Starting phenix.real_space_refine on Mon Jun 16 09:46:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e24_47433/06_2025/9e24_47433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e24_47433/06_2025/9e24_47433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e24_47433/06_2025/9e24_47433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e24_47433/06_2025/9e24_47433.map" model { file = "/net/cci-nas-00/data/ceres_data/9e24_47433/06_2025/9e24_47433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e24_47433/06_2025/9e24_47433.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.017 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 102 5.16 5 C 11334 2.51 5 N 3402 2.21 5 O 3486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18324 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "F" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 10.45, per 1000 atoms: 0.57 Number of scatterers: 18324 At special positions: 0 Unit cell: (124.63, 134.93, 98.88, 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 102 16.00 O 3486 8.00 N 3402 7.00 C 11334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.4 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 12 sheets defined 45.4% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 80 through 97 removed outlier: 3.921A pdb=" N ALA A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 106 through 126 removed outlier: 3.786A pdb=" N ILE A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 removed outlier: 3.726A pdb=" N HIS A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.339A pdb=" N LEU A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 157 " --> pdb=" O PRO A 153 " (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 288 through 296 Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 361 through 372 removed outlier: 4.073A 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 488 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'B' and resid 81 through 97 removed outlier: 3.606A pdb=" N THR B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 107 through 126 removed outlier: 4.047A pdb=" N GLY B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.356A 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 removed outlier: 3.587A pdb=" N ALA B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.796A pdb=" N ARG B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 4.077A pdb=" N ASP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 487 removed outlier: 3.533A pdb=" N ALA B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'C' and resid 81 through 97 removed outlier: 3.775A pdb=" N ILE C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 removed outlier: 3.780A pdb=" N LEU C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 removed outlier: 3.583A pdb=" N GLU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.716A pdb=" N GLN C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.562A 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 removed outlier: 3.578A pdb=" N ALA C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.813A pdb=" N ARG C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 removed outlier: 3.950A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 399 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 489 through 501 removed outlier: 4.392A pdb=" N GLU C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.526A pdb=" N ALA D 103 " --> 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 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 156 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 296 Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.734A pdb=" N ARG D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.017A 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 Processing helix chain 'E' and resid 81 through 97 removed outlier: 4.145A pdb=" N THR E 85 " --> pdb=" O TYR E 81 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 107 through 126 removed outlier: 4.282A pdb=" N GLY E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 147 Processing helix chain 'E' and resid 150 through 157 removed outlier: 4.342A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (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 347 removed outlier: 3.752A pdb=" N ARG E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 372 removed outlier: 3.857A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 368 " --> pdb=" O PHE E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.547A pdb=" N SER E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 487 removed outlier: 3.554A pdb=" N ALA E 484 " --> pdb=" O PHE E 480 " (cutoff:3.500A) 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 103 Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.634A pdb=" N GLU F 113 " --> pdb=" O GLN F 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP F 116 " --> pdb=" O GLU F 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 146 removed outlier: 3.985A pdb=" N VAL F 138 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) 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 removed outlier: 3.707A pdb=" N GLN F 202 " --> pdb=" O ARG F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.647A pdb=" N ALA F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 346 removed outlier: 3.532A pdb=" N LEU F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 361 through 372 removed outlier: 3.906A 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 480 through 488 Processing helix chain 'F' and resid 489 through 501 removed outlier: 4.347A pdb=" N GLU F 501 " --> pdb=" O LEU F 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.038A 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: 6.579A pdb=" N VAL A 304 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 323 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR A 306 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY A 356 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N CYS A 307 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 358 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET A 378 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 356 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 380 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS A 382 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 435 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 424 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE A 433 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 17.474A pdb=" N ARG A 431 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 14.151A pdb=" N THR A 458 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N ILE A 433 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLU A 456 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N HIS A 435 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 454 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 437 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 452 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 439 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN A 450 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TYR A 455 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG A 471 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 457 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 469 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 459 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 182 removed outlier: 4.520A pdb=" N VAL B 171 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.794A 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: 6.617A pdb=" N VAL B 305 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 353 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR B 380 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL B 355 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N HIS B 382 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU B 277 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU B 381 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE B 279 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 278 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA B 423 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER B 280 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N ARG B 425 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B 424 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE B 433 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N ARG B 432 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N GLU B 456 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR B 434 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 454 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 436 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 448 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU B 442 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR B 455 " --> pdb=" O ARG B 471 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 471 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE B 457 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 