Starting phenix.real_space_refine on Thu Mar 5 07:21:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzh_22531/03_2026/7jzh_22531.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzh_22531/03_2026/7jzh_22531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jzh_22531/03_2026/7jzh_22531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzh_22531/03_2026/7jzh_22531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzh_22531/03_2026/7jzh_22531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzh_22531/03_2026/7jzh_22531.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.166 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 138 5.16 5 C 12948 2.51 5 N 3456 2.21 5 O 3786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20328 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3388 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.31, per 1000 atoms: 0.21 Number of scatterers: 20328 At special positions: 0 Unit cell: (138.24, 139.32, 93.96, 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 138 16.00 O 3786 8.00 N 3456 7.00 C 12948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 872.6 milliseconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 12 sheets defined 47.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.803A pdb=" N GLU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 90 through 108 removed outlier: 4.027A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 149 Processing helix chain 'A' and resid 163 through 173 removed outlier: 3.590A pdb=" N HIS A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 169 " --> pdb=" O CYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.874A pdb=" N ILE A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 4.334A pdb=" N LEU A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 removed outlier: 3.515A pdb=" N PHE A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 322 through 359 removed outlier: 3.507A pdb=" N ALA A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLU A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.785A pdb=" N LEU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 451 Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 38 through 54 removed outlier: 3.775A pdb=" N GLU B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 90 through 108 removed outlier: 4.094A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 149 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.940A pdb=" N ILE B 195 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.698A pdb=" N ASP B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 322 through 361 removed outlier: 7.546A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.782A pdb=" N LEU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 451 Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 38 through 54 removed outlier: 3.885A pdb=" N GLU C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 90 through 108 removed outlier: 4.044A pdb=" N ALA C 94 " --> pdb=" O TYR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 149 removed outlier: 3.660A pdb=" N ALA C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 190 through 197 removed outlier: 4.032A pdb=" N ILE C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 234 removed outlier: 4.337A pdb=" N LEU C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 249 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 322 through 334 Processing helix chain 'C' and resid 334 through 361 Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.591A pdb=" N LEU C 395 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C 397 " --> pdb=" O TYR C 393 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 451 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 38 through 54 removed outlier: 3.905A pdb=" N GLU D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 90 through 108 removed outlier: 4.024A pdb=" N ALA D 94 " --> pdb=" O TYR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 149 removed outlier: 3.636A pdb=" N ALA D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 190 through 197 removed outlier: 3.991A pdb=" N ILE D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 234 removed outlier: 4.338A pdb=" N LEU D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA D 226 " --> pdb=" O PRO D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 249 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 322 through 359 removed outlier: 7.336A pdb=" N ARG D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLU D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 401 removed outlier: 4.012A pdb=" N GLU D 397 " --> pdb=" O TYR D 393 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 451 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.978A pdb=" N GLU E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 69 through 80 Processing helix chain 'E' and resid 90 through 108 removed outlier: 4.034A pdb=" N ALA E 94 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 149 Processing helix chain 'E' and resid 163 through 173 removed outlier: 3.655A pdb=" N HIS E 167 " --> pdb=" O GLN E 163 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE E 169 " --> pdb=" O CYS E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 removed outlier: 3.910A pdb=" N ILE E 195 " --> pdb=" O PRO E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 234 removed outlier: 3.539A pdb=" N ASP E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA E 226 " --> pdb=" O PRO E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 249 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 322 through 334 Processing helix chain 'E' and resid 334 through 361 removed outlier: 3.637A pdb=" N GLY E 361 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 401 removed outlier: 3.899A pdb=" N GLU E 397 " --> pdb=" O TYR E 393 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 398 " --> pdb=" O ASP E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 451 Processing helix chain 'F' and resid 6 through 14 Processing helix chain 'F' and resid 38 through 54 removed outlier: 4.210A pdb=" N GLU F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 69 through 79 Processing helix chain 'F' and resid 90 through 108 removed outlier: 4.044A pdb=" N ALA F 94 " --> pdb=" O TYR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 149 Processing helix chain 'F' and resid 163 through 173 removed outlier: 4.108A pdb=" N PHE F 169 " --> pdb=" O CYS F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 removed outlier: 3.996A pdb=" N ILE F 195 " --> pdb=" O PRO F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.569A pdb=" N ASP F 225 " --> pdb=" O GLN F 221 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 249 removed outlier: 3.517A pdb=" N PHE F 249 " --> pdb=" O SER F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 246 through 249' Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 322 through 334 Processing helix chain 'F' and resid 334 through 361 removed outlier: 3.752A pdb=" N GLY F 361 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 401 removed outlier: 3.607A pdb=" N LEU F 395 " --> pdb=" O THR F 391 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU F 397 " --> pdb=" O TYR F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 123 removed outlier: 6.557A pdb=" N MET A 240 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 269 " --> pdb=" O MET A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 367 removed outlier: 5.283A pdb=" N PHE A 365 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS A 381 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 382 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 419 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 123 removed outlier: 6.513A pdb=" N MET B 240 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 269 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 363 through 367 removed