cc_start: 0.8860 (t80) cc_final: 0.8611 (t80) REVERT: A 365 ASP cc_start: 0.8834 (m-30) cc_final: 0.8274 (m-30) REVERT: A 371 ASN cc_start: 0.7907 (t0) cc_final: 0.7671 (t0) REVERT: B 174 GLU cc_start: 0.8195 (tt0) cc_final: 0.7751 (tt0) REVERT: B 189 ASN cc_start: 0.8381 (m-40) cc_final: 0.8094 (t0) REVERT: B 193 MET cc_start: 0.8425 (tpp) cc_final: 0.8078 (tpt) REVERT: B 241 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7316 (mtm180) REVERT: B 270 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8274 (mt) REVERT: B 273 CYS cc_start: 0.8705 (m) cc_final: 0.8338 (t) REVERT: B 339 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7600 (ttm-80) REVERT: B 365 ASP cc_start: 0.8568 (m-30) cc_final: 0.8046 (m-30) REVERT: B 370 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7402 (mmm) REVERT: B 408 THR cc_start: 0.8834 (m) cc_final: 0.8281 (p) REVERT: B 482 ASP cc_start: 0.8954 (m-30) cc_final: 0.8526 (p0) REVERT: B 487 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7995 (t80) REVERT: B 497 LEU cc_start: 0.6638 (mp) cc_final: 0.6281 (pp) REVERT: C 151 LEU cc_start: 0.8875 (tp) cc_final: 0.8573 (mt) REVERT: C 152 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8048 (tm-30) REVERT: C 246 ASP cc_start: 0.8910 (p0) cc_final: 0.8667 (p0) REVERT: C 407 LYS cc_start: 0.8721 (tptm) cc_final: 0.8378 (tppt) REVERT: C 411 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8391 (mt-10) REVERT: C 418 ASP cc_start: 0.7310 (m-30) cc_final: 0.7075 (m-30) REVERT: C 445 ASP cc_start: 0.8335 (t0) cc_final: 0.8037 (t0) REVERT: D 324 GLU cc_start: 0.8656 (tt0) cc_final: 0.8335 (tt0) REVERT: D 390 ILE cc_start: 0.8747 (mt) cc_final: 0.8481 (mt) REVERT: D 407 LYS cc_start: 0.7881 (tptt) cc_final: 0.7577 (tptt) REVERT: D 418 ASP cc_start: 0.7704 (m-30) cc_final: 0.7479 (m-30) REVERT: D 481 TRP cc_start: 0.7421 (t-100) cc_final: 0.7077 (t-100) REVERT: E 202 GLN cc_start: 0.9293 (tt0) cc_final: 0.9047 (tt0) REVERT: E 306 THR cc_start: 0.8858 (m) cc_final: 0.8610 (p) REVERT: E 338 MET cc_start: 0.8191 (tpp) cc_final: 0.7945 (tpp) REVERT: E 345 CYS cc_start: 0.8932 (m) cc_final: 0.8607 (m) REVERT: E 481 TRP cc_start: 0.8017 (t-100) cc_final: 0.7671 (t-100) REVERT: F 164 MET cc_start: 0.8713 (mtm) cc_final: 0.8359 (mpp) REVERT: F 289 THR cc_start: 0.9362 (m) cc_final: 0.8975 (p) REVERT: F 339 ARG cc_start: 0.9232 (tmm-80) cc_final: 0.8813 (ttt90) REVERT: F 391 SER cc_start: 0.8521 (m) cc_final: 0.8069 (p) REVERT: F 395 SER cc_start: 0.8625 (m) cc_final: 0.8199 (t) outliers start: 95 outliers final: 52 residues processed: 591 average time/residue: 0.1424 time to fit residues: 121.9792 Evaluate side-chains 531 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 476 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL 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 A residue 381 LEU Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 260 SER 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 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 GLN 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 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 454 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 277 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 467 VAL Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 190 LEU 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 307 CYS Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 495 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 62 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 55 optimal weight: 30.0000 chunk 226 optimal weight: 8.9990 chunk 216 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 chunk 250 optimal weight: 8.9990 chunk 151 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS C 191 GLN D 450 GLN ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3576 r_free = 0.3576 target = 0.097096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.075522 restraints weight = 44844.989| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.81 r_work: 0.3041 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 18402 Z= 0.198 Angle : 0.681 13.374 24981 Z= 0.351 Chirality : 0.050 0.311 2978 Planarity : 0.006 0.079 3338 Dihedral : 4.376 37.889 2749 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.19 % Allowed : 19.88 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2520 helix: 1.73 (0.16), residues: 1132 sheet: -0.50 (0.22), residues: 528 loop : 0.26 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 471 TYR 0.018 0.001 TYR F 455 PHE 0.030 0.002 PHE F 480 TRP 0.016 0.002 TRP F 481 HIS 0.006 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00463 (18402) covalent geometry : angle 0.68060 (24981) hydrogen bonds : bond 0.03462 ( 958) hydrogen bonds : angle 4.20351 ( 2805) *********************** 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 