469 " --> pdb=" O ILE B 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 182 removed outlier: 4.453A pdb=" N VAL C 171 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.754A 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 322 removed outlier: 6.441A pdb=" N VAL C 304 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU C 277 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU C 381 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 279 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 420 " --> pdb=" O ILE C 436 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE C 436 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N ARG C 432 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N GLU C 456 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR C 434 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 454 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 436 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 448 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU C 442 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR C 455 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG C 471 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE C 457 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 6.366A 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: 3.843A pdb=" N ASP D 162 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.566A pdb=" N VAL D 304 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU D 323 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR D 306 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 305 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY D 356 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS D 307 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL D 358 " --> pdb=" O CYS D 307 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET D 378 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY D 356 " --> pdb=" O MET D 378 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR D 380 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N HIS D 382 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 278 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA D 423 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER D 280 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ARG D 425 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 435 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA D 424 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE D 433 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 17.552A pdb=" N ARG D 431 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 14.173A pdb=" N THR D 458 " --> pdb=" O ARG D 431 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N ILE D 433 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLU D 456 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N HIS D 435 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 454 " --> pdb=" O HIS D 435 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR D 437 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU D 452 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL D 439 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN D 450 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR D 455 " --> pdb=" O ARG D 471 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG D 471 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE D 457 " --> pdb=" O LYS D 469 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS D 469 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 459 " --> pdb=" O VAL D 467 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 178 through 182 removed outlier: 4.567A pdb=" N VAL E 171 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG E 170 " --> pdb=" O ASN E 166 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP E 162 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 320 through 324 removed outlier: 6.304A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE E 353 " --> pdb=" O MET E 378 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N THR E 380 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL E 355 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N HIS E 382 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU E 277 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU E 381 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE E 279 " --> pdb=" O LEU E 381 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 278 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA E 423 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER E 280 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ARG E 425 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA E 424 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE E 433 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N ARG E 432 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N GLU E 456 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR E 434 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL E 454 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE E 436 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL E 448 " --> pdb=" O VAL E 440 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU E 442 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYR E 455 " --> pdb=" O ARG E 471 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG E 471 " --> pdb=" O TYR E 455 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE E 457 " --> pdb=" O LYS E 469 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS E 469 " --> pdb=" O ILE E 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 178 through 182 removed outlier: 4.399A pdb=" N VAL F 171 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 321 through 322 removed outlier: 6.232A pdb=" N VAL F 305 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE F 353 " --> pdb=" O MET F 378 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N THR F 380 " --> pdb=" O ILE F 353 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL F 355 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N HIS F 382 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 379 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL F 278 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA F 423 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER F 280 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ARG F 425 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 11.577A pdb=" N ARG F 432 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLU F 456 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR F 434 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL F 454 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE F 436 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL F 448 " --> pdb=" O VAL F 440 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR F 455 " --> pdb=" O ARG F 471 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 471 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE F 457 " --> pdb=" O LYS F 469 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS F 469 " --> pdb=" O ILE F 457 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 5.81 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: 6522 1.34 - 1.46: 1661 1.46 - 1.57: 10201 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 18552 Sorted by residual: bond pdb=" CG GLN E 368 " pdb=" CD GLN E 368 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CA ILE F 279 " pdb=" CB ILE F 279 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.28e+00 bond pdb=" CA ILE C 279 " pdb=" CB ILE C 279 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.21e+00 bond pdb=" CB GLN C 316 " pdb=" CG GLN C 316 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.17e+00 bond pdb=" N LEU E 107 " pdb=" CA LEU E 107 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.09e+00 ... (remaining 18547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 24917 1.93 - 3.85: 229 3.85 - 5.78: 25 5.78 - 7.71: 4 7.71 - 9.64: 1 Bond angle restraints: 25176 Sorted by residual: angle pdb=" CB MET F 250 " pdb=" CG MET F 250 " pdb=" SD MET F 250 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA GLN F 316 " pdb=" CB GLN F 316 " pdb=" CG GLN F 316 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.50e+00 angle pdb=" CA GLN C 316 " pdb=" CB GLN C 316 " pdb=" CG GLN C 316 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.11e+00 angle pdb=" N GLU C 312 " pdb=" CA GLU C 312 " pdb=" C GLU C 312 " ideal model delta sigma weight residual 113.18 110.00 3.18 1.33e+00 5.65e-01 5.72e+00 angle pdb=" C ALA C 272 " pdb=" N CYS C 273 " pdb=" CA CYS C 273 " ideal model delta sigma weight residual 125.02 120.94 4.08 1.76e+00 3.23e-01 5.37e+00 ... (remaining 25171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10446 17.76 - 35.52: 760 35.52 - 53.28: 141 53.28 - 71.04: 27 71.04 - 88.80: 20 Dihedral angle restraints: 11394 sinusoidal: 4194 harmonic: 7200 Sorted by residual: dihedral pdb=" CA HIS D 435 " pdb=" C HIS D 435 " pdb=" N ILE D 436 " pdb=" CA ILE D 436 