outlier: 5.329A pdb=" N PHE B 365 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS B 381 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 382 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 419 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 120 through 123 removed outlier: 7.021A pdb=" N MET C 240 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N SER C 271 " --> pdb=" O MET C 240 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 242 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N SER C 273 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 363 through 367 removed outlier: 5.117A pdb=" N PHE C 365 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS C 381 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 382 " --> pdb=" O VAL C 419 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 419 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 120 through 123 removed outlier: 6.993A pdb=" N MET D 240 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N SER D 271 " --> pdb=" O MET D 240 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE D 242 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N SER D 273 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 363 through 367 removed outlier: 5.104A pdb=" N PHE D 365 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS D 381 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 382 " --> pdb=" O VAL D 419 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 419 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 120 through 123 removed outlier: 7.036A pdb=" N MET E 240 " --> pdb=" O SER E 269 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N SER E 271 " --> pdb=" O MET E 240 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE E 242 " --> pdb=" O SER E 271 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N SER E 273 " --> pdb=" O ILE E 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 363 through 367 removed outlier: 5.370A pdb=" N PHE E 365 " --> pdb=" O LYS E 381 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS E 381 " --> pdb=" O PHE E 365 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 382 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL E 419 " --> pdb=" O LEU E 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 120 through 123 removed outlier: 7.045A pdb=" N MET F 240 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N SER F 271 " --> pdb=" O MET F 240 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 242 " --> pdb=" O SER F 271 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N SER F 273 " --> pdb=" O ILE F 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 363 through 367 removed outlier: 5.351A pdb=" N PHE F 365 " --> pdb=" O LYS F 381 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS F 381 " --> pdb=" O PHE F 365 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU F 382 " --> pdb=" O VAL F 419 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 419 " --> pdb=" O LEU F 382 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2583 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5951 1.33 - 1.45: 3680 1.45 - 1.58: 10979 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 20826 Sorted by residual: bond pdb=" CA ASP B 261 " pdb=" C ASP B 261 " ideal model delta sigma weight residual 1.523 1.560 -0.037 1.34e-02 5.57e+03 7.50e+00 bond pdb=" CA TRP D 260 " pdb=" CB TRP D 260 " ideal model delta sigma weight residual 1.536 1.498 0.039 1.46e-02 4.69e+03 7.01e+00 bond pdb=" N LYS F 276 " pdb=" CA LYS F 276 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.54e+00 bond pdb=" CA TRP C 260 " pdb=" CB TRP C 260 " ideal model delta sigma weight residual 1.536 1.497 0.039 1.58e-02 4.01e+03 6.08e+00 bond pdb=" CG1 ILE B 258 " pdb=" CD1 ILE B 258 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.31e+00 ... (remaining 20821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 27561 2.69 - 5.38: 594 5.38 - 8.06: 40 8.06 - 10.75: 19 10.75 - 13.44: 4 Bond angle restraints: 28218 Sorted by residual: angle pdb=" N VAL D 259 " pdb=" CA VAL D 259 " pdb=" C VAL D 259 " ideal model delta sigma weight residual 107.73 121.17 -13.44 1.56e+00 4.11e-01 7.42e+01 angle pdb=" N VAL C 259 " pdb=" CA VAL C 259 " pdb=" C VAL C 259 " ideal model delta sigma weight residual 106.85 118.27 -11.42 1.42e+00 4.96e-01 6.47e+01 angle pdb=" N GLY F 215 " pdb=" CA GLY F 215 " pdb=" C GLY F 215 " ideal model delta sigma weight residual 112.77 122.95 -10.18 1.28e+00 6.10e-01 6.32e+01 angle pdb=" C LEU A 295 " pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta sigma weight residual 120.21 127.77 -7.56 9.60e-01 1.09e+00 6.21e+01 angle pdb=" N GLY B 215 " pdb=" CA GLY B 215 " pdb=" C GLY B 215 " ideal model delta sigma weight residual 112.77 122.79 -10.02 1.28e+00 6.10e-01 6.12e+01 ... (remaining 28213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 10156 18.10 - 36.21: 1527 36.21 - 54.31: 519 54.31 - 72.42: 144 72.42 - 90.52: 50 Dihedral angle restraints: 12396 sinusoidal: 5022 harmonic: 7374 Sorted by residual: dihedral pdb=" CA GLU D 218 " pdb=" C GLU D 218 " pdb=" N PHE D 219 " pdb=" CA PHE D 219 " ideal model delta harmonic sigma weight residual -180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" C TYR D 213 " pdb=" N TYR D 213 " pdb=" CA TYR D 213 " pdb=" CB TYR D 213 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" N TYR D 213 " pdb=" C TYR D 213 " pdb=" CA TYR D 213 " pdb=" CB TYR D 213 " ideal model delta harmonic sigma weight residual 122.80 135.80 -13.00 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 12393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2882 0.119 - 0.238: 91 0.238 - 0.357: 5 0.357 - 0.476: 0 0.476 - 0.596: 4 Chirality restraints: 2982 Sorted by residual: chirality pdb=" CA TYR D 213 " pdb=" N TYR D 213 " pdb=" C TYR D 213 " pdb=" CB TYR D 213 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CA TYR B 213 " pdb=" N TYR B 213 " pdb=" C TYR B 213 " pdb=" CB TYR B 213 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.79e+00 chirality pdb=" CA TYR C 213 " pdb=" N TYR C 213 " pdb=" C TYR C 213 " pdb=" CB TYR C 213 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 2979 not shown) Planarity restraints: 3690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 141 " 0.028 2.00e-02 2.50e+03 5.44e-02 2.95e+01 pdb=" C TRP C 141 " -0.094 2.00e-02 2.50e+03 pdb=" O TRP C 141 " 0.035 2.00e-02 2.50e+03 pdb=" N ARG C 142 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 210 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C GLY B 210 " -0.061 2.00e-02 2.50e+03 pdb=" O GLY B 210 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL B 211 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 219 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO C 220 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 220 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 220 " 0.037 5.00e-02 4.00e+02 ... (remaining 3687 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 450 2.66 - 3.22: 19435 3.22 - 3.78: 30811 3.78 - 4.34: 40596 4.34 - 4.90: 66344 Nonbonded interactions: 157636 Sorted by model distance: nonbonded pdb=" N GLU B 89 " pdb=" OE1 GLU B 89 " model vdw 2.095 3.120 nonbonded pdb=" OD1 ASP E 86 " pdb=" N LYS E 87 " model vdw 2.162 3.120 nonbonded pdb=" OD1 ASP A 86 " pdb=" N LYS A 87 " model vdw 2.175 3.120 nonbonded pdb=" N GLN B 297 " pdb=" OE1 GLN B 297 " model vdw 2.179 3.120 nonbonded pdb=" O GLN E 163 " pdb=" ND1 HIS E 167 " model vdw 2.202 3.120 ... (remaining 157631 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: 0.01 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.006 0.081 20826 Z= 0.301 Angle : 0.956 13.438 28218 Z= 0.565 Chirality : 0.056 0.596 2982 Planarity : 0.006 0.066 3690 Dihedral : 20.562 90.525 7656 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.67 % Favored : 91.29 % Rotamer: Outliers : 16.34 % Allowed : 33.24 % Favored : 50.42 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.14), residues: 2526 helix: -2.06 (0.13), residues: 1110 sheet: -1.10 (0.33), residues: 240 loop : -2.71 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 17 TYR 0.012 0.002 TYR B 328 PHE 0.028 0.002 PHE E 230 TRP 0.033 0.003 TRP F 67 HIS 0.011 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00649 (20826) covalent geometry : angle 0.95581 (28218) hydrogen bonds : bond 0.16089 ( 888) hydrogen bonds : angle 7.16055 ( 2583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 348 poor density : 483 time to evaluate : 0.669 Fit side-chains REVERT: A 45 ILE cc_start: 0.8944 (mt) cc_final: 0.8671 (mt) REVERT: A 49 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: A 81 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7791 (m110) REVERT: A 145 MET cc_start: 0.6634 (tpp) cc_final: 0.6045 (mmt) REVERT: A 150 LYS cc_start: 0.8980 (mppt) cc_final: 0.8302 (ttpt) REVERT: A 297 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7149 (mm-40) REVERT: A 336 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7698 (ttm170) REVERT: A 398 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7836 (mmp-170) REVERT: B 37 MET cc_start: 0.7883 (ptp) cc_final: 0.7472 (ptp) REVERT: B 44 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7399 (mm-40) REVERT: B 45 ILE cc_start: 0.8909 (mt) cc_final: 0.8638 (mt) REVERT: B 49 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: B 84 TRP cc_start: 0.6859 (p-90) cc_final: 0.6555 (p-90) REVERT: B 139 TRP cc_start: 0.6420 (t-100) cc_final: 0.6155 (t-100) REVERT: B 157 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6908 (tp) REVERT: B 201 ASN cc_start: 0.5604 (OUTLIER) cc_final: 0.5402 (t0) REVERT: B 218 GLU cc_start: 0.6184 (tt0) cc_final: 0.5913 (mt-10) REVERT: B 336 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: B 346 SER cc_start: 0.8684 (t) cc_final: 0.8461 (m) REVERT: C 10 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.4455 (ptp-170) REVERT: C 57 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.7758 (tpt-90) REVERT: C 63 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: C 84 TRP cc_start: 0.6372 (p-90) cc_final: 0.5838 (p-90) REVERT: C 109 HIS cc_start: 0.6488 (m-70) cc_final: 0.6223 (m170) REVERT: C 131 MET cc_start: 0.4014 (OUTLIER) cc_final: 0.3562 (ttt) REVERT: C 154 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6148 (ptmm) REVERT: C 176 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5706 (tt0) REVERT: C 218 GLU cc_start: 0.6344 (tt0) cc_final: 0.5679 (mt-10) REVERT: C 236 ILE cc_start: 0.5351 (OUTLIER) cc_final: 0.4754 (mm) REVERT: C 291 ASP cc_start: 0.7504 (p0) cc_final: 0.7269 (p0) REVERT: C 402 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.6964 (mmt180) REVERT: D 28 GLU cc_start: 0.7218 (tp30) cc_final: 0.6874 (tp30) REVERT: D 34 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 57 ARG cc_start: 0.8485 (tpt-90) cc_final: 0.7377 (tpt-90) REVERT: D 63 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: D 82 LYS cc_start: 0.7768 (pttm) cc_final: 0.7385 (mtmm) REVERT: D 84 TRP cc_start: 0.6215 (p-90) cc_final: 0.5587 (p-90) REVERT: D 109 HIS cc_start: 0.6459 (m-70) cc_final: 0.6226 (m170) REVERT: D 154 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5819 (ptmm) REVERT: D 171 ARG cc_start: 0.4100 (OUTLIER) cc_final: 0.3838 (tpt-90) REVERT: D 236 ILE cc_start: 0.5508 (OUTLIER) cc_final: 0.5142 (mm) REVERT: D 336 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7530 (mmm-85) REVERT: D 459 GLN cc_start: 0.2921 (OUTLIER) cc_final: 0.1456 (pp30) REVERT: E 15 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7850 (t70) REVERT: E 28 GLU cc_start: 0.7418 (tp30) cc_final: 0.7195 (tp30) REVERT: E 44 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7778 (mm-40) REVERT: E 115 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8380 (p0) REVERT: E 124 ILE cc_start: 0.7483 (mm) cc_final: 0.7108 (pt) REVERT: E 141 TRP cc_start: 0.5747 (OUTLIER) cc_final: 0.4801 (t-100) REVERT: E 150 LYS cc_start: 0.9092 (mppt) cc_final: 0.8373 (tttt) REVERT: E 192 LYS cc_start: -0.1269 (OUTLIER) cc_final: -0.1785 (tptt) REVERT: E 373 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7287 (tm-30) REVERT: E 430 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: E 441 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: F 31 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7478 (mtm-85) REVERT: F 44 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7802 (mm-40) REVERT: F 117 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: F 124 ILE cc_start: 0.7552 (mp) cc_final: 0.7249 (pt) REVERT: F 141 TRP cc_start: 0.5587 (OUTLIER) cc_final: 0.4164 (t-100) REVERT: F 150 LYS cc_start: 0.9076 (mppt) cc_final: 0.8192 (tttt) REVERT: F 381 LYS cc_start: 0.7796 (pttt) cc_final: 0.7345 (pttt) REVERT: F 436 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7264 (mm) REVERT: F 441 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7126 (m-80) outliers start: 348 outliers final: 187 residues processed: 762 average time/residue: 0.1440 time to fit residues: 167.3121 Evaluate side-chains 668 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 448 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 459 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 31 ARG Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 117 GLN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 436 LEU Chi-restraints excluded: chain F residue 441 TYR Chi-restraints excluded: chain F residue 448 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 40.0000 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN C 73 HIS C 117 GLN C 201 ASN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 73 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN F 344 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.204167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.166097 restraints weight = 26110.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.170352 restraints weight = 16572.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.173193 restraints weight = 12619.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.175023 restraints weight = 10666.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.176270 restraints weight = 9586.544| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20826 Z= 0.143 Angle : 0.691 9.466 28218 Z= 0.345 Chirality : 0.045 0.284 2982 Planarity : 0.005 0.064 3690 Dihedral : 11.811 98.593 3162 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 9.34 % Allowed : 31.31 % Favored : 59.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2526 helix: -0.44 (0.15), residues: 1146 sheet: -0.84 (0.33), residues: 246 loop : -2.05 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 398 TYR 0.011 0.001 TYR D 447 PHE 0.035 0.002 PHE B 230 TRP 0.016 0.001 TRP A 84 HIS 0.007 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00328 (20826) covalent geometry : angle 0.69137 (28218) hydrogen bonds : bond 0.04755 ( 888) hydrogen bonds : angle 5.40511 ( 2583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 444 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7492 (mm-40) REVERT: A 45 ILE cc_start: 0.8912 (mt) cc_final: 0.8711 (mt) REVERT: A 49 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: A 84 TRP cc_start: 0.6452 (p-90) cc_final: 0.6201 (p-90) REVERT: A 139 TRP cc_start: 0.5917 (OUTLIER) cc_final: 0.5103 (m100) REVERT: A 150 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8234 (tttt) REVERT: B 37 MET cc_start: 0.7856 (ptp) cc_final: 0.7508 (ptp) REVERT: B 45 ILE cc_start: 0.8905 (mt) cc_final: 0.7712 (mt) REVERT: B 49 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: B 139 TRP cc_start: 0.6403 (t-100) cc_final: 0.6031 (t-100) REVERT: B 333 ARG cc_start: 0.8308 (tmt-80) cc_final: 0.7801 (tmt-80) REVERT: B 359 LYS cc_start: 0.7104 (pttt) cc_final: 0.6807 (ptmm) REVERT: B 400 