Starting phenix.real_space_refine on Mon Aug 25 04:17:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyl_36725/08_2025/8jyl_36725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyl_36725/08_2025/8jyl_36725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jyl_36725/08_2025/8jyl_36725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyl_36725/08_2025/8jyl_36725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jyl_36725/08_2025/8jyl_36725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyl_36725/08_2025/8jyl_36725.map" } resolution = 2.33 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.003 sd= 0.155 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: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 114 5.16 5 C 16296 2.51 5 N 4266 2.21 5 O 4752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25434 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4204 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 23, 'TRANS': 503} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {' MG': 1, 'VUL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 3.87, per 1000 atoms: 0.15 Number of scatterers: 25434 At special positions: 0 Unit cell: (153.45, 150.66, 84.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 Mg 6 11.99 O 4752 8.00 N 4266 7.00 C 16296 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: 2.09 Conformation dependent library (CDL) restraints added in 893.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5928 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 30 sheets defined 40.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.564A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.602A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.501A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.558A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.649A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 483 through 497 removed outlier: 3.823A pdb=" N LEU A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 removed outlier: 3.523A pdb=" N LEU A 506 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.954A pdb=" N LYS A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.564A pdb=" N LEU B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 86 removed outlier: 3.602A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.501A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.559A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.650A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 483 through 497 removed outlier: 3.824A pdb=" N LEU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.523A pdb=" N LEU B 506 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.953A pdb=" N LYS B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 removed outlier: 3.563A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 86 removed outlier: 3.602A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.501A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.558A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 335 through 339 Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.650A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 483 through 497 removed outlier: 3.823A pdb=" N LEU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 507 removed outlier: 3.524A pdb=" N LEU C 506 " --> pdb=" O GLU C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.953A pdb=" N LYS C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.563A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 86 removed outlier: 3.603A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.501A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.558A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.650A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 483 through 497 removed outlier: 3.823A pdb=" N LEU D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 507 removed outlier: 3.524A pdb=" N LEU D 506 " --> pdb=" O GLU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.953A pdb=" N LYS D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.564A pdb=" N LEU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 86 removed outlier: 3.602A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.501A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.558A pdb=" N ALA E 284 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 310 Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.649A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 440 through 449 Processing helix chain 'E' and resid 483 through 497 removed outlier: 3.823A pdb=" N LEU E 487 " --> pdb=" O THR E 483 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE E 494 " --> pdb=" O PHE E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 507 removed outlier: 3.523A pdb=" N LEU E 506 " --> pdb=" O GLU E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 532 removed outlier: 3.954A pdb=" N LYS E 530 " --> pdb=" O LYS E 526 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 removed outlier: 3.564A pdb=" N LEU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 86 removed outlier: 3.602A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 128 removed outlier: 3.629A pdb=" N GLN F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.501A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.558A pdb=" N ALA F 284 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 310 Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.649A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 440 through 449 Processing helix chain 'F' and resid 483 through 497 removed outlier: 3.823A pdb=" N LEU F 487 " --> pdb=" O THR F 483 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE F 494 " --> pdb=" O PHE F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 507 removed outlier: 3.523A pdb=" N LEU F 506 " --> pdb=" O GLU F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 532 removed outlier: 3.954A pdb=" N LYS F 530 " --> pdb=" O LYS F 526 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.704A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR A 218 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 292 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY A 317 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 