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+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 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA HIS F 435 " pdb=" C HIS F 435 " pdb=" N ILE F 436 " pdb=" CA ILE F 436 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 11391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1981 0.032 - 0.063: 573 0.063 - 0.095: 219 0.095 - 0.126: 200 0.126 - 0.158: 21 Chirality restraints: 2994 Sorted by residual: chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA ILE D 240 " pdb=" N ILE D 240 " pdb=" C ILE D 240 " pdb=" CB ILE D 240 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE F 354 " pdb=" N ILE F 354 " pdb=" C ILE F 354 " pdb=" CB ILE F 354 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2991 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 206 " 0.151 9.50e-02 1.11e+02 6.81e-02 3.42e+00 pdb=" NE ARG A 206 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 206 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 206 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 206 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 364 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C PHE E 364 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE E 364 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP E 365 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 349 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO C 350 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 350 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 350 " 0.019 5.00e-02 4.00e+02 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 228 2.59 - 3.16: 17077 3.16 - 3.74: 28469 3.74 - 4.32: 37569 4.32 - 4.90: 64115 Nonbonded interactions: 147458 Sorted by model distance: nonbonded pdb=" OD1 ASN B 371 " pdb=" OG SER B 416 " model vdw 2.008 3.040 nonbonded pdb=" OD1 ASN E 371 " pdb=" OG SER E 416 " model vdw 2.058 3.040 nonbonded pdb=" OG SER D 472 " pdb=" O ALA D 500 " model vdw 2.060 3.040 nonbonded pdb=" O ASP F 451 " pdb=" OG1 THR F 473 " model vdw 2.074 3.040 nonbonded pdb=" N GLN B 316 " pdb=" OE1 GLN B 316 " model vdw 2.094 3.120 ... (remaining 147453 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 42.800 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 18552 Z= 0.132 Angle : 0.496 9.637 25176 Z= 0.271 Chirality : 0.044 0.158 2994 Planarity : 0.003 0.068 3360 Dihedral : 13.401 88.801 6750 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.06 % Allowed : 10.02 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.18), residues: 2520 helix: 1.78 (0.17), residues: 1072 sheet: -0.48 (0.24), residues: 488 loop : 0.16 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 481 HIS 0.003 0.001 HIS A 435 PHE 0.008 0.001 PHE E 480 TYR 0.016 0.001 TYR C 486 ARG 0.013 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.14385 ( 942) hydrogen bonds : angle 6.13999 ( 2748) covalent geometry : bond 0.00271 (18552) covalent geometry : angle 0.49590 (25176) *********************** 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 738 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 737 time to evaluate : 2.303 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: 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 172 PHE cc_start: 0.8167 (m-80) cc_final: 0.7871 (m-10) REVERT: A 287 LYS cc_start: 0.8276 (pttm) cc_final: 0.7957 (pttt) REVERT: A 339 ARG cc_start: 0.8314 (mtp85) cc_final: 0.7870 (tpp80) REVERT: A 346 LEU cc_start: 0.8896 (mt) cc_final: 0.7954 (mt) REVERT: A 391 SER cc_start: 0.8887 (t) cc_final: 0.8578 (m) REVERT: B 294 MET cc_start: 0.8642 (mmm) cc_final: 0.7989 (mmm) REVERT: B 313 LEU cc_start: 0.8215 (mp) cc_final: 0.7894 (mp) REVERT: B 342 VAL cc_start: 0.7531 (t) cc_final: 0.7181 (t) REVERT: B 346 LEU cc_start: 0.8475 (mt) cc_final: 0.8236 (mt) REVERT: B 365 ASP cc_start: 0.7907 (m-30) cc_final: 0.7681 (m-30) REVERT: B 448 VAL cc_start: 0.8866 (t) cc_final: 0.8545 (p) REVERT: C 239 THR cc_start: 0.7773 (m) cc_final: 0.7289 (p) REVERT: C 270 ILE cc_start: 0.8118 (mt) cc_final: 0.7689 (mm) REVERT: C 314 GLN cc_start: 0.7071 (pt0) cc_final: 0.6849 (pt0) REVERT: C 317 GLN cc_start: 0.8715 (mm-40) cc_final: 0.7371 (mm-40) REVERT: C 358 VAL cc_start: 0.8447 (t) cc_final: 0.8052 (m) REVERT: C 367 LEU cc_start: 0.8446 (mp) cc_final: 0.7815 (mp) REVERT: C 381 LEU cc_start: 0.7720 (tp) cc_final: 0.7420 (tp) REVERT: C 410 LYS cc_start: 0.7747 (mttm) cc_final: 0.7039 (mtmm) REVERT: C 411 GLU cc_start: 0.8855 (tp30) cc_final: 0.8615 (tp30) REVERT: C 454 VAL cc_start: 0.7931 (t) cc_final: 0.7653 (p) REVERT: D 207 VAL cc_start: 0.7304 (p) cc_final: 0.6526 (p) REVERT: D 240 ILE cc_start: 0.7152 (mm) cc_final: 0.6751 (mm) REVERT: D 247 LYS cc_start: 0.8730 (mptt) cc_final: 0.8432 (mmtt) REVERT: D 308 GLU cc_start: 0.7725 (pt0) cc_final: 0.7176 (pt0) REVERT: D 410 LYS cc_start: 0.8606 (mttm) cc_final: 0.8270 (mttm) REVERT: D 454 VAL cc_start: 0.8216 (t) cc_final: 0.7933 (p) REVERT: E 175 VAL cc_start: 0.8384 (p) cc_final: 0.8042 (m) REVERT: E 243 PHE cc_start: 0.7955 (t80) cc_final: 0.6867 (t80) REVERT: E 294 MET cc_start: 0.7002 (mmm) cc_final: 0.6177 (mmm) REVERT: E 312 GLU cc_start: 0.8321 (tp30) cc_final: 0.8022 (tp30) REVERT: E 325 THR cc_start: 0.8250 (p) cc_final: 0.7810 (p) REVERT: E 395 SER cc_start: 0.9272 (m) cc_final: 0.8990 (p) REVERT: F 269 VAL cc_start: 0.9169 (t) cc_final: 0.8931 (t) REVERT: F 289 THR cc_start: 0.9118 (m) cc_final: 0.8825 (t) REVERT: F 290 LEU cc_start: 0.9352 (tp) cc_final: 0.9145 (tt) REVERT: F 380 THR cc_start: 0.7409 (p) cc_final: 0.6977 (p) REVERT: F 382 HIS cc_start: 0.7023 (t-90) cc_final: 0.5615 (t-170) REVERT: F 437 THR cc_start: 0.7100 (p) cc_final: 0.6764 (t) REVERT: F 489 LEU cc_start: 0.8806 (mm) cc_final: 0.8480 (mp) outliers start: 1 outliers final: 0 residues processed: 737 average time/residue: 0.4097 time to fit residues: 431.2769 Evaluate side-chains 502 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 40.0000 chunk 191 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 40.0000 chunk 102 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 147 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN B 382 HIS D 191 GLN D 374 HIS E 371 ASN F 384 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.087068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065433 restraints weight = 55412.249| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.72 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18552 Z= 0.185 Angle : 0.728 10.202 25176 Z= 0.377 Chirality : 0.051 0.229 2994 Planarity : 0.006 0.068 3360 Dihedral : 4.317 32.211 2754 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.55 % Allowed : 18.13 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2520 helix: 1.48 (0.16), residues: 1100 sheet: -0.57 (0.21), residues: 588 loop : 0.59 (0.24), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP D 481 HIS 0.006 0.001 HIS C 374 PHE 0.031 0.002 PHE A 243 TYR 0.019 0.002 TYR D 402 ARG 0.010 0.001 ARG C 471 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 942) hydrogen bonds : angle 4.84352 ( 2748) covalent geometry : bond 0.00416 (18552) covalent geometry : angle 0.72764 (25176) *********************** 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 597 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 534 time to evaluate : 2.032 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: symmetry clash REVERT: A 172 PHE cc_start: 0.8438 (m-80) cc_final: 0.8126 (m-10) REVERT: A 243 PHE cc_start: 0.8049 (p90) cc_final: 0.7666 (p90) REVERT: A 314 GLN cc_start: 0.8325 (tp40) cc_final: 0.8110 (tp40) REVERT: A 339 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7887 (ttm-80) REVERT: A 342 VAL cc_start: 0.8988 (t) cc_final: 0.8720 (t) REVERT: A 345 CYS cc_start: 0.7903 (m) cc_final: 0.7625 (m) REVERT: A 391 SER cc_start: 0.8738 (t) cc_final: 0.8374 (m) REVERT: A 408 THR cc_start: 0.7950 (p) cc_final: 0.7672 (p) REVERT: A 411 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8711 (tm-30) REVERT: A 456 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: B 151 LEU cc_start: 0.9332 (mt) cc_final: 0.9129 (mt) REVERT: B 162 ASP cc_start: 0.7176 (m-30) cc_final: 0.6724 (t0) REVERT: B 164 MET cc_start: 0.7713 (mtm) cc_final: 0.7324 (mpp) REVERT: B 313 LEU cc_start: 0.8480 (mp) cc_final: 0.8166 (mp) REVERT: B 314 GLN cc_start: 0.8281 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 342 VAL cc_start: 0.7583 (t) cc_final: 0.7274 (t) REVERT: B 364 PHE cc_start: 0.8940 (t80) cc_final: 0.8600 (t80) REVERT: B 394 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8281 (mt-10) REVERT: B 410 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8043 (mmmt) REVERT: B 414 VAL cc_start: 0.8046 (t) cc_final: 0.7802 (t) REVERT: B 445 ASP cc_start: 0.8412 (m-30) cc_final: 0.8122 (m-30) REVERT: C 174 GLU cc_start: 0.8491 (tt0) cc_final: 0.8248 (tt0) REVERT: C 317 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8434 (mm-40) REVERT: C 343 LYS cc_start: 0.8743 (mttp) cc_final: 0.8408 (mttp) REVERT: C 345 CYS cc_start: 0.7875 (m) cc_final: 0.7395 (m) REVERT: C 358 VAL cc_start: 0.8589 (t) cc_final: 0.8078 (m) REVERT: C 364 PHE cc_start: 0.8324 (t80) cc_final: 0.7713 (t80) REVERT: C 368 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8013 (mm110) REVERT: C 381 LEU cc_start: 0.8027 (tp) cc_final: 0.7625 (tp) REVERT: C 411 GLU cc_start: 0.8926 (tp30) cc_final: 0.8567 (tp30) REVERT: C 450 GLN cc_start: 0.8025 (pp30) cc_final: 0.7815 (pp30) REVERT: C 454 VAL cc_start: 0.8257 (t) cc_final: 0.7813 (p) REVERT: D 390 ILE cc_start: 0.9012 (mt) cc_final: 0.8797 (mt) REVERT: D 407 LYS cc_start: 0.8600 (mtpp) cc_final: 0.7986 (mmmm) REVERT: D 411 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8743 (mt-10) REVERT: D 491 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8056 (ptm-80) REVERT: E 180 GLN cc_start: 0.7750 (pp30) cc_final: 0.7478 (pp30) REVERT: E 243 PHE cc_start: 0.7773 (t80) cc_final: 0.6644 (t80) REVERT: E 256 PHE cc_start: 0.8465 (m-10) cc_final: 0.8220 (m-10) REVERT: E 341 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7222 (mm) REVERT: E 345 CYS cc_start: 0.8729 (m) cc_final: 0.8372 (m) REVERT: E 399 MET cc_start: 0.7911 (mtm) cc_final: 0.7595 (ptp) REVERT: E 402 TYR cc_start: 0.8131 (m-80) cc_final: 0.7584 (m-80) REVERT: E 481 TRP cc_start: 0.8618 (t-100) cc_final: 0.8195 (t-100) REVERT: F 178 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8971 (tmmt) REVERT: F 202 GLN cc_start: 0.7816 (mp10) cc_final: 0.7315 (mp10) REVERT: F 256 PHE cc_start: 0.9081 (m-10) cc_final: 0.8819 (m-10) REVERT: F 289 THR cc_start: 0.9284 (m) cc_final: 0.8950 (t) REVERT: F 290 LEU cc_start: 0.9458 (tp) cc_final: 0.9185 (tt) REVERT: F 324 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6590 (tp30) REVERT: F 342 VAL cc_start: 0.9385 (t) cc_final: 0.9170 (p) REVERT: F 345 CYS cc_start: 0.8533 (m) cc_final: 0.8066 (m) REVERT: F 399 MET cc_start: 0.9282 (ptm) cc_final: 0.9077 (ppp) REVERT: F 402 TYR cc_start: 0.7749 (m-80) cc_final: 0.7435 (m-10) REVERT: F 407 LYS cc_start: 0.8830 (tppt) cc_final: 0.8584 (tppt) REVERT: F 410 LYS cc_start: 0.8218 (mttm) cc_final: 0.7996 (mtpt) REVERT: F 411 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8633 (pp20) outliers start: 63 outliers final: 34 residues processed: 561 average time/residue: 0.3683 time to fit residues: 306.4333 Evaluate side-chains 479 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 443 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 384 ASN Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 171 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN A 316 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 HIS ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS F 292 ASN F 422 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.086715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065110 restraints weight = 55110.470| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.73 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18552 Z= 0.174 Angle : 0.678 10.878 25176 Z= 0.347 Chirality : 0.049 0.197 2994 Planarity : 0.005 0.052 3360 Dihedral : 4.162 31.754 2754 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.50 % Allowed : 19.99 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2520 helix: 1.52 (0.16), residues: 1104 sheet: -0.59 (0.21), residues: 566 loop : 0.30 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 481 HIS 0.005 0.001 HIS F 382 PHE 0.024 0.002 PHE A 243 TYR 0.014 0.001 TYR D 402 ARG 0.008 0.001 ARG E 339 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 942) hydrogen bonds : angle 4.64551 ( 2748) covalent geometry : bond 0.00400 (18552) covalent geometry : angle 0.67819 (25176) *********************** 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 543 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 463 time to evaluate : 4.560 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: A 172 PHE cc_start: 0.8620 (m-80) cc_final: 0.8298 (m-10) REVERT: A 243 PHE cc_start: 0.8133 (p90) cc_final: 0.7677 (p90) REVERT: A 256 PHE cc_start: 0.9076 (m-10) cc_final: 0.8844 (m-10) REVERT: A 314 GLN cc_start: 0.8619 (tp40) cc_final: 0.7871 (tm-30) REVERT: A 315 LEU cc_start: 0.9326 (mt) cc_final: 0.9089 (mm) REVERT: A 391 SER cc_start: 0.8912 (t) cc_final: 0.8573 (m) REVERT: B 239 THR cc_start: 0.8742 (m) cc_final: 0.8479 (p) REVERT: B 273 CYS cc_start: 0.8558 (m) cc_final: 0.7938 (p) REVERT: B 313 LEU cc_start: 0.8855 (mp) cc_final: 0.8425 (mp) REVERT: B 314 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8110 (tm-30) REVERT: B 339 ARG cc_start: 0.8951 (ttp80) cc_final: 0.8655 (ttm-80) REVERT: B 364 PHE cc_start: 0.9087 (t80) cc_final: 0.8511 (t80) REVERT: B 370 MET cc_start: 0.7707 (mmt) cc_final: 0.7487 (mmt) REVERT: B 427 ARG cc_start: 0.8676 (tmm-80) cc_final: 0.8183 (ttp-170) REVERT: C 174 GLU cc_start: 0.8592 (tt0) cc_final: 0.8368 (tt0) REVERT: C 244 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8596 (tptp) REVERT: C 248 LEU cc_start: 0.7285 (pp) cc_final: 0.7080 (pp) REVERT: C 317 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8208 (mm-40) REVERT: C 364 PHE cc_start: 0.8662 (t80) cc_final: 0.7755 (t80) REVERT: C 368 GLN cc_start: 0.8694 (mm-40) cc_final: 0.7973 (mm110) REVERT: C 370 MET cc_start: 0.8303 (tpp) cc_final: 0.8081 (tpp) REVERT: C 399 MET cc_start: 0.8909 (ptp) cc_final: 0.8654 (ppp) REVERT: C 411 GLU cc_start: 0.9058 (tp30) cc_final: 0.8850 (tp30) REVERT: C 450 GLN cc_start: 0.8082 (pp30) cc_final: 0.7367 (pp30) REVERT: C 453 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5737 (t80) REVERT: C 482 ASP cc_start: 0.9336 (OUTLIER) cc_final: 0.9127 (p0) REVERT: D 193 MET cc_start: 0.8064 (tpp) cc_final: 0.7835 (tpt) REVERT: D 245 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8940 (mmmt) REVERT: D 378 MET cc_start: 0.7490 (mtp) cc_final: 0.7287 (mtp) REVERT: D 407 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8247 (mmmm) REVERT: D 410 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8484 (mmtm) REVERT: D 411 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8846 (mt-10) REVERT: D 426 LEU cc_start: 0.8714 (mt) cc_final: 0.8487 (mt) REVERT: D 448 VAL cc_start: 0.9101 (t) cc_final: 0.8730 (p) REVERT: D 491 ARG cc_start: 0.8784 (ttp80) cc_final: 0.8499 (ttp80) REVERT: E 180 GLN cc_start: 0.8113 (pp30) cc_final: 0.7715 (pp30) REVERT: E 256 PHE cc_start: 0.8517 (m-10) cc_final: 0.8267 (m-10) REVERT: E 308 GLU cc_start: 0.8428 (pm20) cc_final: 0.7983 (mp0) REVERT: E 312 GLU cc_start: 0.8321 (tp30) cc_final: 0.7973 (mp0) REVERT: E 341 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7248 (mm) REVERT: E 345 CYS cc_start: 0.9124 (m) cc_final: 0.8740 (m) REVERT: E 388 GLU cc_start: 0.9318 (tp30) cc_final: 0.8974 (tt0) REVERT: E 399 MET cc_start: 0.8021 (mtm) cc_final: 0.7710 (ptp) REVERT: E 418 ASP cc_start: 0.7916 (m-30) cc_final: 0.7370 (m-30) REVERT: E 446 VAL cc_start: 0.8892 (t) cc_final: 0.8597 (p) REVERT: E 481 TRP cc_start: 0.8696 (t-100) cc_final: 0.8243 (t-100) REVERT: F 178 LYS cc_start: 0.9347 (ttpp) cc_final: 0.9074 (ttpp) REVERT: F 202 GLN cc_start: 0.8249 (mp10) cc_final: 0.7725 (mp10) REVERT: F 256 PHE cc_start: 0.9196 (m-10) cc_final: 0.8875 (m-10) REVERT: F 289 THR cc_start: 0.9437 (m) cc_final: 0.9103 (t) REVERT: F 297 PHE cc_start: 0.9188 (m-80) cc_final: 0.8910 (m-80) REVERT: F 324 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7022 (tp30) REVERT: F 370 MET cc_start: 0.8796 (mtm) cc_final: 0.8543 (mtm) REVERT: F 399 MET cc_start: 0.9339 (ptm) cc_final: 0.9078 (ppp) REVERT: F 407 LYS cc_start: 0.8900 (tppt) cc_final: 0.8682 (tppt) outliers start: 80 outliers final: 39 residues processed: 506 average time/residue: 0.4220 time to fit residues: 323.1433 Evaluate side-chains 458 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 416 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 168 optimal weight: 110.0000 chunk 137 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN B 463 HIS D 374 HIS E 344 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065072 restraints weight = 54358.845| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.60 r_work: 0.2866 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18552 Z= 0.175 Angle : 0.659 11.601 25176 Z= 0.337 Chirality : 0.048 0.225 2994 Planarity : 0.005 0.047 3360 Dihedral : 4.154 31.252 2754 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.95 % Allowed : 21.57 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2520 helix: 1.50 (0.16), residues: 1108 sheet: -0.38 (0.22), residues: 530 loop : 0.08 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 481 HIS 0.004 0.001 HIS D 382 PHE 0.018 0.002 PHE A 243 TYR 0.013 0.001 TYR F 402 ARG 0.011 0.001 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 942) hydrogen bonds : angle 4.56977 ( 2748) covalent geometry : bond 0.00405 (18552) covalent geometry : angle 0.65946 (25176) *********************** 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 527 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 439 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8775 (m-80) cc_final: 0.8469 (m-10) REVERT: A 243 PHE cc_start: 0.8404 (p90) cc_final: 0.7951 (p90) REVERT: A 256 PHE cc_start: 0.9160 (m-10) cc_final: 0.8953 (m-10) REVERT: A 298 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 