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7368 (ttm-80) REVERT: C 57 ARG cc_start: 0.8382 (tpt-90) cc_final: 0.7769 (tpt-90) REVERT: C 76 MET cc_start: 0.8290 (tmm) cc_final: 0.7776 (tmm) REVERT: C 78 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8674 (mm) REVERT: C 84 TRP cc_start: 0.6196 (p-90) cc_final: 0.5965 (p-90) REVERT: C 176 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5688 (tt0) REVERT: C 402 ARG cc_start: 0.7101 (mmm-85) cc_final: 0.6779 (mmt180) REVERT: D 31 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7831 (ttm-80) REVERT: D 48 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: D 84 TRP cc_start: 0.5995 (p-90) cc_final: 0.5665 (p-90) REVERT: D 145 MET cc_start: 0.5697 (mmt) cc_final: 0.5449 (mmm) REVERT: E 115 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8162 (p0) REVERT: E 131 MET cc_start: 0.5013 (ttp) cc_final: 0.4793 (ttt) REVERT: E 137 MET cc_start: 0.7349 (mmm) cc_final: 0.6874 (mmt) REVERT: E 141 TRP cc_start: 0.5940 (OUTLIER) cc_final: 0.3996 (t-100) REVERT: E 145 MET cc_start: 0.6726 (mmm) cc_final: 0.5914 (mmt) REVERT: E 150 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8247 (tttt) REVERT: E 324 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7793 (m) REVERT: E 381 LYS cc_start: 0.7849 (ptpt) cc_final: 0.7632 (ptpt) REVERT: E 441 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: F 137 MET cc_start: 0.7488 (mmm) cc_final: 0.6732 (mmt) REVERT: F 141 TRP cc_start: 0.5811 (OUTLIER) cc_final: 0.4140 (t-100) REVERT: F 145 MET cc_start: 0.6662 (mmm) cc_final: 0.5664 (mmt) REVERT: F 150 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8162 (tttt) REVERT: F 333 ARG cc_start: 0.8305 (tmt-80) cc_final: 0.7903 (tmt-80) REVERT: F 441 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7434 (m-80) outliers start: 199 outliers final: 105 residues processed: 597 average time/residue: 0.1494 time to fit residues: 135.6793 Evaluate side-chains 531 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 409 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 122 optimal weight: 20.0000 chunk 2 optimal weight: 0.0470 chunk 68 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 57 optimal weight: 40.0000 chunk 245 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 59 ASN B 71 ASN C 73 HIS D 73 HIS D 297 GLN E 73 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 ASN F 344 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.201050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.164562 restraints weight = 25987.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.168685 restraints weight = 16474.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.171401 restraints weight = 12500.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.173178 restraints weight = 10531.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.174305 restraints weight = 9444.520| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20826 Z= 0.178 Angle : 0.694 10.775 28218 Z= 0.339 Chirality : 0.045 0.234 2982 Planarity : 0.005 0.054 3690 Dihedral : 9.716 92.648 2929 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 9.01 % Allowed : 31.13 % Favored : 59.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.16), residues: 2526 helix: 0.05 (0.15), residues: 1158 sheet: -0.75 (0.35), residues: 240 loop : -1.84 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 398 TYR 0.019 0.001 TYR D 363 PHE 0.032 0.002 PHE B 230 TRP 0.019 0.002 TRP B 84 HIS 0.005 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00426 (20826) covalent geometry : angle 0.69368 (28218) hydrogen bonds : bond 0.05099 ( 888) hydrogen bonds : angle 5.27033 ( 2583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 420 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.7895 (ptp) cc_final: 0.7315 (ptp) REVERT: A 44 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7574 (mm-40) REVERT: A 45 ILE cc_start: 0.8971 (mt) cc_final: 0.7870 (mt) REVERT: A 49 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: A 75 LEU cc_start: 0.8740 (tp) cc_final: 0.8511 (tp) REVERT: A 84 TRP cc_start: 0.6451 (p-90) cc_final: 0.6132 (p-90) REVERT: A 132 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7191 (tt) REVERT: A 137 MET cc_start: 0.7132 (mmp) cc_final: 0.6710 (mmm) REVERT: A 150 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8140 (ttmt) REVERT: A 192 LYS cc_start: -0.0323 (OUTLIER) cc_final: -0.1587 (tptt) REVERT: B 37 MET cc_start: 0.7882 (ptp) cc_final: 0.7378 (ptp) REVERT: B 45 ILE cc_start: 0.8951 (mt) cc_final: 0.7930 (mt) REVERT: B 49 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: B 137 MET cc_start: 0.7220 (mmp) cc_final: 0.6788 (mmm) REVERT: B 139 TRP cc_start: 0.6414 (t-100) cc_final: 0.6091 (t-100) REVERT: B 201 ASN cc_start: 0.5846 (OUTLIER) cc_final: 0.5597 (t0) REVERT: B 216 ASN cc_start: 0.6737 (p0) cc_final: 0.6445 (p0) REVERT: B 333 ARG cc_start: 0.8371 (tmt-80) cc_final: 0.7834 (tmt-80) REVERT: B 359 LYS cc_start: 0.7167 (pttt) cc_final: 0.6773 (ptmm) REVERT: B 421 MET cc_start: 0.8648 (ttp) cc_final: 0.8445 (ttp) REVERT: C 57 ARG cc_start: 0.8409 (tpt-90) cc_final: 0.7848 (tpt-90) REVERT: C 76 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7817 (tmm) REVERT: C 78 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8593 (mm) REVERT: C 84 TRP cc_start: 0.6280 (p-90) cc_final: 0.5973 (p-90) REVERT: C 137 MET cc_start: 0.6953 (mpp) cc_final: 0.6376 (mpp) REVERT: C 139 TRP cc_start: 0.6146 (OUTLIER) cc_final: 0.5349 (m100) REVERT: C 176 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5657 (tt0) REVERT: C 402 ARG cc_start: 0.7082 (mmm-85) cc_final: 0.6783 (mmt180) REVERT: D 84 TRP cc_start: 0.5985 (p-90) cc_final: 0.5568 (p-90) REVERT: D 145 MET cc_start: 0.5565 (mmt) cc_final: 0.5309 (mmm) REVERT: E 31 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7671 (mtp85) REVERT: E 76 MET cc_start: 0.8261 (tmt) cc_final: 0.7895 (tmm) REVERT: E 135 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6246 (mtt) REVERT: E 141 TRP cc_start: 0.6031 (OUTLIER) cc_final: 0.4014 (t-100) REVERT: E 145 MET cc_start: 0.6695 (mmm) cc_final: 0.5810 (mmt) REVERT: E 150 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8159 (ttmt) REVERT: E 381 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7671 (ptpt) REVERT: E 426 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7716 (ptt90) REVERT: E 441 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: F 30 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8155 (mmmm) REVERT: F 137 MET cc_start: 0.7552 (mmm) cc_final: 0.7087 (mmp) REVERT: F 141 TRP cc_start: 0.6067 (OUTLIER) cc_final: 0.4399 (t-100) REVERT: F 145 MET cc_start: 0.6740 (mmm) cc_final: 0.5837 (mmt) REVERT: F 150 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8141 (ttmt) REVERT: F 333 ARG cc_start: 0.8332 (tmt-80) cc_final: 0.7916 (tmt-80) REVERT: F 381 LYS cc_start: 0.7885 (pttt) cc_final: 0.7028 (pttt) REVERT: F 441 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7487 (m-80) outliers start: 192 outliers final: 113 residues processed: 562 average time/residue: 0.1520 time to fit residues: 129.7004 Evaluate side-chains 532 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 401 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 426 ARG Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 23 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 201 optimal weight: 0.0970 chunk 152 optimal weight: 0.4980 chunk 139 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 55 optimal weight: 30.0000 chunk 151 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 overall best weight: 3.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN C 59 ASN C 73 HIS C 201 ASN E 73 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN F 405 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.201827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.165864 restraints weight = 25779.