294 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.407A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU A 90 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR A 174 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N MET A 92 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR A 172 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 185 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A 174 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS A 183 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 363 removed outlier: 5.161A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 433 Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 463 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.704A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR B 218 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 292 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY B 317 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE B 294 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.407A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU B 90 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR B 174 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N MET B 92 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 172 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 185 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B 174 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS B 183 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 363 removed outlier: 5.161A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 430 through 433 Processing sheet with id=AB1, first strand: chain 'B' and resid 455 through 463 Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.704A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C 218 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 292 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY C 317 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE C 294 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.408A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU C 90 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR C 174 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N MET C 92 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR C 172 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C 185 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR C 174 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS C 183 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 359 through 363 removed outlier: 5.161A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 430 through 433 Processing sheet with id=AB6, first strand: chain 'C' and resid 455 through 463 Processing sheet with id=AB7, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.704A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR D 218 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL D 292 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLY D 317 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE D 294 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.407A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU D 90 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR D 174 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N MET D 92 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR D 172 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 185 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR D 174 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS D 183 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 359 through 363 removed outlier: 5.161A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 430 through 433 Processing sheet with id=AC2, first strand: chain 'D' and resid 455 through 463 Processing sheet with id=AC3, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.704A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR E 218 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL E 292 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY E 317 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE E 294 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.407A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU E 90 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR E 174 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N MET E 92 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR E 172 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL E 185 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR E 174 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS E 183 " --> pdb=" O TYR E 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 359 through 363 removed outlier: 5.161A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 430 through 433 Processing sheet with id=AC7, first strand: chain 'E' and resid 455 through 463 Processing sheet with id=AC8, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.705A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR F 218 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL F 292 " --> pdb=" O PHE F 315 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY F 317 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE F 294 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY F 319 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.408A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU F 90 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR F 174 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N MET F 92 " --> pdb=" O TYR F 174 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR F 172 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL F 185 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR F 174 " --> pdb=" O LYS F 183 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS F 183 " --> pdb=" O TYR F 174 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 359 through 363 removed outlier: 5.162A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 430 through 433 Processing sheet with id=AD3, first strand: chain 'F' and resid 455 through 463 996 hydrogen bonds defined for protein. 