564 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 474 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8198 (m-80) cc_final: 0.7874 (m-80) REVERT: A 191 GLN cc_start: 0.8936 (tt0) cc_final: 0.8583 (tt0) REVERT: A 202 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8577 (tm-30) REVERT: A 244 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8334 (tppt) REVERT: A 248 LEU cc_start: 0.8033 (mt) cc_final: 0.7828 (tp) REVERT: A 270 ILE cc_start: 0.8990 (mt) cc_final: 0.8554 (mt) REVERT: A 351 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8100 (mp0) REVERT: A 364 PHE cc_start: 0.9064 (t80) cc_final: 0.8678 (t80) REVERT: A 365 ASP cc_start: 0.9020 (m-30) cc_final: 0.8696 (m-30) REVERT: A 407 LYS cc_start: 0.9538 (tptp) cc_final: 0.9199 (tptp) REVERT: B 174 GLU cc_start: 0.8429 (tt0) cc_final: 0.7992 (tt0) REVERT: B 189 ASN cc_start: 0.8209 (m-40) cc_final: 0.7935 (t0) REVERT: B 193 MET cc_start: 0.8614 (tpp) cc_final: 0.8006 (tpt) REVERT: B 197 GLN cc_start: 0.8492 (mt0) cc_final: 0.8050 (mp10) REVERT: B 339 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7888 (ttm-80) REVERT: B 365 ASP cc_start: 0.8920 (m-30) cc_final: 0.8512 (m-30) REVERT: B 448 VAL cc_start: 0.8998 (t) cc_final: 0.8728 (p) REVERT: B 487 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8071 (t80) REVERT: C 206 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8209 (ttp80) REVERT: C 324 GLU cc_start: 0.8737 (tt0) cc_final: 0.8527 (tt0) REVERT: C 411 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8574 (mt-10) REVERT: D 333 SER cc_start: 0.9586 (m) cc_final: 0.9369 (p) REVERT: D 351 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7863 (mp0) REVERT: D 390 ILE cc_start: 0.9212 (mt) cc_final: 0.8991 (mt) REVERT: D 481 TRP cc_start: 0.7838 (t-100) cc_final: 0.7387 (t-100) REVERT: D 491 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7438 (ttp80) REVERT: E 202 GLN cc_start: 0.9289 (tt0) cc_final: 0.9033 (tt0) REVERT: E 252 ASN cc_start: 0.8310 (m110) cc_final: 0.7165 (m-40) REVERT: E 255 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8851 (pt0) REVERT: E 256 PHE cc_start: 0.8712 (m-10) cc_final: 0.8217 (m-10) REVERT: E 343 LYS cc_start: 0.9366 (ttmt) cc_final: 0.9154 (ttmm) REVERT: E 345 CYS cc_start: 0.8946 (m) cc_final: 0.8548 (m) REVERT: E 359 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8333 (ttm110) REVERT: E 365 ASP cc_start: 0.9262 (m-30) cc_final: 0.9050 (m-30) REVERT: E 407 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7807 (tttm) REVERT: E 438 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6941 (tm-30) REVERT: E 469 LYS cc_start: 0.8592 (pptt) cc_final: 0.8233 (pptt) REVERT: F 289 THR cc_start: 0.9538 (m) cc_final: 0.9157 (p) REVERT: F 309 ASP cc_start: 0.8705 (m-30) cc_final: 0.8448 (m-30) REVERT: F 339 ARG cc_start: 0.9340 (tmm-80) cc_final: 0.8818 (ttm-80) REVERT: F 347 ARG cc_start: 0.8871 (ttp-110) cc_final: 0.8577 (ptm-80) REVERT: F 391 SER cc_start: 0.8882 (m) cc_final: 0.8419 (p) REVERT: F 395 SER cc_start: 0.9243 (m) cc_final: 0.8906 (t) outliers start: 90 outliers final: 45 residues processed: 523 average time/residue: 0.1336 time to fit residues: 102.4727 Evaluate side-chains 464 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 417 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL 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 402 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 260 SER 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 367 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 307 CYS 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 454 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 312 GLU 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 190 LEU Chi-restraints excluded: chain F residue 200 VAL 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 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 129 optimal weight: 50.0000 chunk 11 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS C 292 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3562 r_free = 0.3562 target = 0.096335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.074371 restraints weight = 44392.162| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.76 r_work: 0.2985 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.8500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18402 Z= 0.185 Angle : 0.667 11.656 24981 Z= 0.336 Chirality : 0.048 0.221 2978 Planarity : 0.005 0.056 3338 Dihedral : 4.257 39.104 2749 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.73 % Allowed : 21.27 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.17), residues: 2520 helix: 1.77 (0.16), residues: 1134 sheet: -0.64 (0.21), residues: 536 loop : 0.25 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 485 TYR 0.024 0.002 TYR C 486 PHE 0.016 0.002 PHE F 297 TRP 0.008 0.001 TRP F 