314 GLN cc_start: 0.9056 (tp40) cc_final: 0.8802 (tm-30) REVERT: A 316 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: A 324 GLU cc_start: 0.8888 (pp20) cc_final: 0.8679 (pp20) REVERT: A 370 MET cc_start: 0.8301 (tpp) cc_final: 0.8086 (tpp) REVERT: A 391 SER cc_start: 0.9106 (t) cc_final: 0.8808 (m) REVERT: B 184 VAL cc_start: 0.8396 (t) cc_final: 0.7960 (p) REVERT: B 273 CYS cc_start: 0.9138 (m) cc_final: 0.8708 (p) REVERT: B 297 PHE cc_start: 0.8998 (m-80) cc_final: 0.8761 (m-10) REVERT: B 313 LEU cc_start: 0.9049 (mp) cc_final: 0.8685 (mp) REVERT: B 314 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8485 (tm-30) REVERT: B 339 ARG cc_start: 0.9196 (ttp80) cc_final: 0.8838 (ttm-80) REVERT: B 343 LYS cc_start: 0.9125 (mttp) cc_final: 0.8866 (mttm) REVERT: B 450 GLN cc_start: 0.9352 (pt0) cc_final: 0.9111 (pt0) REVERT: C 148 TYR cc_start: 0.8229 (m-10) cc_final: 0.7925 (m-10) REVERT: C 174 GLU cc_start: 0.8733 (tt0) cc_final: 0.8386 (tt0) REVERT: C 180 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (pp30) REVERT: C 270 ILE cc_start: 0.9299 (mt) cc_final: 0.9058 (mm) REVERT: C 317 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8419 (mm-40) REVERT: C 340 ASP cc_start: 0.8851 (m-30) cc_final: 0.8628 (m-30) REVERT: C 343 LYS cc_start: 0.9148 (mttp) cc_final: 0.8839 (mttp) REVERT: C 364 PHE cc_start: 0.8850 (t80) cc_final: 0.8264 (t80) REVERT: C 368 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8645 (mm110) REVERT: C 399 MET cc_start: 0.9197 (ptp) cc_final: 0.8868 (ppp) REVERT: C 411 GLU cc_start: 0.9324 (tp30) cc_final: 0.9093 (tp30) REVERT: C 453 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.6088 (t80) REVERT: C 482 ASP cc_start: 0.9442 (OUTLIER) cc_final: 0.9220 (p0) REVERT: D 233 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8848 (mm) REVERT: D 308 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6956 (pt0) REVERT: D 312 GLU cc_start: 0.8536 (mp0) cc_final: 0.8235 (mp0) REVERT: D 343 LYS cc_start: 0.8857 (mttp) cc_final: 0.8545 (mmtm) REVERT: D 426 LEU cc_start: 0.8871 (mt) cc_final: 0.8612 (mt) REVERT: D 443 GLU cc_start: 0.7844 (mp0) cc_final: 0.7496 (mp0) REVERT: D 448 VAL cc_start: 0.9189 (t) cc_final: 0.8894 (p) REVERT: E 180 GLN cc_start: 0.8497 (pp30) cc_final: 0.8102 (pp30) REVERT: E 243 PHE cc_start: 0.8083 (t80) cc_final: 0.7733 (t80) REVERT: E 256 PHE cc_start: 0.8770 (m-10) cc_final: 0.8519 (m-10) REVERT: E 312 GLU cc_start: 0.8603 (tp30) cc_final: 0.8284 (mp0) REVERT: E 345 CYS cc_start: 0.9527 (m) cc_final: 0.9249 (m) REVERT: E 388 GLU cc_start: 0.9516 (tp30) cc_final: 0.9112 (tt0) REVERT: E 399 MET cc_start: 0.8446 (mtm) cc_final: 0.8105 (ptp) REVERT: E 410 LYS cc_start: 0.8582 (mttm) cc_final: 0.8023 (mtpt) REVERT: E 418 ASP cc_start: 0.8467 (m-30) cc_final: 0.7757 (m-30) REVERT: E 481 TRP cc_start: 0.8879 (t-100) cc_final: 0.8517 (t-100) REVERT: F 148 TYR cc_start: 0.8841 (m-80) cc_final: 0.8632 (m-10) REVERT: F 178 LYS cc_start: 0.9485 (ttpp) cc_final: 0.9164 (tmmt) REVERT: F 180 GLN cc_start: 0.8915 (pm20) cc_final: 0.8337 (pm20) REVERT: F 193 MET cc_start: 0.9268 (tpp) cc_final: 0.9066 (tpp) REVERT: F 202 GLN cc_start: 0.8800 (mp10) cc_final: 0.8172 (mp10) REVERT: F 256 PHE cc_start: 0.9327 (m-10) cc_final: 0.8976 (m-10) REVERT: F 297 PHE cc_start: 0.9397 (m-80) cc_final: 0.9054 (m-80) REVERT: F 324 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7618 (tp30) REVERT: F 399 MET cc_start: 0.9444 (ptm) cc_final: 0.9096 (ppp) REVERT: F 407 LYS cc_start: 0.8931 (tppt) cc_final: 0.8687 (tppt) outliers start: 88 outliers final: 46 residues processed: 492 average time/residue: 0.4655 time to fit residues: 353.3554 Evaluate side-chains 441 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 388 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 440 VAL 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 482 ASP Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 345 CYS Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 42 optimal weight: 100.0000 chunk 184 optimal weight: 0.0970 chunk 30 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 chunk 37 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN D 374 HIS E 371 ASN F 422 GLN F 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.087579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.066507 restraints weight = 54129.599| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.61 r_work: 0.2896 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18552 Z= 0.127 Angle : 0.637 9.523 25176 Z= 0.321 Chirality : 0.047 0.205 2994 Planarity : 0.005 0.048 3360 Dihedral : 4.076 29.943 2754 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.62 % Allowed : 21.79 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2520 helix: 1.49 (0.16), residues: 1108 sheet: -0.37 (0.21), residues: 554 loop : 0.17 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 481 HIS 0.002 0.000 HIS F 319 PHE 0.015 0.002 PHE B 364 TYR 0.014 0.001 TYR F 402 ARG 0.008 0.000 ARG D 491 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 942) hydrogen bonds : angle 4.42820 ( 2748) covalent geometry : bond 0.00291 (18552) covalent geometry : angle 0.63699 (25176) *********************** 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 500 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 418 time to evaluate : 2.157 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: 0.8766 (m-80) cc_final: 0.8484 (m-10) REVERT: A 243 PHE cc_start: 0.8419 (p90) cc_final: 0.7987 (p90) REVERT: A 256 PHE cc_start: 0.9178 (m-10) cc_final: 0.8965 (m-10) REVERT: A 316 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8495 (tm-30) REVERT: A 324 GLU cc_start: 0.8839 (pp20) cc_final: 0.8590 (pp20) REVERT: A 342 VAL cc_start: 0.9474 (t) cc_final: 0.9251 (p) REVERT: A 391 SER cc_start: 0.9072 (t) cc_final: 0.8778 (m) REVERT: A 435 HIS cc_start: 0.8807 (m90) cc_final: 0.8363 (m90) REVERT: B 180 GLN cc_start: 0.9446 (tm-30) cc_final: 0.9083 (tm-30) REVERT: B 256 PHE cc_start: 0.9025 (m-10) cc_final: 0.8752 (m-10) REVERT: B 273 CYS cc_start: 0.9168 (m) cc_final: 0.8891 (p) REVERT: B 313 LEU cc_start: 0.9116 (mp) cc_final: 0.8773 (mp) REVERT: B 314 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8431 (tm-30) REVERT: B 339 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8752 (ttm-80) REVERT: B 343 LYS cc_start: 0.9109 (mttp) cc_final: 0.8830 (mttm) REVERT: B 346 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8655 (mm) REVERT: B 370 MET cc_start: 0.8104 (mmt) cc_final: 0.7830 (mmt) REVERT: B 399 MET cc_start: 0.8909 (ptp) cc_final: 0.8666 (ptp) REVERT: B 450 GLN cc_start: 0.9343 (pt0) cc_final: 0.9129 (pt0) REVERT: C 148 TYR cc_start: 0.8288 (m-10) cc_final: 0.7940 (m-10) REVERT: C 180 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8483 (pp30) REVERT: C 244 LYS cc_start: 0.9419 (mmmt) cc_final: 0.8824 (tptt) REVERT: C 250 MET cc_start: 0.8477 (ttt) cc_final: 0.8273 (pmm) REVERT: C 270 ILE cc_start: 0.9357 (mt) cc_final: 0.9120 (mm) REVERT: C 317 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8583 (mm-40) REVERT: C 364 PHE cc_start: 0.8822 (t80) cc_final: 0.8058 (t80) REVERT: C 367 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8693 (mm) REVERT: C 368 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8560 (mm110) REVERT: C 396 MET cc_start: 0.8217 (tpp) cc_final: 0.7942 (mtt) REVERT: C 399 MET cc_start: 0.9230 (ptp) cc_final: 0.8877 (ppp) REVERT: C 411 GLU cc_start: 0.9359 (tp30) cc_final: 0.9144 (tp30) REVERT: C 469 LYS cc_start: 0.9300 (mmmt) cc_final: 0.9045 (tptp) REVERT: C 482 ASP cc_start: 0.9441 (OUTLIER) cc_final: 0.9228 (p0) REVERT: D 308 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7065 (pt0) REVERT: D 343 LYS cc_start: 0.8800 (mttp) cc_final: 0.8580 (mtmm) REVERT: D 426 LEU cc_start: 0.8907 (mt) cc_final: 0.8615 (mt) REVERT: D 443 GLU cc_start: 0.7968 (mp0) cc_final: 0.7555 (mp0) REVERT: D 448 VAL cc_start: 0.9216 (t) cc_final: 0.8912 (p) REVERT: E 154 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8852 (pp) REVERT: E 180 GLN cc_start: 0.8589 (pp30) cc_final: 0.8205 (pp30) REVERT: E 256 PHE cc_start: 0.8801 (m-10) cc_final: 0.8538 (m-10) REVERT: E 312 GLU cc_start: 0.8527 (tp30) cc_final: 0.8226 (mp0) REVERT: E 345 CYS cc_start: 0.9566 (m) cc_final: 0.9253 (m) REVERT: E 388 GLU cc_start: 0.9502 (tp30) cc_final: 0.9134 (tt0) REVERT: E 410 LYS cc_start: 0.8568 (mttm) cc_final: 0.8058 (mtpt) REVERT: E 456 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8657 (mp0) REVERT: E 469 LYS cc_start: 0.9457 (ttpp) cc_final: 0.9154 (tmmt) REVERT: E 481 TRP cc_start: 0.8855 (t-100) cc_final: 0.8384 (t-100) REVERT: F 148 TYR cc_start: 0.8837 (m-80) cc_final: 0.8591 (m-10) REVERT: F 178 LYS cc_start: 0.9479 (ttpp) cc_final: 0.9168 (tmmt) REVERT: F 180 GLN cc_start: 0.8877 (pm20) cc_final: 0.8347 (pm20) REVERT: F 202 GLN cc_start: 0.8883 (mp10) cc_final: 0.8225 (mp10) REVERT: F 256 PHE cc_start: 0.9330 (m-10) cc_final: 0.8962 (m-10) REVERT: F 297 PHE cc_start: 0.9383 (m-80) cc_final: 0.9131 (m-80) REVERT: F 324 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7651 (tp30) REVERT: F 399 MET cc_start: 0.9452 (ptm) cc_final: 