2682 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: 4.42 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4284 1.31 - 1.43: 6478 1.43 - 1.56: 15020 1.56 - 1.68: 30 1.68 - 1.81: 198 Bond restraints: 26010 Sorted by residual: bond pdb=" C14 VUL E 601 " pdb=" C15 VUL E 601 " ideal model delta sigma weight residual 1.541 1.303 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C14 VUL A 601 " pdb=" C15 VUL A 601 " ideal model delta sigma weight residual 1.541 1.303 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C14 VUL D 601 " pdb=" C15 VUL D 601 " ideal model delta sigma weight residual 1.541 1.303 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C14 VUL C 601 " pdb=" C15 VUL C 601 " ideal model delta sigma weight residual 1.541 1.303 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C14 VUL F 601 " pdb=" C15 VUL F 601 " ideal model delta sigma weight residual 1.541 1.304 0.237 2.00e-02 2.50e+03 1.41e+02 ... (remaining 26005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 34599 2.21 - 4.42: 548 4.42 - 6.63: 91 6.63 - 8.84: 24 8.84 - 11.05: 12 Bond angle restraints: 35274 Sorted by residual: angle pdb=" N ALA F 207 " pdb=" CA ALA F 207 " pdb=" C ALA F 207 " ideal model delta sigma weight residual 111.07 115.21 -4.14 1.07e+00 8.73e-01 1.49e+01 angle pdb=" N ALA B 207 " pdb=" CA ALA B 207 " pdb=" C ALA B 207 " ideal model delta sigma weight residual 111.07 115.19 -4.12 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 111.07 115.16 -4.09 1.07e+00 8.73e-01 1.46e+01 angle pdb=" N ALA D 207 " pdb=" CA ALA D 207 " pdb=" C ALA D 207 " ideal model delta sigma weight residual 111.07 115.16 -4.09 1.07e+00 8.73e-01 1.46e+01 angle pdb=" N ALA E 207 " pdb=" CA ALA E 207 " pdb=" C ALA E 207 " ideal model delta sigma weight residual 111.07 115.16 -4.09 1.07e+00 8.73e-01 1.46e+01 ... (remaining 35269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 13362 16.61 - 33.23: 1685 33.23 - 49.84: 494 49.84 - 66.45: 137 66.45 - 83.07: 42 Dihedral angle restraints: 15720 sinusoidal: 6510 harmonic: 9210 Sorted by residual: dihedral pdb=" CA GLY F 324 " pdb=" C GLY F 324 " pdb=" N PRO F 325 " pdb=" CA PRO F 325 " ideal model delta harmonic sigma weight residual -180.00 -121.20 -58.80 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA GLY E 324 " pdb=" C GLY E 324 " pdb=" N PRO E 325 " pdb=" CA PRO E 325 " ideal model delta harmonic sigma weight residual -180.00 -121.24 -58.76 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA GLY A 324 " pdb=" C GLY A 324 " pdb=" N PRO A 325 " pdb=" CA PRO A 325 " ideal model delta harmonic sigma weight residual -180.00 -121.24 -58.76 0 5.00e+00 4.00e-02 1.38e+02 ... (remaining 15717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3825 0.109 - 0.218: 123 0.218 - 0.327: 6 0.327 - 0.435: 12 0.435 - 0.544: 12 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CA TRP B 230 " pdb=" N TRP B 230 " pdb=" C TRP B 230 " pdb=" CB TRP B 230 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" CA TRP C 230 " pdb=" N TRP C 230 " pdb=" C TRP C 230 " pdb=" CB TRP C 230 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CA TRP D 230 " pdb=" N TRP D 230 " pdb=" C TRP D 230 " pdb=" CB TRP D 230 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.38e+00 ... (remaining 3975 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 324 " 0.062 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO B 325 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 324 " 0.061 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO F 325 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO F 325 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 325 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 324 " -0.061 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO A 325 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.050 5.00e-02 4.00e+02 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1258 2.73 - 3.27: 25365 3.27 - 3.81: 46557 3.81 - 4.36: 61177 4.36 - 4.90: 96172 Nonbonded interactions: 230529 Sorted by model distance: nonbonded pdb=" O3 VUL F 601 " pdb="MG MG F 602 " model vdw 2.183 2.170 nonbonded pdb=" O3 VUL E 601 " pdb="MG MG E 602 " model vdw 2.183 2.170 nonbonded pdb=" O3 VUL A 601 " pdb="MG MG A 602 " model vdw 2.183 2.170 nonbonded pdb=" O3 VUL D 601 " pdb="MG MG D 602 " model vdw 2.183 2.170 nonbonded pdb=" O3 VUL C 601 " pdb="MG MG C 602 " model vdw 2.183 2.170 ... (remaining 230524 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.170 Find NCS groups from input model: 0.180 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:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.009 0.238 26010 Z= 0.443 Angle : 0.710 11.048 35274 Z= 0.361 Chirality : 0.060 0.544 3978 Planarity : 0.006 0.094 4470 Dihedral : 17.200 83.068 9792 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.61 % Allowed : 18.51 % Favored : 80.88 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.14), residues: 3150 helix: 0.35 (0.15), residues: 1074 sheet: -0.51 (0.19), residues: 582 loop : -0.02 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 383 TYR 0.021 0.002 TYR D 245 PHE 0.017 0.002 PHE F 287 TRP 0.009 0.002 TRP C 402 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00877 (26010) covalent geometry : angle 0.71006 (35274) hydrogen bonds : bond 0.22428 ( 996) hydrogen bonds : angle 8.05245 ( 2682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 396 time to evaluate : 1.141 Fit side-chains REVERT: B 256 ASN cc_start: 0.7757 (t0) cc_final: 0.7414 (t0) REVERT: B 281 LYS cc_start: 0.7539 (tttt) cc_final: 0.7052 (tttm) REVERT: B 311 ASP cc_start: 0.7061 (t0) cc_final: 0.6832 (m-30) REVERT: B 338 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6319 (mm-30) REVERT: B 418 GLU cc_start: 0.6218 (pm20) cc_final: 0.6014 (pm20) REVERT: B 442 GLU cc_start: 0.6927 (tt0) cc_final: 0.6139 (tm-30) REVERT: B 468 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6977 (mt-10) REVERT: C 197 MET cc_start: 0.8709 (mmm) cc_final: 0.8432 (mpm) REVERT: C 224 MET cc_start: 0.9126 (mtp) cc_final: 0.8797 (mtp) REVERT: C 275 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7974 (mt) REVERT: C 466 TRP cc_start: 0.8202 (m100) cc_final: 0.7973 (m100) REVERT: C 468 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7121 (mt-10) REVERT: C 507 LEU cc_start: 