481 HIS 0.005 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00441 (18402) covalent geometry : angle 0.66731 (24981) hydrogen bonds : bond 0.03203 ( 958) hydrogen bonds : angle 4.10572 ( 2805) *********************** 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 509 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 427 time to evaluate : 0.507 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: 0.8986 (tt0) cc_final: 0.8596 (tt0) REVERT: A 202 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8647 (tm-30) REVERT: A 244 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8456 (tppt) REVERT: A 270 ILE cc_start: 0.9074 (mt) cc_final: 0.8685 (mt) REVERT: A 273 CYS cc_start: 0.8397 (m) cc_final: 0.7672 (p) REVERT: A 339 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8766 (tpp80) REVERT: A 340 ASP cc_start: 0.9043 (t70) cc_final: 0.8700 (m-30) REVERT: A 351 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 365 ASP cc_start: 0.9149 (m-30) cc_final: 0.8854 (m-30) REVERT: B 174 GLU cc_start: 0.8553 (tt0) cc_final: 0.8185 (tt0) REVERT: B 189 ASN cc_start: 0.8432 (m-40) cc_final: 0.8213 (t0) REVERT: B 193 MET cc_start: 0.8837 (tpp) cc_final: 0.8552 (tpt) REVERT: B 339 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8018 (ttm170) REVERT: B 359 ARG cc_start: 0.9373 (mtm-85) cc_final: 0.9073 (mtm-85) REVERT: B 365 ASP cc_start: 0.9039 (m-30) cc_final: 0.8775 (m-30) REVERT: B 378 MET cc_start: 0.8611 (mtm) cc_final: 0.8406 (mtm) REVERT: B 473 THR cc_start: 0.8757 (m) cc_final: 0.8466 (p) REVERT: C 324 GLU cc_start: 0.8761 (tt0) cc_final: 0.8561 (tt0) REVERT: C 339 ARG cc_start: 0.8623 (ttp-170) cc_final: 0.8117 (ttm-80) REVERT: C 351 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: C 370 MET cc_start: 0.8924 (mtt) cc_final: 0.8489 (mtt) REVERT: D 343 LYS cc_start: 0.8615 (mttp) cc_final: 0.8411 (mttp) REVERT: D 481 TRP cc_start: 0.7980 (t-100) cc_final: 0.7767 (t-100) REVERT: D 491 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7520 (ttp80) REVERT: E 196 CYS cc_start: 0.9038 (p) cc_final: 0.8823 (m) REVERT: E 244 LYS cc_start: 0.8646 (ptmm) cc_final: 0.8182 (ptmm) REVERT: E 255 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8880 (pt0) REVERT: E 256 PHE cc_start: 0.8896 (m-10) cc_final: 0.8437 (m-10) REVERT: E 343 LYS cc_start: 0.9425 (ttmt) cc_final: 0.9177 (ttmm) REVERT: E 345 CYS cc_start: 0.8992 (m) cc_final: 0.8627 (m) REVERT: E 357 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7786 (tm-30) REVERT: E 365 ASP cc_start: 0.9267 (m-30) cc_final: 0.9018 (m-30) REVERT: E 396 MET cc_start: 0.9410 (ttm) cc_final: 0.9088 (ttm) REVERT: E 438 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6879 (tm-30) REVERT: E 469 LYS cc_start: 0.8627 (pptt) cc_final: 0.8361 (pptt) REVERT: F 188 ASP cc_start: 0.8820 (t0) cc_final: 0.8503 (p0) REVERT: F 289 THR cc_start: 0.9561 (m) cc_final: 0.9345 (p) REVERT: F 391 SER cc_start: 0.9154 (m) cc_final: 0.8734 (p) REVERT: F 395 SER cc_start: 0.9262 (m) cc_final: 0.9013 (t) REVERT: F 410 LYS cc_start: 0.8821 (mttm) cc_final: 0.8582 (mttm) REVERT: F 473 THR cc_start: 0.8088 (p) cc_final: 0.7817 (p) outliers start: 82 outliers final: 41 residues processed: 479 average time/residue: 0.1339 time to fit residues: 94.1251 Evaluate side-chains 425 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 382 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 260 SER 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 371 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 151 LEU 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 325 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 365 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 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 182 THR 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 457 ILE Chi-restraints excluded: chain E residue 277 LEU 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 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 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 133 optimal weight: 30.0000 chunk 116 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 ASN C 292 ASN F 225 ASN ** F 292 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 = 0.3550 r_free = 0.3550 target = 0.095776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.073672 restraints weight = 44229.574| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.75 r_work: 0.2971 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.8985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18402 Z= 0.162 Angle : 0.625 8.622 24981 Z= 0.318 Chirality : 0.047 0.179 2978 Planarity : 0.005 0.055 3338 Dihedral : 4.206 39.583 2749 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.98 % Allowed : 22.65 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2520 helix: 1.88 (0.16), residues: 1124 sheet: -0.54 (0.22), residues: 