0.9078 (ppp) REVERT: F 407 LYS cc_start: 0.9000 (tppt) cc_final: 0.8582 (tppt) REVERT: F 411 GLU cc_start: 0.9336 (tm-30) cc_final: 0.9047 (pt0) outliers start: 82 outliers final: 52 residues processed: 462 average time/residue: 0.3015 time to fit residues: 211.5522 Evaluate side-chains 448 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 390 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 201 optimal weight: 10.0000 chunk 212 optimal weight: 40.0000 chunk 97 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 371 ASN D 225 ASN E 314 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.063795 restraints weight = 55530.775| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.80 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18552 Z= 0.190 Angle : 0.684 15.707 25176 Z= 0.343 Chirality : 0.048 0.234 2994 Planarity : 0.005 0.049 3360 Dihedral : 4.153 29.884 2754 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.67 % Allowed : 22.64 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2520 helix: 1.47 (0.16), residues: 1108 sheet: -0.54 (0.21), residues: 586 loop : 0.17 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 481 HIS 0.005 0.001 HIS C 470 PHE 0.018 0.002 PHE C 453 TYR 0.015 0.001 TYR F 402 ARG 0.013 0.001 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 942) hydrogen bonds : angle 4.48818 ( 2748) covalent geometry : bond 0.00421 (18552) covalent geometry : angle 0.68352 (25176) *********************** 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 471 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 388 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8984 (m-80) cc_final: 0.8588 (m-10) REVERT: A 197 GLN cc_start: 0.8835 (tt0) cc_final: 0.8563 (tm-30) REVERT: A 205 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8437 (mpp80) REVERT: A 243 PHE cc_start: 0.8420 (p90) cc_final: 0.7898 (p90) REVERT: A 316 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8548 (tm-30) REVERT: A 342 VAL cc_start: 0.9494 (t) cc_final: 0.9293 (p) REVERT: A 365 ASP cc_start: 0.8967 (p0) cc_final: 0.8700 (p0) REVERT: A 450 GLN cc_start: 0.8620 (pt0) cc_final: 0.8132 (tm-30) REVERT: B 180 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8826 (tm-30) REVERT: B 256 PHE cc_start: 0.9048 (m-10) cc_final: 0.8787 (m-10) REVERT: B 314 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7787 (tm-30) REVERT: B 339 ARG cc_start: 0.9159 (ttp80) cc_final: 0.8407 (mmm-85) REVERT: B 343 LYS cc_start: 0.9203 (mttp) cc_final: 0.8808 (mttm) REVERT: B 364 PHE cc_start: 0.9217 (t80) cc_final: 0.8770 (t80) REVERT: B 368 GLN cc_start: 0.8360 (mt0) cc_final: 0.7703 (mt0) REVERT: B 370 MET cc_start: 0.8383 (mmt) cc_final: 0.8137 (mmt) REVERT: B 399 MET cc_start: 0.8921 (ptp) cc_final: 0.8599 (ptp) REVERT: B 438 GLU cc_start: 0.8091 (mp0) cc_final: 0.7868 (mp0) REVERT: C 180 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8601 (pp30) REVERT: C 234 ASP cc_start: 0.8527 (t0) cc_final: 0.8250 (t0) REVERT: C 243 PHE cc_start: 0.8577 (t80) cc_final: 0.8221 (t80) REVERT: C 244 LYS cc_start: 0.9561 (mmmt) cc_final: 0.9039 (tptp) REVERT: C 270 ILE cc_start: 0.9435 (mt) cc_final: 0.9228 (mm) REVERT: C 309 ASP cc_start: 0.8129 (p0) cc_final: 0.7852 (p0) REVERT: C 312 GLU cc_start: 0.8443 (tp30) cc_final: 0.8149 (tm-30) REVERT: C 343 LYS cc_start: 0.9218 (mttp) cc_final: 0.8933 (mttp) REVERT: C 364 PHE cc_start: 0.8993 (t80) cc_final: 0.8364 (t80) REVERT: C 367 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8840 (mm) REVERT: C 368 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8659 (mm110) REVERT: C 370 MET cc_start: 0.8757 (tpp) cc_final: 0.8552 (tpp) REVERT: C 410 LYS cc_start: 0.8162 (mttm) cc_final: 0.7804 (mtpp) REVERT: C 411 GLU cc_start: 0.9295 (tp30) cc_final: 0.9077 (tp30) REVERT: C 469 LYS cc_start: 0.9402 (mmmt) cc_final: 0.9157 (tptp) REVERT: C 482 ASP cc_start: 0.9399 (OUTLIER) cc_final: 0.9134 (p0) REVERT: D 202 GLN cc_start: 0.8798 (tt0) cc_final: 0.8500 (mm110) REVERT: D 233 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8952 (mm) REVERT: D 308 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6082 (pt0) REVERT: D 426 LEU cc_start: 0.8831 (mt) cc_final: 0.8466 (mp) REVERT: D 443 GLU cc_start: 0.8037 (mp0) cc_final: 0.7713 (mp0) REVERT: D 448 VAL cc_start: 0.9341 (t) cc_final: 0.9105 (p) REVERT: E 180 GLN cc_start: 0.8422 (pp30) cc_final: 0.8041 (pp30) REVERT: E 256 PHE cc_start: 0.8833 (m-10) cc_final: 0.8556 (m-10) REVERT: E 312 GLU cc_start: 0.8416 (tp30) cc_final: 0.8050 (mp0) REVERT: E 324 GLU cc_start: 0.8145 (pt0) cc_final: 0.7851 (pt0) REVERT: E 345 CYS cc_start: 0.9240 (m) cc_final: 0.8872 (m) REVERT: E 388 GLU cc_start: 0.9307 (tp30) cc_final: 0.8979 (tt0) REVERT: E 396 MET cc_start: 0.8653 (tpp) cc_final: 0.8446 (tpp) REVERT: E 406 SER cc_start: 0.9079 (m) cc_final: 0.8736 (t) REVERT: E 418 ASP cc_start: 0.7912 (m-30) cc_final: 0.7352 (m-30) REVERT: E 481 TRP cc_start: 0.8850 (t-100) cc_final: 0.8587 (t-100) REVERT: F 148 TYR cc_start: 0.8999 (m-80) cc_final: 0.8752 (m-10) REVERT: F 178 LYS cc_start: 0.9458 (ttpp) cc_final: 0.9159 (ttpp) REVERT: F 180 GLN cc_start: 0.8720 (pm20) cc_final: 0.8142 (pm20) REVERT: F 202 GLN cc_start: 0.8921 (mp10) cc_final: 0.8060 (mp10) REVERT: F 256 PHE cc_start: 0.9385 (m-10) cc_final: 0.8985 (m-10) REVERT: F 314 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7542 (tm-30) REVERT: F 368 GLN cc_start: 0.9197 (tp40) cc_final: 0.8990 (mm-40) REVERT: F 399 MET cc_start: 0.9402 (ptm) cc_final: 0.9035 (ppp) REVERT: F 407 LYS cc_start: 0.8986 (tppt) cc_final: 0.8657 (tppt) outliers start: 83 outliers final: 55 residues processed: 439 average time/residue: 0.2917 time to fit residues: 194.0645 Evaluate side-chains 418 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 358 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 3 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 48 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 50 optimal weight: 7.9990 chunk 171 optimal weight: 40.0000 chunk 101 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 174 optimal weight: 40.0000 chunk 241 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 314 GLN F 422 GLN F 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064829 restraints weight = 55166.503| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.78 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.7313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18552 Z= 0.147 Angle : 0.671 11.805 25176 Z= 0.330 Chirality : 0.048 0.262 2994 Planarity : 0.004 0.048 3360 Dihedral : 4.107 31.443 2754 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.28 % Allowed : 23.93 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2520 helix: 1.52 (0.16), residues: 1108 sheet: -0.46 (0.21), residues: 578 loop : 0.19 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 481 HIS 0.002 0.001 HIS D 470 PHE 0.023 0.002 PHE A 256 TYR 0.010 0.001 TYR C 148 ARG 0.009 0.000 ARG D 491 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 942) hydrogen bonds : angle 4.37837 ( 2748) covalent geometry : bond 0.00349 (18552) covalent geometry : angle 0.67138 (25176) *********************** 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 449 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 373 time to evaluate : 2.214 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: 0.9007 (m-80) cc_final: 0.8623 (m-10) REVERT: A 205 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8510 (mmm-85) REVERT: A 243 PHE cc_start: 0.8443 (p90) cc_final: 0.7991 (p90) REVERT: A 256 PHE cc_start: 0.9173 (m-10) cc_final: 0.8973 (m-10) REVERT: A 347 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8839 (ttp-110) REVERT: B 180 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8864 (tm-30) REVERT: B 256 PHE cc_start: 0.9084 (m-10) cc_final: 0.8820 (m-10) REVERT: B 324 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8172 (mt-10) REVERT: B 339 ARG cc_start: 0.9187 (ttp80) cc_final: 0.8426 (mmm-85) REVERT: B 343 LYS cc_start: 0.9251 (mttp) cc_final: 0.8855 (mttm) REVERT: B 364 PHE cc_start: 0.9213 (t80) cc_final: 0.8858 (t80) REVERT: B 368 GLN cc_start: 0.8341 (mt0) cc_final: 0.7856 (mt0) REVERT: B 378 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8072 (mtp) REVERT: B 399 MET cc_start: 0.8972 (ptp) cc_final: 0.8628 (ptp) REVERT: B 438 GLU cc_start: 0.8177 (mp0) cc_final: 0.7950 (mp0) REVERT: C 180 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8439 (pp30) REVERT: C 244 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9069 (tptp) REVERT: C 343 LYS cc_start: 0.9251 (mttp) cc_final: 0.8994 (mttp) REVERT: C 364 PHE cc_start: 0.8920 (t80) cc_final: 0.8349 (t80) REVERT: C 367 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8816 (mm) REVERT: C 399 MET cc_start: 0.9270 (ptp) cc_final: 0.8941 (ppp) REVERT: C 411 GLU cc_start: 0.9310 (tp30) cc_final: 0.9082 (tp30) REVERT: C 469 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9180 (tptp) REVERT: C 482 ASP cc_start: 0.9427 (OUTLIER) cc_final: 0.9136 (p0) REVERT: D 202 GLN cc_start: 0.8879 (tt0) cc_final: 0.8510 (mm110) REVERT: D 233 