0.7601 (tp) cc_final: 0.7391 (tp) REVERT: D 197 MET cc_start: 0.8708 (mmm) cc_final: 0.8432 (mpm) REVERT: D 224 MET cc_start: 0.9125 (mtp) cc_final: 0.8796 (mtp) REVERT: D 466 TRP cc_start: 0.8199 (m100) cc_final: 0.7971 (m100) REVERT: D 468 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7128 (mt-10) REVERT: D 507 LEU cc_start: 0.7601 (tp) cc_final: 0.7390 (tp) REVERT: F 256 ASN cc_start: 0.7761 (t0) cc_final: 0.7392 (t0) REVERT: F 281 LYS cc_start: 0.7542 (tttt) cc_final: 0.7057 (tttm) REVERT: F 311 ASP cc_start: 0.7061 (t0) cc_final: 0.6832 (m-30) REVERT: F 338 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6324 (mm-30) REVERT: F 418 GLU cc_start: 0.6221 (pm20) cc_final: 0.6021 (pm20) REVERT: F 442 GLU cc_start: 0.6928 (tt0) cc_final: 0.6140 (tm-30) REVERT: F 468 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6983 (mt-10) outliers start: 17 outliers final: 12 residues processed: 409 average time/residue: 0.6704 time to fit residues: 317.7266 Evaluate side-chains 385 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 372 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 228 HIS Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 108 HIS A 160 ASN A 195 HIS A 267 HIS A 390 ASN B 17 ASN B 29 GLN B 108 HIS B 160 ASN B 195 HIS B 267 HIS B 390 ASN C 17 ASN C 29 GLN C 108 HIS C 160 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS C 344 GLN C 390 ASN D 17 ASN D 29 GLN D 108 HIS D 160 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 HIS D 344 GLN D 390 ASN E 29 GLN E 108 HIS E 160 ASN E 195 HIS E 267 HIS E 390 ASN F 17 ASN F 29 GLN F 108 HIS F 160 ASN F 195 HIS F 226 HIS F 267 HIS F 390 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.177841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137890 restraints weight = 20392.582| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.53 r_work: 0.2978 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26010 Z= 0.199 Angle : 0.624 6.707 35274 Z= 0.329 Chirality : 0.049 0.230 3978 Planarity : 0.006 0.100 4470 Dihedral : 7.014 59.753 3644 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.28 % Allowed : 14.61 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.14), residues: 3150 helix: 0.89 (0.15), residues: 1104 sheet: -0.49 (0.19), residues: 582 loop : -0.18 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.022 0.002 TYR D 245 PHE 0.023 0.003 PHE C 187 TRP 0.013 0.002 TRP C 402 HIS 0.007 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00448 (26010) covalent geometry : angle 0.62423 (35274) hydrogen bonds : bond 0.05773 ( 996) hydrogen bonds : angle 6.26840 ( 2682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 382 time to evaluate : 1.018 Fit side-chains REVERT: A 119 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8027 (mm-30) REVERT: A 484 GLU cc_start: 0.5283 (OUTLIER) cc_final: 0.4363 (pm20) REVERT: B 61 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7661 (mmtm) REVERT: B 118 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: B 119 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: B 309 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: B 338 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6671 (mm-30) REVERT: B 468 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7139 (mt-10) REVERT: C 118 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (pt0) REVERT: C 119 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: C 350 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8213 (mttm) REVERT: C 484 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.4550 (pm20) REVERT: D 118 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: D 119 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: D 275 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (mt) REVERT: D 350 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8208 (mttm) REVERT: D 484 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.4559 (pm20) REVERT: E 119 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8043 (mm-30) REVERT: E 484 GLU cc_start: 0.5278 (OUTLIER) cc_final: 0.4359 (pm20) REVERT: F 61 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7649 (mmtm) REVERT: F 118 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: F 119 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: F 309 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: F 338 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6679 (mm-30) REVERT: F 443 LEU cc_start: 0.7631 (mt) cc_final: 0.7408 (mt) REVERT: F 468 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7138 (mt-10) outliers start: 91 outliers final: 26 residues processed: 445 average time/residue: 0.6607 time to fit residues: 340.9089 Evaluate side-chains 412 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 365 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 131 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 278 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 160 ASN A 195 HIS B 226 HIS C 160 ASN C 195 HIS D 160 ASN D 195 HIS E 17 ASN E 160 ASN E 195 HIS F 226 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139760 restraints weight = 20483.796| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.45 r_work: 0.3022 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26010 Z= 0.141 Angle : 0.557 5.950 35274 Z= 0.291 Chirality : 0.046 0.216 3978 Planarity : 0.005 0.099 4470 Dihedral : 6.277 55.887 3630 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.98 % Allowed : 15.80 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.14), residues: 3150 helix: 1.13 (0.15), residues: 1104 sheet: -0.35 (0.20), residues: 582 loop : -0.20 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 190 TYR 0.016 0.001 TYR D 245 PHE 0.017 0.002 PHE E 81 TRP 0.011 0.001 TRP D 402 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00313 (26010) covalent geometry : angle 0.55731 (35274) hydrogen bonds : bond 0.04683 ( 996) hydrogen bonds : angle 5.87676 ( 2682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 368 time to evaluate : 1.081 Fit side-chains REVERT: A 256 ASN cc_start: 0.8127 (t0) cc_final: 0.7900 (t0) REVERT: A 484 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4334 (pm20) REVERT: B 61 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7616 (mmtm) REVERT: B 119 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: B 309 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: B 338 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6665 (mm-30) REVERT: B 468 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7135 (mt-10) REVERT: C 113 ILE cc_start: 0.8330 (mt) cc_final: 0.8059 (mt) REVERT: C 118 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: C 275 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8225 (mt) REVERT: C 484 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.4682 (pm20) REVERT: D 113 ILE cc_start: 0.8331 (mt) cc_final: 0.8060 (mt) REVERT: D 118 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: D 275 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8233 (mt) REVERT: D 484 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.4690 (pm20) REVERT: E 256 ASN cc_start: 0.8119 (t0) cc_final: 0.7892 (t0) REVERT: E 484 GLU cc_start: 0.5120 (OUTLIER) cc_final: 0.4335 (pm20) REVERT: F 61 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7617 (mmtm) REVERT: F 119 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: F 309 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: F 338 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6658 (mm-30) REVERT: F 443 LEU cc_start: 0.7623 (mt) cc_final: 0.7383 (mt) REVERT: F 468 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7143 (mt-10) outliers start: 55 outliers final: 20 residues processed: 413 average time/residue: 0.6486 time to fit residues: 312.3737 Evaluate side-chains 401 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 367 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 258 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 161 optimal weight: 0.0370 chunk 70 optimal weight: 0.6980 chunk 155 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 overall best weight: 3.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN B 206 ASN B 226 HIS C 160 ASN D 160 ASN D 344 GLN E 160 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 206 ASN F 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.178323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135786 restraints weight = 20964.940| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.12 r_work: 0.2966 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26010 Z= 0.236 Angle : 0.652 6.922 35274 Z= 0.340 Chirality : 0.051 0.236 3978 Planarity : 0.006 0.105 4470 Dihedral : 6.758 61.276 3630 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.17 % Allowed : 14.86 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.14), residues: 3150 helix: 1.01 (0.15), residues: 1104 sheet: -0.46 (0.19), residues: 582 loop : -0.25 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 190 TYR 0.026 0.002 TYR D 245 PHE 0.024 0.003 PHE C 187 TRP 0.015 0.002 TRP D 402 HIS 0.008 0.002 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00536 (26010) covalent geometry : angle 0.65224 (35274) hydrogen bonds : bond 0.05487 ( 996) hydrogen bonds : angle 6.03989 ( 2682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 379 time to evaluate : 1.059 Fit side-chains REVERT: A 119 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: A 163 ASP cc_start: 0.8437 (m-30) cc_final: 0.8085 (t70) REVERT: A 256 ASN cc_start: 0.8051 (t0) cc_final: 0.7708 (t0) REVERT: A 281 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7274 (tttt) REVERT: A 350 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8512 (mttm) REVERT: A 484 GLU cc_start: 0.5163 (OUTLIER) cc_final: 0.4345 (pm20) REVERT: B 61 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7768 (mmtm) REVERT: B 118 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: B 119 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: B 309 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: B 338 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6690 (mm-30) REVERT: C 118 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8110 (pt0) REVERT: C 119 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: C 275 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8223 (mt) REVERT: C 350 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8164 (mttm) REVERT: C 484 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.4667 (pm20) REVERT: D 118 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: D 119 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: D 275 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8215 (mt) REVERT: D 350 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8162 (mttm) REVERT: D 484 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.4694 (pm20) REVERT: E 119 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: E 163 ASP cc_start: 0.8443 (m-30) cc_final: 0.8088 (t70) REVERT: E 256 ASN cc_start: 0.8044 (t0) cc_final: 0.7700 (t0) REVERT: E 281 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7284 (tttt) REVERT: E 350 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8513 (mttm) REVERT: E 484 GLU cc_start: 0.5166 (OUTLIER) cc_final: 0.4344 (pm20) REVERT: F 61 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7778 (mmtm) REVERT: F 118 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: F 119 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7781 (mm-30) REVERT: F 309 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: F 338 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6684 (mm-30) REVERT: F 443 LEU cc_start: 0.7674 (mt) cc_final: 0.7449 (mt) outliers start: 88 outliers final: 30 residues processed: 432 average time/residue: 0.6519 time to fit residues: 327.6935 Evaluate side-chains 425 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 369 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 203 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 195 HIS B 226 HIS C 160 ASN D 160 ASN E 160 ASN E 195 HIS F 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.161448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123427 restraints weight = 19913.120| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 0.84 r_work: 0.3037 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26010 Z= 0.164 Angle : 0.582 6.164 35274 Z= 0.303 Chirality : 0.047 0.221 3978 Planarity : 0.006 