540 loop : 0.20 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 347 TYR 0.022 0.002 TYR C 486 PHE 0.026 0.002 PHE A 172 TRP 0.010 0.001 TRP F 481 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00387 (18402) covalent geometry : angle 0.62528 (24981) hydrogen bonds : bond 0.03070 ( 958) hydrogen bonds : angle 3.94610 ( 2805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 385 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8603 (pm20) cc_final: 0.8061 (pm20) REVERT: A 191 GLN cc_start: 0.8996 (tt0) cc_final: 0.8634 (tt0) REVERT: A 202 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8653 (tm-30) REVERT: A 244 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8564 (tppt) REVERT: A 270 ILE cc_start: 0.9124 (mt) cc_final: 0.8757 (mt) REVERT: A 273 CYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7785 (p) REVERT: A 339 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8780 (tpp80) REVERT: A 340 ASP cc_start: 0.9022 (t70) cc_final: 0.8744 (m-30) REVERT: A 365 ASP cc_start: 0.9230 (m-30) cc_final: 0.8961 (m-30) REVERT: A 407 LYS cc_start: 0.9615 (tptp) cc_final: 0.8979 (tptt) REVERT: B 174 GLU cc_start: 0.8575 (tt0) cc_final: 0.8129 (tt0) REVERT: B 180 GLN cc_start: 0.8979 (pt0) cc_final: 0.8692 (pt0) REVERT: B 193 MET cc_start: 0.8763 (tpp) cc_final: 0.8075 (tpt) REVERT: B 197 GLN cc_start: 0.8575 (mt0) cc_final: 0.8227 (mp10) REVERT: B 244 LYS cc_start: 0.8373 (tppt) cc_final: 0.8054 (tptp) REVERT: B 246 ASP cc_start: 0.8750 (p0) cc_final: 0.7747 (p0) REVERT: B 339 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8121 (ttm170) REVERT: B 359 ARG cc_start: 0.9365 (mtm-85) cc_final: 0.9162 (ttm110) REVERT: B 365 ASP cc_start: 0.9036 (m-30) cc_final: 0.8812 (m-30) REVERT: B 448 VAL cc_start: 0.9139 (t) cc_final: 0.8933 (p) REVERT: C 162 ASP cc_start: 0.7918 (p0) cc_final: 0.7710 (p0) REVERT: C 206 ARG cc_start: 0.8568 (ttp80) cc_final: 0.8304 (ptm-80) REVERT: C 339 ARG cc_start: 0.8696 (ttp-170) cc_final: 0.8217 (ttm-80) REVERT: C 347 ARG cc_start: 0.9156 (mtm-85) cc_final: 0.8855 (mtp85) REVERT: C 351 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: C 370 MET cc_start: 0.8977 (mtt) cc_final: 0.8520 (mtt) REVERT: D 351 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8161 (mp0) REVERT: D 370 MET cc_start: 0.8943 (mtp) cc_final: 0.8708 (mtt) REVERT: D 481 TRP cc_start: 0.8030 (t-100) cc_final: 0.7713 (t-100) REVERT: E 251 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8767 (mmmm) REVERT: E 255 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8810 (pt0) REVERT: E 256 PHE cc_start: 0.8987 (m-10) cc_final: 0.8481 (m-10) REVERT: E 339 ARG cc_start: 0.9021 (ttp-170) cc_final: 0.8795 (ttm-80) REVERT: E 343 LYS cc_start: 0.9440 (ttmt) cc_final: 0.9188 (ttmm) REVERT: E 345 CYS cc_start: 0.8933 (m) cc_final: 0.8635 (m) REVERT: E 365 ASP cc_start: 0.9278 (m-30) cc_final: 0.8954 (m-30) REVERT: E 368 GLN cc_start: 0.9033 (tt0) cc_final: 0.8827 (tm-30) REVERT: E 396 MET cc_start: 0.9416 (ttm) cc_final: 0.9098 (ttm) REVERT: E 438 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6904 (tm-30) REVERT: F 188 ASP cc_start: 0.8706 (t0) cc_final: 0.8489 (t70) REVERT: F 202 GLN cc_start: 0.9155 (tt0) cc_final: 0.8850 (tm-30) REVERT: F 410 LYS cc_start: 0.9013 (mttm) cc_final: 0.8692 (mttm) outliers start: 69 outliers final: 39 residues processed: 426 average time/residue: 0.1254 time to fit residues: 79.9294 Evaluate side-chains 408 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 402 TYR 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 447 ILE Chi-restraints excluded: chain B residue 497 LEU 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 325 THR Chi-restraints excluded: chain C residue 351 GLU 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 182 THR 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 457 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 407 LYS 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 258 SER Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 215 optimal weight: 50.0000 chunk 24 optimal weight: 0.3980 chunk 229 optimal weight: 3.9990 chunk 249 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 240 optimal weight: 0.3980 chunk 222 optimal weight: 0.6980 chunk 129 optimal weight: 50.