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.170035 restraints weight = 16237.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.172765 restraints weight = 12250.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.174414 restraints weight = 10277.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.175715 restraints weight = 9211.205| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20826 Z= 0.139 Angle : 0.651 11.541 28218 Z= 0.314 Chirality : 0.042 0.246 2982 Planarity : 0.004 0.040 3690 Dihedral : 9.098 92.915 2901 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 8.50 % Allowed : 30.75 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.17), residues: 2526 helix: 0.55 (0.15), residues: 1146 sheet: -0.58 (0.36), residues: 240 loop : -1.73 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 398 TYR 0.018 0.001 TYR D 363 PHE 0.031 0.001 PHE A 230 TRP 0.011 0.001 TRP B 84 HIS 0.006 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00332 (20826) covalent geometry : angle 0.65134 (28218) hydrogen bonds : bond 0.04424 ( 888) hydrogen bonds : angle 4.97248 ( 2583) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 406 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.7889 (ptp) cc_final: 0.7263 (ptp) REVERT: A 44 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7598 (mm-40) REVERT: A 45 ILE cc_start: 0.8974 (mt) cc_final: 0.7734 (mt) REVERT: A 49 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: A 75 LEU cc_start: 0.8661 (tp) cc_final: 0.8440 (tp) REVERT: A 84 TRP cc_start: 0.6452 (p-90) cc_final: 0.6115 (p-90) REVERT: A 115 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7879 (p0) REVERT: A 132 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7203 (tt) REVERT: A 150 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8266 (tmtt) REVERT: A 192 LYS cc_start: 0.0082 (OUTLIER) cc_final: -0.1241 (tptt) REVERT: A 400 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7352 (ttm-80) REVERT: B 30 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7766 (mtmt) REVERT: B 37 MET cc_start: 0.7867 (ptp) cc_final: 0.7599 (ptp) REVERT: B 44 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7386 (mm-40) REVERT: B 45 ILE cc_start: 0.8956 (mt) cc_final: 0.7826 (mt) REVERT: B 49 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: B 201 ASN cc_start: 0.5812 (OUTLIER) cc_final: 0.5601 (t0) REVERT: B 333 ARG cc_start: 0.8325 (tmt-80) cc_final: 0.7752 (tmt-80) REVERT: B 359 LYS cc_start: 0.7041 (pttt) cc_final: 0.6701 (ptmm) REVERT: B 400 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7475 (ttm-80) REVERT: B 441 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: C 57 ARG cc_start: 0.8379 (tpt-90) cc_final: 0.7868 (tpt-90) REVERT: C 76 MET cc_start: 0.8395 (tmm) cc_final: 0.7821 (tmm) REVERT: C 78 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8618 (mp) REVERT: C 137 MET cc_start: 0.6845 (mpp) cc_final: 0.6598 (mpp) REVERT: C 139 TRP cc_start: 0.6230 (OUTLIER) cc_final: 0.5345 (m100) REVERT: C 168 LYS cc_start: 0.7420 (mmpt) cc_final: 0.7209 (mmpt) REVERT: C 402 ARG cc_start: 0.7234 (mmm-85) cc_final: 0.6875 (mmt180) REVERT: C 459 GLN cc_start: 0.3390 (OUTLIER) cc_final: 0.1944 (pp30) REVERT: D 145 MET cc_start: 0.5198 (mmt) cc_final: 0.4965 (mmm) REVERT: D 168 LYS cc_start: 0.7098 (mmpt) cc_final: 0.6852 (mmpt) REVERT: D 169 PHE cc_start: 0.8433 (t80) cc_final: 0.8224 (t80) REVERT: D 176 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5679 (tt0) REVERT: E 76 MET cc_start: 0.8163 (tmt) cc_final: 0.7810 (tmm) REVERT: E 135 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6272 (mtm) REVERT: E 141 TRP cc_start: 0.5817 (OUTLIER) cc_final: 0.3823 (t-100) REVERT: E 145 MET cc_start: 0.6638 (mmm) cc_final: 0.5873 (mmt) REVERT: E 150 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8357 (tmtt) REVERT: E 441 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: F 31 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7587 (mtp85) REVERT: F 141 TRP cc_start: 0.5994 (OUTLIER) cc_final: 0.4228 (t-100) REVERT: F 145 MET cc_start: 0.6845 (mmm) cc_final: 0.5907 (mmt) REVERT: F 150 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8214 (ttmt) REVERT: F 333 ARG cc_start: 0.8308 (tmt-80) cc_final: 0.7883 (tmt-80) REVERT: F 400 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7028 (ttm-80) REVERT: F 441 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7496 (m-80) outliers start: 181 outliers final: 120 residues processed: 544 average time/residue: 0.1474 time to fit residues: 121.6078 Evaluate side-chains 525 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 382 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 400 ARG Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 159 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 224 optimal weight: 0.1980 chunk 207 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN D 216 ASN D 297 GLN D 405 GLN E 73 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.206242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.169179 restraints weight = 25965.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.173445 restraints weight = 16569.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.176231 restraints weight = 12624.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.178033 restraints weight = 10665.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.179211 restraints weight = 9583.320| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20826 Z= 0.106 Angle : 0.612 11.839 28218 Z= 0.292 Chirality : 0.041 0.278 2982 Planarity : 0.004 0.039 3690 Dihedral : 8.407 89.178 2889 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 7.75 % Allowed : 31.27 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2526 helix: 1.19 (0.16), residues: 1116 sheet: -0.42 (0.37), residues: 240 loop : -1.67 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 31 TYR 0.015 0.001 TYR B 328 PHE 0.032 0.001 PHE A 230 TRP 0.010 0.001 TRP B 84 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00243 (20826) covalent geometry : angle 0.61175 (28218) hydrogen bonds : bond 0.03571 ( 888) hydrogen bonds : angle 4.61312 ( 2583) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 404 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7844 (ptp) cc_final: 0.7208 (ptp) REVERT: A 45 ILE cc_start: 0.8961 (mt) cc_final: 0.8611 (mt) REVERT: A 75 LEU cc_start: 0.8684 (tp) cc_final: 0.8479 (tp) REVERT: A 115 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7809 (p0) REVERT: A 132 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7124 (tt) REVERT: B 30 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7977 (mmmt) REVERT: B 37 MET cc_start: 0.7870 (ptp) cc_final: 0.7605 (ptp) REVERT: B 45 ILE cc_start: 0.8960 (mt) cc_final: 0.8679 (mt) REVERT: B 150 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8306 (tmtt) REVERT: B 333 ARG cc_start: 0.8380 (tmt-80) cc_final: 0.7832 (tmt-80) REVERT: B 359 LYS cc_start: 0.6965 (pttt) cc_final: 0.6697 (ptmm) REVERT: B 373 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: B 383 LYS cc_start: 0.5783 (OUTLIER) cc_final: 0.4808 (mtpp) REVERT: B 384 ASP cc_start: 0.6221 (t0) cc_final: 0.6013 (t0) REVERT: C 57 ARG cc_start: 0.8377 (tpt-90) cc_final: 0.7853 (tpt-90) REVERT: C 63 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: C 76 MET cc_start: 0.8444 (tmm) cc_final: 0.7856 (tmm) REVERT: C 139 TRP cc_start: 0.6273 (OUTLIER) cc_final: 0.5315 (m100) REVERT: C 168 LYS cc_start: 0.7399 (mmpt) cc_final: 0.7179 (mmpt) REVERT: C 373 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7210 (tp30) REVERT: C 402 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6954 (mmt180) REVERT: D 48 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6447 (m-30) REVERT: D 57 ARG cc_start: 0.8226 (tpt-90) cc_final: 0.7821 (tpt-90) REVERT: D 168 LYS cc_start: 0.6831 (mmpt) cc_final: 0.6548 (mmpt) REVERT: D 176 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5801 (tt0) REVERT: E 76 MET cc_start: 0.8091 (tmt) cc_final: 0.7784 (tmm) REVERT: E 84 TRP cc_start: 0.6794 (p-90) cc_final: 0.6285 (p-90) REVERT: E 135 MET cc_start: 0.7203 (tpt) cc_final: 0.6237 (mtm) REVERT: E 141 TRP cc_start: 0.5677 (OUTLIER) cc_final: 0.3477 (t-100) REVERT: E 145 MET cc_start: 0.6331 (mmm) cc_final: 0.5883 (mmt) REVERT: E 150 LYS cc_start: 0.8707 (mppt) cc_final: 0.8453 (tttt) REVERT: E 382 LEU cc_start: 0.7448 (mt) cc_final: 0.7088 (pp) REVERT: E 441 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: E 455 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6058 (mt0) REVERT: F 31 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7455 (mmm-85) REVERT: F 48 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6043 (m-30) REVERT: F 141 TRP cc_start: 0.5945 (OUTLIER) cc_final: 0.4775 (t60) REVERT: F 145 MET cc_start: 0.6615 (mmm) cc_final: 0.6316 (mmt) REVERT: F 150 LYS cc_start: 0.8705 (mppt) cc_final: 0.8353 (tttt) REVERT: F 333 ARG cc_start: 0.8380 (tmt-80) cc_final: 0.8064 (tmt-80) REVERT: F 441 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7429 (m-80) outliers start: 165 outliers final: 101 residues processed: 528 average time/residue: 0.1456 time to fit residues: 118.0498 Evaluate side-chains 498 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 382 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 430 GLU Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 243 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 212 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN B 71 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN E 73 HIS E 201 ASN E 405 GLN F 73 HIS ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN F 405 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.207908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.173001 restraints weight = 25751.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.177223 restraints weight = 16181.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.179986 restraints weight = 12154.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.181695 restraints weight = 10149.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.182975 restraints weight = 9041.963| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20826 Z= 0.101 Angle : 0.619 13.146 28218 Z= 0.288 Chirality : 0.041 0.324 2982 Planarity : 0.004 0.037 3690 Dihedral : 7.884 84.037 2868 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 7.65 % Allowed : 31.69 % Favored : 60.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2526 helix: 1.42 (0.16), residues: 1128 sheet: 0.01 (0.39), residues: 228 loop : -1.71 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 400 TYR 0.016 0.001 TYR C 363 PHE 0.032 0.001 PHE A 230 TRP 0.016 0.001 TRP F 173 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00234 (20826) covalent geometry : angle 0.61937 (28218) hydrogen bonds : bond 0.03346 ( 888) hydrogen bonds : angle 4.45889 ( 2583) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 392 time to evaluate : 0.667 Fit side-chains REVERT: A 37 MET cc_start: 0.7765 (ptp) cc_final: 0.7217 (ptp) REVERT: A 75 LEU cc_start: 0.8654 (tp) cc_final: 0.8444 (tp) REVERT: A 137 MET cc_start: 0.7103 (mmm) cc_final: 0.6835 (mmm) REVERT: A 243 ASP cc_start: 0.8444 (t0) cc_final: 0.8197 (t0) REVERT: A 400 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7396 (ttm-80) REVERT: B 37 MET cc_start: 0.7838 (ptp) cc_final: 0.7345 (ptp) REVERT: B 333 ARG cc_start: 0.8407 (tmt-80) cc_final: 0.7887 (tmt-80) REVERT: B 373 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: B 383 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.4829 (mtpp) REVERT: C 57 ARG cc_start: 0.8364 (tpt-90) cc_final: 0.7844 (tpt-90) REVERT: C 63 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: C 76 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7835 (tmm) REVERT: C 139 TRP cc_start: 0.6298 (OUTLIER) cc_final: 0.5315 (m100) REVERT: C 168 LYS cc_start: 0.7435 (mmpt) cc_final: 0.7205 (mmpt) REVERT: C 169 PHE cc_start: 0.8483 (t80) cc_final: 0.8206 (t80) REVERT: C 381 LYS cc_start: 0.7404 (ptpt) cc_final: 0.6894 (ptpt) REVERT: C 402 ARG cc_start: 0.7258 (mmm-85) cc_final: 0.6895 (mmt180) REVERT: C 459 GLN cc_start: 0.3437 (OUTLIER) cc_final: 0.2044 (pp30) REVERT: D 48 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.6435 (m-30) REVERT: D 57 ARG cc_start: 0.8219 (tpt-90) cc_final: 0.7809 (tpt-90) REVERT: D 168 LYS cc_start: 0.6822 (mmpt) cc_final: 0.6600 (mmpt) REVERT: D 323 GLN cc_start: 0.7889 (pt0) cc_final: 0.7586 (mt0) REVERT: E 57 ARG cc_start: 0.8496 (tpt-90) cc_final: 0.8244 (tpp-160) REVERT: E 76 MET cc_start: 0.8060 (tmt) cc_final: 0.7723 (tmm) REVERT: E 135 MET cc_start: 0.7343 (tpt) cc_final: 0.6154 (mtm) REVERT: E 139 TRP cc_start: 0.6129 (OUTLIER) cc_final: 0.5726 (m-10) REVERT: E 141 TRP cc_start: 0.5724 (OUTLIER) cc_final: 0.3640 (t-100) REVERT: E 145 MET cc_start: 0.6630 (mmm) cc_final: 0.6270 (mmm) REVERT: E 441 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: E 455 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5956 (mt0) REVERT: F 48 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6206 (m-30) REVERT: F 141 TRP cc_start: 0.5809 (OUTLIER) cc_final: 0.4785 (t60) REVERT: F 150 LYS cc_start: 0.8576 (mppt) cc_final: 0.8351 (tmtt) REVERT: F 154 LYS cc_start: 0.6364 (mmmm) cc_final: 0.5329 (tttm) REVERT: F 333 ARG cc_start: 0.8361 (tmt-80) cc_final: 0.8086 (tmt-80) REVERT: F 416 THR cc_start: 0.6528 (OUTLIER) cc_final: 0.6327 (m) REVERT: F 441 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7605 (m-80) outliers start: 163 outliers final: 106 residues processed: 510 average time/residue: 0.1380 time to fit residues: 108.5312 Evaluate side-chains 499 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 377 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 139 TRP Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 405 GLN Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 247 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN E 73 HIS E 201 ASN E 405 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN F 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.205909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.169404 restraints weight = 25772.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.173667 restraints weight = 16489.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.176486 restraints weight = 12553.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.178314 restraints weight = 10570.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.179337 restraints weight = 9462.213| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20826 Z= 0.115 Angle : 0.634 13.875 28218 Z= 0.295 Chirality : 0.042 0.399 2982 Planarity : 0.004 0.038 3690 Dihedral : 7.309 59.979 2858 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.81 % Allowed : 32.21 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2526 helix: 1.49 (0.15), residues: 1116 sheet: 0.04 (0.38), residues: 228 loop : -1.59 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 31 TYR 0.014 0.001 TYR C 363 PHE 0.032 0.001 PHE A 230 TRP 0.008 0.001 TRP F 173 HIS 0.004 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00275 (20826) covalent geometry : angle 0.63412 (28218) hydrogen bonds : bond 0.03589 ( 888) hydrogen bonds : angle 4.44831 ( 2583) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 392 time to evaluate : 0.722 Fit side-chains REVERT: A 37 MET cc_start: 0.7812 (ptp) cc_final: 0.7243 (ptp) REVERT: A 75 LEU cc_start: 0.8668 (tp) cc_final: 0.8458 (tp) REVERT: A 137 MET cc_start: 0.7145 (mmm) cc_final: 0.6655 (mmm) REVERT: A 243 ASP cc_start: 0.8480 (t0) cc_final: 0.8093 (t0) REVERT: A 400 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7422 (ttm-80) REVERT: B 37 MET cc_start: 0.7790 (ptp) cc_final: 0.7524 (ptp) REVERT: B 330 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7934 (tp30) REVERT: B 333 ARG cc_start: 0.8401 (tmt-80) cc_final: 0.7872 (tmt-80) REVERT: B 373 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: B 383 LYS cc_start: 0.5737 (OUTLIER) cc_final: 0.4559 (mtpp) REVERT: C 47 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7471 (m-40) REVERT: C 57 ARG cc_start: 0.8378 (tpt-90) cc_final: 0.7847 (tpt-90) REVERT: C 63 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: C 76 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7863 (tmm) REVERT: C 139 TRP cc_start: 0.6375 (OUTLIER) cc_final: 0.5460 (m100) REVERT: C 168 LYS cc_start: 0.7451 (mmpt) cc_final: 0.7205 (mmpt) REVERT: C 169 PHE cc_start: 0.8559 (t80) cc_final: 0.8329 (t80) REVERT: C 402 ARG cc_start: 0.7281 (mmm-85) cc_final: 0.6938 (mmt180) REVERT: C 459 GLN cc_start: 0.3389 (OUTLIER) cc_final: 0.2003 (pp30) REVERT: D 57 ARG cc_start: 0.8304 (tpt-90) cc_final: 0.7874 (tpt-90) REVERT: D 76 MET cc_start: 0.8272 (ttp) cc_final: 0.7841 (tmm) REVERT: D 323 GLN cc_start: 0.7892 (pt0) cc_final: 0.7546 (mt0) REVERT: E 76 MET cc_start: 0.8083 (tmt) cc_final: 0.7747 (tmm) REVERT: E 135 MET cc_start: 0.7391 (tpt) cc_final: 0.6325 (mtm) REVERT: E 141 TRP cc_start: 0.5750 (OUTLIER) cc_final: 0.4691 (t60) REVERT: E 441 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: F 141 TRP cc_start: 0.5823 (OUTLIER) cc_final: 0.4804 (t60) REVERT: F 145 MET cc_start: 0.6697 (mmm) cc_final: 0.6474 (mmt) REVERT: F 150 LYS cc_start: 0.8598 (mppt) cc_final: 0.8369 (tmtt) REVERT: F 154 LYS cc_start: 0.6359 (mmmm) cc_final: 0.5270 (tttm) REVERT: F 333 ARG cc_start: 0.8375 (tmt-80) cc_final: 0.8075 (tmt-80) REVERT: F 441 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7568 (m-80) outliers start: 145 outliers final: 117 residues processed: 494 average time/residue: 0.1338 time to fit residues: 103.4966 Evaluate side-chains 510 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 381 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 359 LYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 0.0870 chunk 53 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 193 optimal weight: 2.9990 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 231 GLN F 58 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.206046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.169090 restraints weight = 25859.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.173397 restraints weight = 16617.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.176231 restraints weight = 12659.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.178063 restraints weight = 10656.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.179208 restraints weight = 9558.862| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20826 Z= 0.115 Angle : 0.646 14.313 28218 Z= 0.299 Chirality : 0.042 0.379 2982 Planarity : 0.004 0.037 3690 Dihedral : 7.287 59.877 2858 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.71 % Allowed : 32.11 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2526 helix: 1.56 (0.15), residues: 1116 sheet: -0.03 (0.37), residues: 240 loop : -1.53 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 31 TYR 0.012 0.001 TYR C 363 PHE 0.028 0.001 PHE A 230 TRP 0.008 0.001 TRP D 84 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00276 (20826) covalent geometry : angle 0.64569 (28218) hydrogen bonds : bond 0.03597 ( 888) hydrogen bonds : angle 4.44966 ( 2583) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 385 time to evaluate : 0.781 Fit side-chains REVERT: A 14 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6701 (pp) REVERT: A 37 MET cc_start: 0.7797 (ptp) cc_final: 0.7220 (ptp) REVERT: A 75 LEU cc_start: 0.8652 (tp) cc_final: 0.8449 (tp) REVERT: A 400 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7408 (ttm-80) REVERT: B 37 MET cc_start: 0.7781 (ptp) cc_final: 0.7535 (ptp) REVERT: B 145 MET cc_start: 0.5206 (mmm) cc_final: 0.4734 (mmm) REVERT: B 373 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: B 383 LYS cc_start: 0.5494 (OUTLIER) cc_final: 0.4317 (mtpp) REVERT: C 47 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7444 (m-40) REVERT: C 57 ARG cc_start: 0.8420 (tpt-90) cc_final: 0.7901 (tpt-90) REVERT: C 63 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7015 (m-80) REVERT: C 76 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7853 (tmm) REVERT: C 139 TRP cc_start: 0.6340 (OUTLIER) cc_final: 0.5393 (m100) REVERT: C 168 LYS cc_start: 0.7350 (mmpt) cc_final: 0.7092 (mmpt) REVERT: C 402 ARG cc_start: 0.7286 (mmm-85) cc_final: 0.6934 (mmt180) REVERT: C 459 GLN cc_start: 0.3366 (OUTLIER) cc_final: 0.2003 (pp30) REVERT: D 57 ARG cc_start: 0.8311 (tpt-90) cc_final: 0.7888 (tpt-90) REVERT: D 76 MET cc_start: 0.8306 (ttp) cc_final: 0.7901 (tmm) REVERT: D 323 GLN cc_start: 0.7860 (pt0) cc_final: 0.7576 (mt0) REVERT: E 76 MET cc_start: 0.8123 (tmt) cc_final: 0.7742 (tmm) REVERT: E 84 TRP cc_start: 0.7009 (p-90) cc_final: 0.6456 (p-90) REVERT: E 135 MET cc_start: 0.7388 (tpt) cc_final: 0.6349 (mtt) REVERT: E 441 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: F 48 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6168 (m-30) REVERT: F 141 TRP cc_start: 0.5837 (OUTLIER) cc_final: 0.4869 (t60) REVERT: F 154 LYS cc_start: 0.6680 (mmmm) cc_final: 0.5736 (tttm) REVERT: F 333 ARG cc_start: 0.8361 (tmt-80) cc_final: 0.8048 (tmt-80) REVERT: F 441 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7610 (m-80) outliers start: 143 outliers final: 117 residues processed: 488 average time/residue: 0.1343 time to fit residues: 102.2296 Evaluate side-chains 507 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 377 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 431 MET Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 TYR Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 42 optimal weight: 50.0000 chunk 113 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 220 optimal weight: 0.0670 chunk 171 optimal weight: 30.0000 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 250 optimal weight: 9.9990 overall best weight: 4.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 ASN D 297 GLN ** F 163 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 = 0.4093 r_free = 0.4093 target = 0.202195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.165318 restraints weight = 25696.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.169502 restraints weight = 16514.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.172250 restraints weight = 12588.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.174032 restraints weight = 10637.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.175073 restraints weight = 9547.467| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20826 Z= 0.162 Angle : 0.703 14.956 28218 Z= 0.327 Chirality : 0.044 0.352 2982 Planarity : 0.004 0.038 3690 Dihedral : 7.477 59.945 2856 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.38 % Allowed : 32.82 % Favored : 60.