0.102 4470 Dihedral : 6.469 57.921 3630 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.81 % Allowed : 14.90 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.14), residues: 3150 helix: 1.12 (0.15), residues: 1104 sheet: -0.41 (0.19), residues: 582 loop : -0.24 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 47 TYR 0.019 0.002 TYR C 245 PHE 0.019 0.002 PHE E 81 TRP 0.012 0.002 TRP D 402 HIS 0.007 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00368 (26010) covalent geometry : angle 0.58244 (35274) hydrogen bonds : bond 0.04725 ( 996) hydrogen bonds : angle 5.84840 ( 2682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 369 time to evaluate : 1.135 Fit side-chains REVERT: A 145 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: A 256 ASN cc_start: 0.8105 (t0) cc_final: 0.7881 (t0) REVERT: A 484 GLU cc_start: 0.4985 (OUTLIER) cc_final: 0.4324 (pm20) REVERT: B 61 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7717 (mmtm) REVERT: B 119 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: B 309 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: B 338 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6545 (mm-30) REVERT: B 428 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6962 (pttp) REVERT: C 113 ILE cc_start: 0.8493 (mt) cc_final: 0.8224 (mt) REVERT: C 118 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: C 275 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8254 (mt) REVERT: C 484 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.4639 (pm20) REVERT: D 113 ILE cc_start: 0.8488 (mt) cc_final: 0.8223 (mt) REVERT: D 118 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: D 275 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8274 (mt) REVERT: D 484 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.4643 (pm20) REVERT: E 145 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: E 256 ASN cc_start: 0.8089 (t0) cc_final: 0.7867 (t0) REVERT: E 484 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.4323 (pm20) REVERT: F 61 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7710 (mmtm) REVERT: F 119 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: F 309 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: F 338 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6557 (mm-30) REVERT: F 428 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6954 (pttp) REVERT: F 443 LEU cc_start: 0.7764 (mt) cc_final: 0.7520 (mt) outliers start: 78 outliers final: 34 residues processed: 427 average time/residue: 0.6627 time to fit residues: 328.5323 Evaluate side-chains 413 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 361 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 204 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 223 optimal weight: 0.0070 chunk 258 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 226 HIS C 160 ASN C 344 GLN D 160 ASN E 160 ASN F 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.160922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122608 restraints weight = 19855.421| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 0.85 r_work: 0.3021 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26010 Z= 0.185 Angle : 0.602 6.325 35274 Z= 0.313 Chirality : 0.048 0.223 3978 Planarity : 0.006 0.104 4470 Dihedral : 6.556 58.811 3630 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.85 % Allowed : 15.12 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.14), residues: 3150 helix: 1.11 (0.15), residues: 1104 sheet: -0.41 (0.19), residues: 582 loop : -0.23 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 141 TYR 0.022 0.002 TYR C 245 PHE 0.020 0.002 PHE A 81 TRP 0.013 0.002 TRP D 402 HIS 0.007 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00416 (26010) covalent geometry : angle 0.60184 (35274) hydrogen bonds : bond 0.04910 ( 996) hydrogen bonds : angle 5.86928 ( 2682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 360 time to evaluate : 0.990 Fit side-chains REVERT: A 119 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: A 256 ASN cc_start: 0.8077 (t0) cc_final: 0.7867 (t0) REVERT: A 350 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8592 (mttm) REVERT: A 484 GLU cc_start: 0.4971 (OUTLIER) cc_final: 0.4329 (pm20) REVERT: B 61 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7780 (mmtm) REVERT: B 119 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: B 309 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: B 338 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6845 (mt-10) REVERT: C 113 ILE cc_start: 0.8553 (mt) cc_final: 0.8288 (mt) REVERT: C 118 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: C 275 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (mt) REVERT: C 350 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8216 (mttm) REVERT: C 484 GLU cc_start: 0.5464 (OUTLIER) cc_final: 0.4639 (pm20) REVERT: D 113 ILE cc_start: 0.8549 (mt) cc_final: 0.8286 (mt) REVERT: D 118 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: D 275 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8262 (mt) REVERT: D 350 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8222 (mttm) REVERT: D 484 GLU cc_start: 0.5475 (OUTLIER) cc_final: 0.4642 (pm20) REVERT: E 119 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: E 256 ASN cc_start: 0.8063 (t0) cc_final: 0.7854 (t0) REVERT: E 350 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8591 (mttm) REVERT: E 484 GLU cc_start: 0.4984 (OUTLIER) cc_final: 0.4336 (pm20) REVERT: F 61 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7760 (mmtm) REVERT: F 119 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: F 309 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: F 338 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6858 (mt-10) REVERT: F 443 LEU cc_start: 0.7759 (mt) cc_final: 0.7515 (mt) outliers start: 79 outliers final: 41 residues processed: 418 average time/residue: 0.6594 time to fit residues: 321.0781 Evaluate side-chains 426 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 365 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 434 SER Chi-restraints excluded: chain F residue 468 GLU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 2 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 