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9060 (mm) REVERT: D 323 LEU cc_start: 0.9033 (mt) cc_final: 0.8663 (mp) REVERT: D 359 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.8399 (ttm110) REVERT: D 364 PHE cc_start: 0.8452 (t80) cc_final: 0.8174 (t80) REVERT: D 426 LEU cc_start: 0.8806 (mt) cc_final: 0.8418 (mp) REVERT: D 443 GLU cc_start: 0.8104 (mp0) cc_final: 0.7817 (mp0) REVERT: D 448 VAL cc_start: 0.9315 (t) cc_final: 0.9102 (p) REVERT: E 180 GLN cc_start: 0.8467 (pp30) cc_final: 0.8079 (pp30) REVERT: E 256 PHE cc_start: 0.8888 (m-10) cc_final: 0.8586 (m-10) REVERT: E 312 GLU cc_start: 0.8286 (tp30) cc_final: 0.7887 (mp0) REVERT: E 324 GLU cc_start: 0.8128 (pt0) cc_final: 0.7857 (pt0) REVERT: E 345 CYS cc_start: 0.9278 (m) cc_final: 0.8897 (m) REVERT: E 388 GLU cc_start: 0.9316 (tp30) cc_final: 0.9020 (tp30) REVERT: E 399 MET cc_start: 0.8540 (mtm) cc_final: 0.8336 (ptp) REVERT: E 406 SER cc_start: 0.9042 (m) cc_final: 0.8706 (t) REVERT: E 418 ASP cc_start: 0.7896 (m-30) cc_final: 0.7277 (m-30) REVERT: F 148 TYR cc_start: 0.9019 (m-80) cc_final: 0.8786 (m-10) REVERT: F 178 LYS cc_start: 0.9465 (ttpp) cc_final: 0.9219 (ttpp) REVERT: F 180 GLN cc_start: 0.8663 (pm20) cc_final: 0.8066 (pm20) REVERT: F 202 GLN cc_start: 0.9025 (mp10) cc_final: 0.8195 (mp10) REVERT: F 256 PHE cc_start: 0.9382 (m-10) cc_final: 0.8968 (m-10) REVERT: F 297 PHE cc_start: 0.9232 (m-80) cc_final: 0.8907 (m-10) REVERT: F 399 MET cc_start: 0.9406 (ptm) cc_final: 0.9024 (ppp) REVERT: F 407 LYS cc_start: 0.9047 (tppt) cc_final: 0.8732 (tppt) REVERT: F 412 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8782 (ttm) REVERT: F 422 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8074 (tp-100) outliers start: 76 outliers final: 49 residues processed: 424 average time/residue: 0.3016 time to fit residues: 195.0434 Evaluate side-chains 407 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 350 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.085973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063926 restraints weight = 55157.855| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.77 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18552 Z= 0.176 Angle : 0.677 11.636 25176 Z= 0.338 Chirality : 0.048 0.246 2994 Planarity : 0.005 0.049 3360 Dihedral : 4.121 31.866 2754 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.77 % Allowed : 24.44 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2520 helix: 1.55 (0.16), residues: 1108 sheet: -0.52 (0.21), residues: 582 loop : 0.15 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 481 HIS 0.003 0.001 HIS F 319 PHE 0.020 0.002 PHE D 186 TYR 0.013 0.001 TYR C 148 ARG 0.011 0.001 ARG E 352 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 942) hydrogen bonds : angle 4.42839 ( 2748) covalent geometry : bond 0.00413 (18552) covalent geometry : angle 0.67748 (25176) *********************** 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 409 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 342 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.9118 (m-80) cc_final: 0.8663 (m-10) REVERT: A 202 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 243 PHE cc_start: 0.8548 (p90) cc_final: 0.8087 (p90) REVERT: A 347 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8927 (ttp-110) REVERT: A 348 MET cc_start: 0.9228 (mtm) cc_final: 0.8670 (mtm) REVERT: A 438 GLU cc_start: 0.7679 (pm20) cc_final: 0.7421 (pm20) REVERT: B 180 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8846 (tm-30) REVERT: B 193 MET cc_start: 0.8734 (tpt) cc_final: 0.8023 (tmm) REVERT: B 256 PHE cc_start: 0.9103 (m-10) cc_final: 0.8826 (m-10) REVERT: B 324 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 339 ARG cc_start: 0.9201 (ttp80) cc_final: 0.8454 (mmm-85) REVERT: B 343 LYS cc_start: 0.9257 (mttp) cc_final: 0.8887 (mttm) REVERT: B 364 PHE cc_start: 0.9261 (t80) cc_final: 0.8988 (t80) REVERT: B 368 GLN cc_start: 0.8395 (mt0) cc_final: 0.7991 (mt0) REVERT: B 399 MET cc_start: 0.8949 (ptp) cc_final: 0.8709 (ptp) REVERT: C 180 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8417 (pp30) REVERT: C 244 LYS cc_start: 0.9598 (mmmt) cc_final: 0.9118 (tptp) REVERT: C 347 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8331 (ttm110) REVERT: C 364 PHE cc_start: 0.8932 (t80) cc_final: 0.8507 (t80) REVERT: C 410 LYS cc_start: 0.8352 (mttm) cc_final: 0.8103 (mtpt) REVERT: C 469 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9179 (tptp) REVERT: C 482 ASP cc_start: 0.9421 (OUTLIER) cc_final: 0.9112 (p0) REVERT: D 233 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9157 (mm) REVERT: D 323 LEU cc_start: 0.9059 (mt) cc_final: 0.8722 (mp) REVERT: D 426 LEU cc_start: 0.8861 (mt) cc_final: 0.8451 (mp) REVERT: D 438 GLU cc_start: 0.7140 (pt0) cc_final: 0.6833 (pt0) REVERT: D 448 VAL cc_start: 0.9358 (t) cc_final: 0.9123 (p) REVERT: D 450 GLN cc_start: 0.8791 (pt0) cc_final: 0.8540 (pt0) REVERT: E 180 GLN cc_start: 0.8480 (pp30) cc_final: 0.8104 (pp30) REVERT: E 211 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8560 (p) REVERT: E 256 PHE cc_start: 0.8947 (m-10) cc_final: 0.8628 (m-10) REVERT: E 312 GLU cc_start: 0.8516 (tp30) cc_final: 0.8131 (mp0) REVERT: E 324 GLU cc_start: 0.8269 (pt0) cc_final: 0.7950 (pt0) REVERT: E 345 CYS cc_start: 0.9257 (m) cc_final: 0.8958 (m) REVERT: E 359 ARG cc_start: 0.8918 (ttp80) cc_final: 0.8495 (ttp80) REVERT: E 388 GLU cc_start: 0.9317 (tp30) cc_final: 0.8855 (tp30) REVERT: E 406 SER cc_start: 0.9103 (m) cc_final: 0.8788 (t) REVERT: E 418 ASP cc_start: 0.7979 (m-30) cc_final: 0.7567 (m-30) REVERT: E 433 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9324 (mp) REVERT: F 148 TYR cc_start: 0.9090 (m-80) cc_final: 0.8871 (m-10) REVERT: F 178 LYS cc_start: 0.9495 (ttpp) cc_final: 0.9227 (ttpp) REVERT: F 180 GLN cc_start: 0.8681 (pm20) cc_final: 0.8038 (pm20) REVERT: F 202 GLN cc_start: 0.9044 (mp10) cc_final: 0.8256 (mp10) REVERT: F 256 PHE cc_start: 0.9381 (m-10) cc_final: 0.8931 (m-10) REVERT: F 297 PHE cc_start: 0.9264 (m-80) cc_final: 0.8955 (m-10) REVERT: F 314 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7920 (tm-30) REVERT: F 399 MET cc_start: 0.9406 (ptm) cc_final: 0.8982 (ppp) REVERT: F 407 LYS cc_start: 0.9037 (tppt) cc_final: 0.8717 (tppt) REVERT: F 422 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8045 (tp-100) outliers start: 67 outliers final: 50 residues processed: 391 average time/residue: 0.3206 time to fit residues: 188.8107 Evaluate side-chains 373 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 315 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 126 optimal weight: 120.0000 chunk 93 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 129 optimal weight: 50.0000 chunk 61 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.063347 restraints weight = 55850.412| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.81 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.8343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18552 Z= 0.184 Angle : 0.704 11.954 25176 Z= 0.350 Chirality : 0.049 0.239 2994 Planarity : 0.005 0.052 3360 Dihedral : 4.158 32.363 2754 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.11 % Allowed : 24.77 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2520 helix: 1.49 (0.16), residues: 1108 sheet: -0.60 (0.22), residues: 562 loop : 0.14 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 481 HIS 0.003 0.001 HIS A 382 PHE 0.025 0.002 PHE D 243 TYR 0.018 0.001 TYR B 402 ARG 0.010 0.001 ARG D 491 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 942) hydrogen bonds : angle 4.46468 ( 2748) covalent geometry : bond 0.00434 (18552) covalent geometry : angle 0.70368 (25176) *********************** 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: 73 poor density : 321 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.9172 (m-80) cc_final: 0.8795 (m-10) REVERT: A 202 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 243 PHE cc_start: 0.8651 (p90) cc_final: 0.8184 (p90) REVERT: A 314 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 347 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8848 (ttp-110) REVERT: A 348 MET cc_start: 0.9272 (mtm) cc_final: 0.8746 (mtm) REVERT: A 438 GLU cc_start: 0.7842 (pm20) cc_final: 0.7607 (pm20) REVERT: A 457 ILE cc_start: 0.8805 (mm) cc_final: 0.8556 (mm) REVERT: B 180 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8801 (tm-30) REVERT: B 191 GLN cc_start: 0.9029 (tt0) cc_final: 0.8760 (pt0) REVERT: B 324 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 338 MET cc_start: 0.9303 (tpp) cc_final: 0.8619 (mmt) REVERT: B 339 ARG cc_start: 0.9207 (ttp80) cc_final: 0.8473 (mmm-85) REVERT: B 343 LYS cc_start: 0.9282 (mttp) cc_final: 0.8907 (mttm) REVERT: B 364 PHE cc_start: 0.9379 (t80) cc_final: 0.9059 (t80) REVERT: B 368 GLN cc_start: 0.8382 (mt0) cc_final: 0.7987 (mt0) REVERT: B 399 MET cc_start: 0.9011 (ptp) cc_final: 0.8796 (ptp) REVERT: C 158 ASP cc_start: 0.9041 (p0) cc_final: 0.8824 (p0) REVERT: C 180 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8380 (pp30) REVERT: C 244 LYS cc_start: 0.9611 (mmmt) cc_final: 0.9019 (tptp) REVERT: C 248 