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN B 189 ASN B 368 GLN C 292 ASN C 384 ASN ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.075994 restraints weight = 44220.268| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.77 r_work: 0.3012 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.9157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18402 Z= 0.121 Angle : 0.617 10.562 24981 Z= 0.314 Chirality : 0.046 0.177 2978 Planarity : 0.005 0.054 3338 Dihedral : 4.120 38.638 2749 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.17 % Allowed : 24.09 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.17), residues: 2520 helix: 1.95 (0.16), residues: 1124 sheet: -0.48 (0.22), residues: 504 loop : 0.16 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 491 TYR 0.017 0.001 TYR C 486 PHE 0.020 0.002 PHE D 364 TRP 0.009 0.001 TRP F 481 HIS 0.004 0.001 HIS F 319 Details of bonding type rmsd covalent geometry : bond 0.00281 (18402) covalent geometry : angle 0.61651 (24981) hydrogen bonds : bond 0.02880 ( 958) hydrogen bonds : angle 3.83011 ( 2805) *********************** 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 450 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 395 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8498 (pm20) cc_final: 0.7943 (pm20) REVERT: A 191 GLN cc_start: 0.9024 (tt0) cc_final: 0.8667 (tt0) REVERT: A 244 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8587 (tppt) REVERT: A 270 ILE cc_start: 0.9040 (mt) cc_final: 0.8633 (mt) REVERT: A 273 CYS cc_start: 0.8483 (m) cc_final: 0.7790 (p) REVERT: A 339 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8635 (tpp80) REVERT: A 340 ASP cc_start: 0.8927 (t70) cc_final: 0.8676 (m-30) REVERT: A 365 ASP cc_start: 0.9234 (m-30) cc_final: 0.8887 (m-30) REVERT: A 411 GLU cc_start: 0.8674 (mp0) cc_final: 0.8406 (mp0) REVERT: B 174 GLU cc_start: 0.8537 (tt0) cc_final: 0.8189 (tt0) REVERT: B 180 GLN cc_start: 0.8969 (pt0) cc_final: 0.8708 (pt0) REVERT: B 189 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8134 (t0) REVERT: B 193 MET cc_start: 0.8769 (tpp) cc_final: 0.8145 (tpt) REVERT: B 202 GLN cc_start: 0.9570 (tt0) cc_final: 0.9183 (mt0) REVERT: B 244 LYS cc_start: 0.8325 (tppt) cc_final: 0.7920 (tptp) REVERT: B 339 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8124 (ttm-80) REVERT: B 365 ASP cc_start: 0.9040 (m-30) cc_final: 0.8811 (m-30) REVERT: B 491 ARG cc_start: 0.8823 (mtp-110) cc_final: 0.8587 (ttp80) REVERT: C 162 ASP cc_start: 0.7725 (p0) cc_final: 0.7496 (p0) REVERT: C 245 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8774 (ptpp) REVERT: C 339 ARG cc_start: 0.8632 (ttp-170) cc_final: 0.8198 (ttm-80) REVERT: C 345 CYS cc_start: 0.9021 (m) cc_final: 0.8710 (m) REVERT: C 347 ARG cc_start: 0.9122 (mtm-85) cc_final: 0.8776 (mtp85) REVERT: C 351 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: C 370 MET cc_start: 0.8890 (mtt) cc_final: 0.8539 (mtt) REVERT: D 196 CYS cc_start: 0.9361 (m) cc_final: 0.9160 (m) REVERT: D 215 ASP cc_start: 0.8121 (t70) cc_final: 0.7840 (t0) REVERT: D 243 PHE cc_start: 0.8773 (t80) cc_final: 0.8563 (t80) REVERT: D 351 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8138 (mp0) REVERT: D 394 GLU cc_start: 0.9320 (tm-30) cc_final: 0.9117 (tm-30) REVERT: D 422 GLN cc_start: 0.8487 (tp40) cc_final: 0.6948 (tp40) REVERT: D 481 TRP cc_start: 0.8019 (t-100) cc_final: 0.7756 (t-100) REVERT: D 491 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7492 (ttp80) REVERT: E 244 LYS cc_start: 0.8579 (ptmm) cc_final: 0.8227 (ptmm) REVERT: E 251 LYS cc_start: 0.9263 (ttmm) cc_final: 0.8969 (mmmm) REVERT: E 255 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8772 (pt0) REVERT: E 256 PHE cc_start: 0.8974 (m-10) cc_final: 0.8517 (m-10) REVERT: E 324 GLU cc_start: 0.8835 (tt0) cc_final: 0.8467 (tp30) REVERT: E 343 LYS cc_start: 0.9452 (ttmt) cc_final: 0.9203 (ttmm) REVERT: E 345 CYS cc_start: 0.8862 (m) cc_final: 0.8654 (m) REVERT: E 357 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7645 (tm-30) REVERT: E 365 ASP cc_start: 0.9271 (m-30) cc_final: 0.8931 (m-30) REVERT: E 396 MET cc_start: 0.9378 (ttm) cc_final: 0.9019 (ttm) REVERT: E 438 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6633 (tm-30) REVERT: F 188 ASP cc_start: 0.8638 (t0) cc_final: 0.8360 (t70) REVERT: F 316 GLN cc_start: 0.8813 (pm20) cc_final: 0.8603 (pm20) outliers start: 55 outliers final: 32 residues processed: 425 average time/residue: 0.1344 time to fit residues: 85.3154 Evaluate side-chains 385 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 349 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 213 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 404 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 182 THR 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 353 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 217 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 169 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 202 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.095656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.073913 restraints weight = 44735.165| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.75 r_work: 0.2968 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.9461 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= 0.157 Angle : 0.640 9.355 24981 Z= 0.326 Chirality : 0.047 0.179 2978 Planarity : 0.005 0.053 3338 Dihedral : 4.140 38.336 2749 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.17 % Allowed : 24.