308 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 149 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 226 HIS C 36 HIS C 160 ASN D 36 HIS D 160 ASN E 160 ASN F 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.159356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121922 restraints weight = 19737.284| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 0.84 r_work: 0.2980 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26010 Z= 0.271 Angle : 0.692 7.775 35274 Z= 0.360 Chirality : 0.053 0.252 3978 Planarity : 0.006 0.107 4470 Dihedral : 6.945 63.073 3630 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.10 % Allowed : 15.01 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.14), residues: 3150 helix: 0.94 (0.15), residues: 1104 sheet: -0.53 (0.19), residues: 582 loop : -0.27 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 190 TYR 0.028 0.003 TYR D 245 PHE 0.025 0.003 PHE C 187 TRP 0.017 0.003 TRP D 402 HIS 0.006 0.002 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00618 (26010) covalent geometry : angle 0.69212 (35274) hydrogen bonds : bond 0.05668 ( 996) hydrogen bonds : angle 6.06754 ( 2682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 375 time to evaluate : 1.251 Fit side-chains REVERT: A 119 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: A 163 ASP cc_start: 0.8441 (m-30) cc_final: 0.8149 (t70) REVERT: A 256 ASN cc_start: 0.8046 (t0) cc_final: 0.7822 (t0) REVERT: A 350 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (mttm) REVERT: A 484 GLU cc_start: 0.5088 (OUTLIER) cc_final: 0.4371 (pm20) REVERT: B 61 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7839 (mmtm) REVERT: B 119 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: B 309 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: B 338 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6882 (mt-10) REVERT: C 118 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: C 119 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: C 275 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8270 (mt) REVERT: C 350 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8219 (mttm) REVERT: C 484 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.4721 (pm20) REVERT: D 118 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: D 119 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: D 275 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8288 (mt) REVERT: D 350 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8227 (mttm) REVERT: D 484 GLU cc_start: 0.5604 (OUTLIER) cc_final: 0.4728 (pm20) REVERT: E 119 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: E 163 ASP cc_start: 0.8444 (m-30) cc_final: 0.8152 (t70) REVERT: E 256 ASN cc_start: 0.8037 (t0) cc_final: 0.7810 (t0) REVERT: E 350 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8536 (mttm) REVERT: E 484 GLU cc_start: 0.5088 (OUTLIER) cc_final: 0.4372 (pm20) REVERT: F 61 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7884 (mmtm) REVERT: F 119 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: F 309 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: F 338 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6886 (mt-10) REVERT: F 443 LEU cc_start: 0.7901 (mt) cc_final: 0.7675 (mt) outliers start: 86 outliers final: 40 residues processed: 436 average time/residue: 0.6717 time to fit residues: 341.0374 Evaluate side-chains 433 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 371 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 434 SER Chi-restraints excluded: chain F residue 468 GLU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 268 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN B 226 HIS C 160 ASN D 160 ASN E 160 ASN F 160 ASN F 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.161854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124592 restraints weight = 20039.549| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 0.83 r_work: 0.3037 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26010 Z= 0.146 Angle : 0.573 6.958 35274 Z= 0.297 Chirality : 0.047 0.221 3978 Planarity : 0.006 0.105 4470 Dihedral : 6.401 55.600 3630 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.13 % Allowed : 16.13 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.14), residues: 3150 helix: 1.13 (0.15), residues: 1104 sheet: -0.42 (0.19), residues: 582 loop : -0.24 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 190 TYR 0.017 0.001 TYR F 245 PHE 0.019 0.002 PHE A 81 TRP 0.012 0.002 TRP D 402 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00326 (26010) covalent geometry : angle 0.57324 (35274) hydrogen bonds : bond 0.04454 ( 996) hydrogen bonds : angle 5.76614 ( 2682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 365 time to evaluate : 1.014 Fit side-chains REVERT: A 119 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7939 (mm-30) REVERT: A 256 ASN cc_start: 0.8108 (t0) cc_final: 0.7899 (t0) REVERT: A 484 GLU cc_start: 0.4934 (OUTLIER) cc_final: 0.4319 (pm20) REVERT: B 61 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7743 (mmtm) REVERT: B 112 ASP cc_start: 0.8545 (m-30) cc_final: 0.8335 (m-30) REVERT: B 119 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: B 309 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: B 338 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6659 (mt-10) REVERT: C 113 ILE cc_start: 0.8472 (mt) cc_final: 0.8195 (mt) REVERT: C 118 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: C 350 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8238 (mttm) REVERT: C 484 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.4690 (pm20) REVERT: D 113 ILE cc_start: 0.8450 (mt) cc_final: 0.8178 (mt) REVERT: D 118 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: D 275 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8281 (mt) REVERT: D 350 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8236 (mttm) REVERT: D 484 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4665 (pm20) REVERT: E 119 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: E 256 ASN cc_start: 0.8107 (t0) cc_final: 0.7895 (t0) REVERT: E 484 GLU cc_start: 0.4948 (OUTLIER) cc_final: 0.4330 (pm20) REVERT: F 61 