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7952 (pp) REVERT: C 343 LYS cc_start: 0.9366 (mttp) cc_final: 0.8996 (mmtm) REVERT: C 347 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8336 (ttm110) REVERT: C 357 GLU cc_start: 0.7445 (pm20) cc_final: 0.7112 (pm20) REVERT: C 364 PHE cc_start: 0.8969 (t80) cc_final: 0.8639 (t80) REVERT: C 411 GLU cc_start: 0.8698 (mp0) cc_final: 0.8460 (mp0) REVERT: C 482 ASP cc_start: 0.9427 (OUTLIER) cc_final: 0.9109 (p0) REVERT: D 233 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9179 (mm) REVERT: D 323 LEU cc_start: 0.9108 (mt) cc_final: 0.8783 (mp) REVERT: D 343 LYS cc_start: 0.8922 (mttp) cc_final: 0.8414 (mmtm) REVERT: D 364 PHE cc_start: 0.8746 (t80) cc_final: 0.8471 (t80) REVERT: D 426 LEU cc_start: 0.8863 (mt) cc_final: 0.8426 (mp) REVERT: D 438 GLU cc_start: 0.7276 (pt0) cc_final: 0.7046 (pt0) REVERT: D 450 GLN cc_start: 0.8782 (pt0) cc_final: 0.8499 (pt0) REVERT: E 180 GLN cc_start: 0.8592 (pp30) cc_final: 0.8188 (pp30) REVERT: E 211 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8532 (p) REVERT: E 256 PHE cc_start: 0.8997 (m-10) cc_final: 0.8663 (m-10) REVERT: E 312 GLU cc_start: 0.8526 (tp30) cc_final: 0.8137 (mp0) REVERT: E 324 GLU cc_start: 0.8302 (pt0) cc_final: 0.8001 (pt0) REVERT: E 345 CYS cc_start: 0.9243 (m) cc_final: 0.9019 (m) REVERT: E 359 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8582 (ttp80) REVERT: E 388 GLU cc_start: 0.9313 (tp30) cc_final: 0.8782 (tp30) REVERT: E 406 SER cc_start: 0.9170 (m) cc_final: 0.8880 (t) REVERT: E 418 ASP cc_start: 0.8020 (m-30) cc_final: 0.7284 (m-30) REVERT: F 178 LYS cc_start: 0.9489 (ttpp) cc_final: 0.9224 (ttpp) REVERT: F 180 GLN cc_start: 0.8686 (pm20) cc_final: 0.8003 (pm20) REVERT: F 202 GLN cc_start: 0.9068 (mp10) cc_final: 0.8352 (mp10) REVERT: F 256 PHE cc_start: 0.9417 (m-10) cc_final: 0.8968 (m-10) REVERT: F 399 MET cc_start: 0.9420 (ptm) cc_final: 0.8946 (ppp) REVERT: F 407 LYS cc_start: 0.9065 (tppt) cc_final: 0.8746 (tppt) REVERT: F 422 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7662 (tt0) outliers start: 73 outliers final: 53 residues processed: 374 average time/residue: 0.2988 time to fit residues: 169.1622 Evaluate side-chains 364 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 303 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 114 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 65 optimal weight: 0.0370 chunk 183 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 237 optimal weight: 0.2980 chunk 128 optimal weight: 50.0000 chunk 115 optimal weight: 6.9990 overall best weight: 4.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN ** F 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.086344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064766 restraints weight = 54444.712| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.66 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18552 Z= 0.148 Angle : 0.699 11.930 25176 Z= 0.344 Chirality : 0.048 0.259 2994 Planarity : 0.005 0.049 3360 Dihedral : 4.123 32.621 2754 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.55 % Allowed : 25.51 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2520 helix: 1.49 (0.16), residues: 1112 sheet: -0.53 (0.22), residues: 558 loop : 0.08 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 481 HIS 0.003 0.001 HIS D 470 PHE 0.025 0.002 PHE F 364 TYR 0.017 0.001 TYR E 148 ARG 0.010 0.000 ARG D 491 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 942) hydrogen bonds : angle 4.43233 ( 2748) covalent geometry : bond 0.00357 (18552) covalent geometry : angle 0.69922 (25176) ********************** 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 392 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 329 time to evaluate : 2.236 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: 0.9203 (m-80) cc_final: 0.8843 (m-10) REVERT: A 197 GLN cc_start: 0.9043 (tp40) cc_final: 0.8669 (tp40) REVERT: A 202 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8722 (tm-30) REVERT: A 215 ASP cc_start: 0.8787 (t0) cc_final: 0.8423 (t0) REVERT: A 243 PHE cc_start: 0.8645 (p90) cc_final: 0.8195 (p90) REVERT: A 314 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 343 LYS cc_start: 0.9507 (ttmt) cc_final: 0.9150 (ttmm) REVERT: A 348 MET cc_start: 0.9242 (mtm) cc_final: 0.8763 (mtm) REVERT: A 411 GLU cc_start: 0.9108 (tt0) cc_final: 0.8907 (tp30) REVERT: A 438 GLU cc_start: 0.7860 (pm20) cc_final: 0.7512 (pm20) REVERT: A 457 ILE cc_start: 0.8837 (mm) cc_final: 0.8592 (mm) REVERT: B 180 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8814 (tm-30) REVERT: B 191 GLN cc_start: 0.9086 (tt0) cc_final: 0.8824 (pt0) REVERT: B 256 PHE cc_start: 0.8915 (m-10) cc_final: 0.8639 (m-10) REVERT: B 312 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 324 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 338 MET cc_start: 0.9286 (tpp) cc_final: 0.8621 (mmt) REVERT: B 339 ARG cc_start: 0.9203 (ttp80) cc_final: 0.8464 (mmm-85) REVERT: B 343 LYS cc_start: 0.9293 (mttp) cc_final: 0.8937 (mttp) REVERT: B 364 PHE cc_start: 0.9385 (t80) cc_final: 0.9045 (t80) REVERT: B 368 GLN cc_start: 0.8372 (mt0) cc_final: 0.8025 (mt0) REVERT: B 394 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8466 (mt-10) REVERT: B 399 MET cc_start: 0.9077 (ptp) cc_final: 0.8661 (ptp) REVERT: C 158 ASP cc_start: 0.9042 (p0) cc_final: 0.8788 (p0) REVERT: C 180 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: C 244 LYS cc_start: 0.9576 (mmmt) cc_final: 0.9061 (tptp) REVERT: C 343 LYS cc_start: 0.9358 (mttp) cc_final: 0.9028 (mmtp) REVERT: C 347 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8392 (ttm110) REVERT: C 364 PHE cc_start: 0.8854 (t80) cc_final: 0.8555 (t80) REVERT: C 411 GLU cc_start: 0.8633 (mp0) cc_final: 0.8405 (mp0) REVERT: C 482 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.9103 (p0) REVERT: D 233 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9172 (mm) REVERT: D 343 LYS cc_start: 0.8929 (mttp) cc_final: 0.8451 (mmtm) REVERT: D 359 ARG cc_start: 0.9049 (ttm-80) cc_final: 0.8710 (ttm110) REVERT: D 364 PHE cc_start: 0.8670 (t80) cc_final: 0.8391 (t80) REVERT: D 426 LEU cc_start: 0.8863 (mt) cc_final: 0.8426 (mp) REVERT: D 438 GLU cc_start: 0.7262 (pt0) cc_final: 0.7029 (pt0) REVERT: D 450 GLN cc_start: 0.8828 (pt0) cc_final: 0.8570 (pt0) REVERT: E 180 GLN cc_start: 0.8625 (pp30) cc_final: 0.8248 (pp30) REVERT: E 312 GLU cc_start: 0.8484 (tp30) cc_final: 0.8099 (mp0) REVERT: E 324 GLU cc_start: 0.8301 (pt0) cc_final: 0.8001 (pt0) REVERT: E 343 LYS cc_start: 0.9408 (ttmm) cc_final: 0.8940 (ttmm) REVERT: E 345 CYS cc_start: 0.9240 (m) cc_final: 0.8969 (m) REVERT: E 359 ARG cc_start: 0.8953 (ttp80) cc_final: 0.8602 (ttp80) REVERT: E 388 GLU cc_start: 0.9307 (tp30) cc_final: 0.8729 (tp30) REVERT: E 406 SER cc_start: 0.9162 (m) cc_final: 0.8887 (t) REVERT: E 418 ASP cc_start: 0.7957 (m-30) cc_final: 0.7188 (m-30) REVERT: F 178 LYS cc_start: 0.9474 (ttpp) cc_final: 0.9111 (tmmt) REVERT: F 180 GLN cc_start: 0.8652 (pm20) cc_final: 0.7479 (pm20) REVERT: F 191 GLN cc_start: 0.9209 (tp40) cc_final: 0.8725 (tm-30) REVERT: F 243 PHE cc_start: 0.8807 (t80) cc_final: 0.8517 (t80) REVERT: F 256 PHE cc_start: 0.9403 (m-10) cc_final: 0.8954 (m-10) REVERT: F 297 PHE cc_start: 0.9149 (m-10) cc_final: 0.8809 (m-10) REVERT: F 399 MET cc_start: 0.9438 (ptm) cc_final: 0.9204 (ppp) REVERT: F 407 LYS cc_start: 0.9081 (tppt) cc_final: 0.8760 (tppt) outliers start: 63 outliers final: 53 residues processed: 376 average time/residue: 0.3073 time to fit residues: 173.5698 Evaluate side-chains 362 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 305 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 180 optimal weight: 9.9990 chunk 226 optimal weight: 30.0000 chunk 243 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 6 optimal weight: 50.0000 chunk 146 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN F 202 GLN ** F 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.086064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.064546 restraints weight = 54397.470| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.63 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.8851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18552 Z= 0.159 Angle : 0.720 11.962 25176 Z= 0.352 Chirality : 0.049 0.269 2994 Planarity : 0.005 0.049 3360 Dihedral : 4.174 32.433 2754 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.49 % Allowed : 25.45 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2520 helix: 1.46 (0.16), residues: 1114 sheet: -0.52 (0.22), residues: 548 loop : 0.07 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 481 HIS 0.002 0.001 HIS D 470 PHE 0.026 0.002 PHE D 243 TYR 0.010 0.001 TYR E 148 ARG 0.010 0.000 ARG D 491 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 942) hydrogen bonds : angle 4.45026 ( 2748) covalent geometry : bond 0.00381 (18552) covalent geometry : angle 0.71984 (25176) =============================================================================== Job complete usr+sys time: 8864.13 seconds wall clock time: 156 minutes 49.27 seconds (9409.27 seconds total)