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.17), residues: 2520 helix: 1.88 (0.16), residues: 1126 sheet: -0.53 (0.21), residues: 534 loop : 0.18 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 187 TYR 0.017 0.001 TYR C 402 PHE 0.022 0.002 PHE A 364 TRP 0.008 0.001 TRP F 481 HIS 0.005 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00375 (18402) covalent geometry : angle 0.64033 (24981) hydrogen bonds : bond 0.02961 ( 958) hydrogen bonds : angle 3.89577 ( 2805) *********************** 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 400 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 345 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8478 (pm20) cc_final: 0.7936 (pm20) REVERT: A 191 GLN cc_start: 0.9010 (tt0) cc_final: 0.8644 (tt0) REVERT: A 270 ILE cc_start: 0.9076 (mt) cc_final: 0.8631 (mt) REVERT: A 273 CYS cc_start: 0.8550 (m) cc_final: 0.8064 (p) REVERT: A 339 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8614 (tpp80) REVERT: A 340 ASP cc_start: 0.8936 (t70) cc_final: 0.8732 (m-30) REVERT: A 365 ASP cc_start: 0.9240 (m-30) cc_final: 0.8925 (m-30) REVERT: A 411 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: B 174 GLU cc_start: 0.8645 (tt0) cc_final: 0.8277 (tt0) REVERT: B 180 GLN cc_start: 0.9004 (pt0) cc_final: 0.8737 (pt0) REVERT: B 193 MET cc_start: 0.8678 (tpp) cc_final: 0.8067 (tpt) REVERT: B 197 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8482 (mp10) REVERT: B 433 ILE cc_start: 0.9423 (mm) cc_final: 0.9167 (mm) REVERT: C 162 ASP cc_start: 0.7881 (p0) cc_final: 0.7662 (p0) REVERT: C 206 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8316 (ptm-80) REVERT: C 247 LYS cc_start: 0.8749 (mptt) cc_final: 0.8227 (mptt) REVERT: C 339 ARG cc_start: 0.8763 (ttp-170) cc_final: 0.8437 (ttm-80) REVERT: C 345 CYS cc_start: 0.9123 (m) cc_final: 0.8802 (m) REVERT: C 347 ARG cc_start: 0.9156 (mtm-85) cc_final: 0.8797 (mtp85) REVERT: C 351 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: C 370 MET cc_start: 0.9017 (mtt) cc_final: 0.8618 (mtt) REVERT: C 411 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8842 (mt-10) REVERT: D 202 GLN cc_start: 0.9333 (tt0) cc_final: 0.8825 (tm-30) REVERT: D 215 ASP cc_start: 0.8097 (t70) cc_final: 0.7747 (t0) REVERT: D 243 PHE cc_start: 0.8897 (t80) cc_final: 0.8681 (t80) REVERT: D 351 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8219 (mp0) REVERT: D 370 MET cc_start: 0.9004 (mtp) cc_final: 0.8764 (mtt) REVERT: D 481 TRP cc_start: 0.8119 (t-100) cc_final: 0.7661 (t-100) REVERT: E 244 LYS cc_start: 0.8571 (ptmm) cc_final: 0.8232 (ptmm) REVERT: E 248 LEU cc_start: 0.8846 (mt) cc_final: 0.8486 (mm) REVERT: E 251 LYS cc_start: 0.9287 (ttmm) cc_final: 0.8881 (mmmm) REVERT: E 255 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8798 (pt0) REVERT: E 256 PHE cc_start: 0.9042 (m-10) cc_final: 0.8568 (m-10) REVERT: E 339 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8742 (ttt180) REVERT: E 343 LYS cc_start: 0.9459 (ttmt) cc_final: 0.9202 (ttmm) REVERT: E 345 CYS cc_start: 0.8887 (m) cc_final: 0.8619 (m) REVERT: E 357 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7767 (tm-30) REVERT: E 365 ASP cc_start: 0.9263 (m-30) cc_final: 0.8970 (m-30) REVERT: E 396 MET cc_start: 0.9408 (ttm) cc_final: 0.9027 (ttm) REVERT: E 438 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6785 (tm-30) REVERT: F 188 ASP cc_start: 0.8620 (t0) cc_final: 0.8345 (t70) outliers start: 55 outliers final: 36 residues processed: 382 average time/residue: 0.1369 time to fit residues: 77.9958 Evaluate side-chains 374 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 497 LEU 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 404 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain D residue 182 THR 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 E residue 277 LEU Chi-restraints excluded: chain E residue 339 ARG 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 258 SER Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 223 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 chunk 122 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 178 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN B 189 ASN B 202 GLN B 368 GLN ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073495 restraints weight = 44466.354| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.74 r_work: 0.2987 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.9719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18402 Z= 0.132 Angle : 0.634 10.975 24981 Z= 0.320 Chirality : 0.046 0.201 2978 Planarity : 0.005 0.055 3338 Dihedral : 4.099 37.946 2749 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.11 % Allowed : 24.