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2526 helix: 1.39 (0.15), residues: 1110 sheet: -0.14 (0.36), residues: 240 loop : -1.59 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 31 TYR 0.016 0.001 TYR C 363 PHE 0.033 0.002 PHE A 230 TRP 0.009 0.001 TRP E 139 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00395 (20826) covalent geometry : angle 0.70273 (28218) hydrogen bonds : bond 0.04338 ( 888) hydrogen bonds : angle 4.67528 ( 2583) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 389 time to evaluate : 0.599 Fit side-chains REVERT: A 14 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6716 (pp) REVERT: A 75 LEU cc_start: 0.8685 (tp) cc_final: 0.8473 (tp) REVERT: A 137 MET cc_start: 0.6984 (mmm) cc_final: 0.6417 (mmm) REVERT: A 192 LYS cc_start: 0.0446 (OUTLIER) cc_final: -0.1050 (tptt) REVERT: A 400 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7390 (ttm-80) REVERT: B 37 MET cc_start: 0.7831 (ptp) cc_final: 0.7573 (ptp) REVERT: B 145 MET cc_start: 0.5380 (mmm) cc_final: 0.4971 (mmm) REVERT: B 373 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: B 383 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.4723 (mtpp) REVERT: C 47 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7444 (m-40) REVERT: C 57 ARG cc_start: 0.8427 (tpt-90) cc_final: 0.7519 (tpt-90) REVERT: C 76 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7853 (tmm) REVERT: C 139 TRP cc_start: 0.6413 (OUTLIER) cc_final: 0.5369 (m100) REVERT: C 168 LYS cc_start: 0.7443 (mmpt) cc_final: 0.7205 (mmpt) REVERT: C 402 ARG cc_start: 0.7368 (mmm-85) cc_final: 0.7025 (mmt180) REVERT: C 459 GLN cc_start: 0.3459 (OUTLIER) cc_final: 0.1965 (pp30) REVERT: D 57 ARG cc_start: 0.8380 (tpt-90) cc_final: 0.7928 (tpt-90) REVERT: D 76 MET cc_start: 0.8263 (ttp) cc_final: 0.7847 (tmm) REVERT: D 291 ASP cc_start: 0.6951 (p0) cc_final: 0.6742 (t0) REVERT: D 323 GLN cc_start: 0.7901 (pt0) cc_final: 0.7432 (mt0) REVERT: D 363 TYR cc_start: 0.7568 (m-80) cc_final: 0.7352 (m-80) REVERT: E 76 MET cc_start: 0.8232 (tmt) cc_final: 0.7814 (tmm) REVERT: E 84 TRP cc_start: 0.7071 (p-90) cc_final: 0.6501 (p-90) REVERT: E 135 MET cc_start: 0.7344 (tpt) cc_final: 0.6341 (mtt) REVERT: E 141 TRP cc_start: 0.5789 (OUTLIER) cc_final: 0.3734 (t-100) REVERT: F 141 TRP cc_start: 0.6077 (OUTLIER) cc_final: 0.4929 (t60) REVERT: F 154 LYS cc_start: 0.6649 (mmmm) cc_final: 0.5693 (tttm) REVERT: F 333 ARG cc_start: 0.8371 (tmt-80) cc_final: 0.8016 (tmt-80) REVERT: F 441 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7601 (m-80) outliers start: 136 outliers final: 112 residues processed: 490 average time/residue: 0.1366 time to fit residues: 104.8295 Evaluate side-chains 504 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 380 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 177 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 73 HIS C 201 ASN D 115 ASN E 201 ASN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.201994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.165332 restraints weight = 25821.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.169498 restraints weight = 16499.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.172253 restraints weight = 12592.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.174060 restraints weight = 10626.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.175127 restraints weight = 9536.077| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20826 Z= 0.152 Angle : 0.704 15.383 28218 Z= 0.327 Chirality : 0.044 0.357 2982 Planarity : 0.004 0.036 3690 Dihedral : 7.417 59.840 2854 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.20 % Allowed : 33.10 % Favored : 60.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2526 helix: 1.37 (0.15), residues: 1110 sheet: -0.24 (0.35), residues: 240 loop : -1.58 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 31 TYR 0.014 0.001 TYR C 363 PHE 0.034 0.002 PHE A 230 TRP 0.009 0.001 TRP D 84 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00372 (20826) covalent geometry : angle 0.70389 (28218) hydrogen bonds : bond 0.04211 ( 888) hydrogen bonds : angle 4.70106 ( 2583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 380 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6739 (pp) REVERT: A 37 MET cc_start: 0.7798 (ptp) cc_final: 0.7313 (ptp) REVERT: A 75 LEU cc_start: 0.8673 (tp) cc_final: 0.8461 (tp) REVERT: A 192 LYS cc_start: 0.0221 (OUTLIER) cc_final: -0.1217 (tptt) REVERT: A 400 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7424 (ttm-80) REVERT: B 37 MET cc_start: 0.7829 (ptp) cc_final: 0.7561 (ptp) REVERT: B 145 MET cc_start: 0.5450 (mmm) cc_final: 0.5034 (mmm) REVERT: B 243 ASP cc_start: 0.8418 (t0) cc_final: 0.7953 (t0) REVERT: B 291 ASP cc_start: 0.7248 (p0) cc_final: 0.7024 (p0) REVERT: B 373 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: B 383 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.4528 (mtpp) REVERT: C 47 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7437 (m-40) REVERT: C 57 ARG cc_start: 0.8446 (tpt-90) cc_final: 0.7912 (tpt-90) REVERT: C 76 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7867 (tmm) REVERT: C 137 MET cc_start: 0.6850 (mpp) cc_final: 0.6221 (mpp) REVERT: C 139 TRP cc_start: 0.6347 (OUTLIER) cc_final: 0.5362 (m100) REVERT: C 168 LYS cc_start: 0.7401 (mmpt) cc_final: 0.7130 (mmpt) REVERT: C 189 MET cc_start: 0.4654 (ttp) cc_final: 0.4133 (ptm) REVERT: C 402 ARG cc_start: 0.7374 (mmm-85) cc_final: 0.7021 (mmt180) REVERT: C 459 GLN cc_start: 0.3452 (OUTLIER) cc_final: 0.1937 (pp30) REVERT: D 57 ARG cc_start: 0.8382 (tpt-90) cc_final: 0.7883 (tpt-90) REVERT: D 76 MET cc_start: 0.8340 (ttp) cc_final: 0.7941 (tmm) REVERT: D 323 GLN cc_start: 0.7877 (pt0) cc_final: 0.7404 (mt0) REVERT: D 363 TYR cc_start: 0.7735 (m-80) cc_final: 0.7529 (m-80) REVERT: E 76 MET cc_start: 0.8350 (tmt) cc_final: 0.7976 (tmm) REVERT: E 84 TRP cc_start: 0.7108 (p-90) cc_final: 0.6840 (p-90) REVERT: E 135 MET cc_start: 0.7386 (tpt) cc_final: 0.6366 (mtt) REVERT: E 141 TRP cc_start: 0.5693 (OUTLIER) cc_final: 0.3792 (t-100) REVERT: F 141 TRP cc_start: 0.5923 (OUTLIER) cc_final: 0.4851 (t60) REVERT: F 154 LYS cc_start: 0.6368 (mmmm) cc_final: 0.5415 (tttm) REVERT: F 333 ARG cc_start: 0.8384 (tmt-80) cc_final: 0.8028 (tmt-80) REVERT: F 441 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7619 (m-80) outliers start: 132 outliers final: 115 residues processed: 479 average time/residue: 0.1423 time to fit residues: 105.8406 Evaluate side-chains 505 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 378 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 433 PHE Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 141 TRP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 368 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 433 PHE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 402 ARG Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain F residue 141 TRP Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 402 ARG Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 424 MET Chi-restraints excluded: chain F residue 433 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 441 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 130 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 84 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 chunk 141 optimal weight: 50.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 455 GLN C 73 HIS C 201 ASN D 297 GLN E 73 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.202934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.166037 restraints weight = 25690.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.170320 restraints weight = 16473.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.173080 restraints weight = 12548.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.174703 restraints weight = 10597.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.176023 restraints weight = 9564.648| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20826 Z= 0.139 Angle : 0.697 15.139 28218 Z= 0.324 Chirality : 0.043 0.349 2982 Planarity : 0.004 0.039 3690 Dihedral : 7.385 59.826 2854 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 6.15 % Allowed : 33.24 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2526 helix: 1.20 (0.15), residues: 1146 sheet: -0.14 (0.36), residues: 228 loop : -1.48 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 31 TYR 0.014 0.001 TYR C 363 PHE 0.033 0.001 PHE A 230 TRP 0.009 0.001 TRP D 84 HIS 0.004 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00338 (20826) covalent geometry : angle 0.69650 (28218) hydrogen bonds : bond 0.04095 ( 888) hydrogen bonds : angle 4.68101 ( 2583) =============================================================================== Job complete usr+sys time: 3433.16 seconds wall clock time: 60 minutes 3.96 seconds (3603.96 seconds total)