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.17), residues: 2520 helix: 1.93 (0.16), residues: 1124 sheet: -0.49 (0.22), residues: 530 loop : 0.19 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 491 TYR 0.015 0.001 TYR C 402 PHE 0.019 0.002 PHE C 364 TRP 0.008 0.001 TRP F 481 HIS 0.004 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00318 (18402) covalent geometry : angle 0.63369 (24981) hydrogen bonds : bond 0.02912 ( 958) hydrogen bonds : angle 3.88462 ( 2805) *********************** 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 394 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8377 (pm20) cc_final: 0.7795 (pm20) REVERT: A 191 GLN cc_start: 0.9031 (tt0) cc_final: 0.8744 (tt0) REVERT: A 196 CYS cc_start: 0.9404 (m) cc_final: 0.9199 (m) REVERT: A 270 ILE cc_start: 0.9008 (mt) cc_final: 0.8531 (mt) REVERT: A 273 CYS cc_start: 0.8574 (m) cc_final: 0.8106 (p) REVERT: A 365 ASP cc_start: 0.9242 (m-30) cc_final: 0.9033 (m-30) REVERT: A 370 MET cc_start: 0.8774 (mtp) cc_final: 0.8389 (mtp) REVERT: A 411 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: B 174 GLU cc_start: 0.8548 (tt0) cc_final: 0.8161 (tt0) REVERT: B 180 GLN cc_start: 0.9027 (pt0) cc_final: 0.8790 (pt0) REVERT: B 324 GLU cc_start: 0.8785 (tt0) cc_final: 0.8232 (tp30) REVERT: B 433 ILE cc_start: 0.9454 (mm) cc_final: 0.9212 (mm) REVERT: C 162 ASP cc_start: 0.7833 (p0) cc_final: 0.7620 (p0) REVERT: C 247 LYS cc_start: 0.8741 (mptt) cc_final: 0.8296 (mptt) REVERT: C 339 ARG cc_start: 0.8718 (ttp-170) cc_final: 0.8320 (ttm-80) REVERT: C 345 CYS cc_start: 0.9138 (m) cc_final: 0.8833 (m) REVERT: C 347 ARG cc_start: 0.9146 (mtm-85) cc_final: 0.8673 (mtp85) REVERT: C 351 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: C 370 MET cc_start: 0.8972 (mtt) cc_final: 0.8592 (mtt) REVERT: D 215 ASP cc_start: 0.8095 (t70) cc_final: 0.7381 (t0) REVERT: D 251 LYS cc_start: 0.9219 (ttpp) cc_final: 0.8967 (ptmm) REVERT: D 351 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8275 (mp0) REVERT: D 370 MET cc_start: 0.9012 (mtp) cc_final: 0.8802 (mtt) REVERT: D 481 TRP cc_start: 0.8104 (t-100) cc_final: 0.7664 (t-100) REVERT: D 491 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7629 (ttp80) REVERT: E 248 LEU cc_start: 0.8881 (mt) cc_final: 0.8547 (mm) REVERT: E 251 LYS cc_start: 0.9303 (ttmm) cc_final: 0.8946 (mmmm) REVERT: E 255 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8731 (pt0) REVERT: E 256 PHE cc_start: 0.9069 (m-10) cc_final: 0.8584 (m-10) REVERT: E 324 GLU cc_start: 0.8835 (tt0) cc_final: 0.8433 (tp30) REVERT: E 339 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8761 (ttt180) REVERT: E 343 LYS cc_start: 0.9468 (ttmt) cc_final: 0.9212 (ttmm) REVERT: E 345 CYS cc_start: 0.8912 (m) cc_final: 0.8682 (m) REVERT: E 357 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7699 (tm-30) REVERT: E 365 ASP cc_start: 0.9239 (m-30) cc_final: 0.8954 (m-30) REVERT: E 438 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6711 (tm-30) REVERT: E 498 ASP cc_start: 0.8817 (m-30) cc_final: 0.8409 (m-30) REVERT: F 188 ASP cc_start: 0.8619 (t0) cc_final: 0.8347 (t70) REVERT: F 398 THR cc_start: 0.9158 (m) cc_final: 0.8807 (p) REVERT: F 443 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8122 (mp0) outliers start: 54 outliers final: 41 residues processed: 373 average time/residue: 0.1362 time to fit residues: 75.4169 Evaluate side-chains 366 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 322 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 164 MET 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 365 ASP Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 182 THR 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 402 TYR Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 203 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 84 optimal weight: 120.0000 chunk 154 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 142 optimal weight: 8.9990 chunk 90 optimal weight: 40.0000 chunk 3 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN B 189 ASN B 316 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.092328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071071 restraints weight = 45271.070| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.73 r_work: 0.2908 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 1.0215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18402 Z= 0.230 Angle : 0.708 11.722 24981 Z= 0.358 Chirality : 0.049 0.219 2978 Planarity : 0.005 0.052 3338 Dihedral : 4.321 38.911 2749 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.65 % Allowed : 25.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.17), residues: 2520 helix: 1.91 (0.16), residues: 1116 sheet: -0.61 (0.22), residues: 524 loop : 0.12 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 491 TYR 0.018 0.002 TYR C 402 PHE 0.027 0.002 PHE A 364 TRP 0.011 0.002 TRP C 481 HIS 0.005 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00545 (18402) covalent geometry : angle 0.70771 (24981) hydrogen bonds : bond 0.03318 ( 958) hydrogen bonds : angle 4.11414 ( 2805) ********************** 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 371 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLN cc_start: 0.9119 (tt0) cc_final: 0.8841 (tt0) REVERT: A 250 MET cc_start: 0.7906 (mmm) cc_final: 0.7437 (tpt) REVERT: A 270 ILE cc_start: 0.9121 (mt) cc_final: 0.8805 (mt) REVERT: A 273 CYS cc_start: 0.8715 (m) cc_final: 0.8384 (p) REVERT: A 338 MET cc_start: 0.9030 (tpp) cc_final: 0.8619 (mmt) REVERT: A 339 ARG cc_start: 0.9070 (tpp80) cc_final: 0.8644 (tpp80) REVERT: A 365 ASP cc_start: 0.9292 (m-30) cc_final: 0.8827 (m-30) REVERT: A 370 MET cc_start: 0.9065 (mtp) cc_final: 0.8521 (mtp) REVERT: A 391 SER cc_start: 0.9141 (t) cc_final: 0.8885 (p) REVERT: A 411 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: B 174 GLU cc_start: 0.8656 (tt0) cc_final: 0.8244 (tt0) REVERT: B 180 GLN cc_start: 0.9046 (pt0) cc_final: 0.8754 (pt0) REVERT: B 189 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8219 (t0) REVERT: B 324 GLU cc_start: 0.8857 (tt0) cc_final: 0.8272 (tp30) REVERT: C 162 ASP cc_start: 0.8064 (p0) cc_final: 0.7851 (p0) REVERT: C 194 ASN cc_start: 0.9146 (m-40) cc_final: 0.8902 (m-40) REVERT: C 314 GLN cc_start: 0.9074 (tt0) cc_final: 0.8855 (tp40) REVERT: C 339 ARG cc_start: 0.8911 (ttp-170) cc_final: 0.8531 (ttm-80) REVERT: C 345 CYS cc_start: 0.9176 (m) cc_final: 0.8852 (m) REVERT: C 347 ARG cc_start: 0.9156 (mtm-85) cc_final: 0.8742 (mtp85) REVERT: C 351 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: C 370 MET cc_start: 0.9105 (mtt) cc_final: 0.8666 (mtt) REVERT: C 477 ARG cc_start: 0.9172 (tpp-160) cc_final: 0.8808 (tpp80) REVERT: D 202 GLN cc_start: 0.9370 (tt0) cc_final: 0.8837 (tm-30) REVERT: D 215 ASP cc_start: 0.8236 (t70) cc_final: 0.7554 (t0) REVERT: D 251 LYS cc_start: 0.9153 (ttpp) cc_final: 0.8895 (ptmm) REVERT: D 370 MET cc_start: 0.9136 (mtp) cc_final: 0.8873 (mtt) REVERT: D 391 SER cc_start: 0.9340 (t) cc_final: 0.8921 (p) REVERT: D 481 TRP cc_start: 0.8333 (t-100) cc_final: 0.7625 (t-100) REVERT: E 251 LYS cc_start: 0.9354 (ttmm) cc_final: 0.9049 (mmmm) REVERT: E 255 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8783 (pt0) REVERT: E 256 PHE cc_start: 0.9177 (m-10) cc_final: 0.8756 (m-10) REVERT: E 339 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8840 (ttt180) REVERT: E 343 LYS cc_start: 0.9495 (ttmt) cc_final: 0.9242 (ttmm) REVERT: E 365 ASP cc_start: 0.9197 (m-30) cc_final: 0.8922 (m-30) REVERT: E 438 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6890 (tm-30) REVERT: E 469 LYS cc_start: 0.8905 (ptmm) cc_final: 0.8524 (ptmm) REVERT: F 188 ASP cc_start: 0.8692 (t0) cc_final: 0.8379 (t70) REVERT: F 258 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8826 (p) REVERT: F 398 THR cc_start: 0.9314 (m) cc_final: 0.8981 (p) outliers start: 46 outliers final: 27 residues processed: 357 average time/residue: 0.1495 time to fit residues: 77.8815 Evaluate side-chains 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 309 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 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 182 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 E residue 277 LEU Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 190 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 109 optimal weight: 5.9990 chunk 85 optimal weight: 0.0070 chunk 164 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN D 180 GLN D 374 HIS ** F 292 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 = 0.3501 r_free = 0.3501 target = 0.093377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.072251 restraints weight = 44858.262| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.71 r_work: 0.2939 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 1.0414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18402 Z= 0.158 Angle : 0.665 11.537 24981 Z= 0.336 Chirality : 0.047 0.182 2978 Planarity : 0.005 0.051 3338 Dihedral : 4.246 39.054 2749 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.42 % Allowed : 25.42 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2520 helix: 1.93 (0.16), residues: 1120 sheet: -0.59 (0.22), residues: 520 loop : 0.08 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 491 TYR 0.015 0.001 TYR C 402 PHE 0.022 0.002 PHE D 243 TRP 0.010 0.001 TRP F 481 HIS 0.004 0.001 HIS F 319 Details of bonding type rmsd covalent geometry : bond 0.00381 (18402) covalent geometry : angle 0.66511 (24981) hydrogen bonds : bond 0.03080 ( 958) hydrogen bonds : angle 4.02815 ( 2805) =============================================================================== Job complete usr+sys time: 4184.09 seconds wall clock time: 72 minutes 21.95 seconds (4341.95 seconds total)