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7716 (mmtm) REVERT: F 112 ASP cc_start: 0.8555 (m-30) cc_final: 0.8347 (m-30) REVERT: F 119 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: F 309 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: F 338 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6669 (mt-10) REVERT: F 443 LEU cc_start: 0.7893 (mt) cc_final: 0.7649 (mt) outliers start: 59 outliers final: 32 residues processed: 412 average time/residue: 0.6396 time to fit residues: 306.9952 Evaluate side-chains 410 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN B 226 HIS C 160 ASN D 160 ASN E 160 ASN F 160 ASN F 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.122305 restraints weight = 20076.217| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.83 r_work: 0.3010 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26010 Z= 0.227 Angle : 0.653 10.613 35274 Z= 0.339 Chirality : 0.051 0.238 3978 Planarity : 0.006 0.106 4470 Dihedral : 6.757 60.409 3630 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 16.41 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.14), residues: 3150 helix: 1.04 (0.15), residues: 1104 sheet: -0.47 (0.19), residues: 582 loop : -0.25 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 190 TYR 0.025 0.002 TYR D 245 PHE 0.022 0.003 PHE C 187 TRP 0.014 0.002 TRP C 402 HIS 0.006 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00515 (26010) covalent geometry : angle 0.65334 (35274) hydrogen bonds : bond 0.05226 ( 996) hydrogen bonds : angle 5.93823 ( 2682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 365 time to evaluate : 1.056 Fit side-chains REVERT: A 119 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: A 163 ASP cc_start: 0.8347 (m-30) cc_final: 0.8076 (t70) REVERT: A 256 ASN cc_start: 0.8072 (t0) cc_final: 0.7855 (t0) REVERT: A 484 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.4300 (pm20) REVERT: B 61 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7843 (mmtm) REVERT: B 119 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: B 309 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: B 338 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6893 (mt-10) REVERT: C 118 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8109 (pt0) REVERT: C 275 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8254 (mt) REVERT: C 350 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8204 (mttm) REVERT: C 484 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.4682 (pm20) REVERT: D 118 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: D 275 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8262 (mt) REVERT: D 350 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8208 (mttm) REVERT: D 484 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.4669 (pm20) REVERT: E 119 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: E 163 ASP cc_start: 0.8341 (m-30) cc_final: 0.8067 (t70) REVERT: E 256 ASN cc_start: 0.8059 (t0) cc_final: 0.7842 (t0) REVERT: E 484 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.4310 (pm20) REVERT: F 61 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7838 (mmtm) REVERT: F 119 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: F 309 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: F 338 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6903 (mt-10) REVERT: F 443 LEU cc_start: 0.7817 (mt) cc_final: 0.7605 (mt) outliers start: 60 outliers final: 34 residues processed: 413 average time/residue: 0.6238 time to fit residues: 299.5027 Evaluate side-chains 416 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 364 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 171 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN B 226 HIS C 160 ASN D 160 ASN E 160 ASN F 160 ASN F 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.161369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 135)---------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112320 restraints weight = 19812.159| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.63 r_work: 0.2977 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26010 Z= 0.181 Angle : 0.613 11.108 35274 Z= 0.317 Chirality : 0.049 0.230 3978 Planarity : 0.006 0.106 4470 Dihedral : 6.576 57.756 3630 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.09 % Allowed : 16.49 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3150 helix: 1.07 (0.15), residues: 1104 sheet: -0.46 (0.19), residues: 582 loop : -0.25 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 190 TYR 0.021 0.002 TYR D 245 PHE 0.021 0.002 PHE A 81 TRP 0.013 0.002 TRP D 466 HIS 0.007 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00410 (26010) covalent geometry : angle 0.61320 (35274) hydrogen bonds : bond 0.04796 ( 996) hydrogen bonds : angle 5.83538 ( 2682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 364 time to evaluate : 1.069 Fit side-chains REVERT: A 119 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: A 256 ASN cc_start: 0.7944 (t0) cc_final: 0.7716 (t0) REVERT: A 484 GLU cc_start: 0.4871 (OUTLIER) cc_final: 0.4233 (pm20) REVERT: B 61 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7701 (mmtm) REVERT: B 119 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: B 309 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: C 113 ILE cc_start: 0.8511 (mt) cc_final: 0.8252 (mt) REVERT: C 118 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7952 (pt0) REVERT: C 275 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8107 (mt) REVERT: C 350 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8124 (mttm) REVERT: C 484 GLU cc_start: 0.5401 (OUTLIER) cc_final: 0.4577 (pm20) REVERT: D 113 ILE cc_start: 0.8507 (mt) cc_final: 0.8247 (mt) REVERT: D 118 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: D 275 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8105 (mt) REVERT: D 350 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8127 (mttm) REVERT: D 484 GLU cc_start: 0.5414 (OUTLIER) cc_final: 0.4582 (pm20) REVERT: E 119 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7813 (mm-30) REVERT: E 256 ASN cc_start: 0.7936 (t0) cc_final: 0.7706 (t0) REVERT: E 484 GLU cc_start: 0.4872 (OUTLIER) cc_final: 0.4233 (pm20) REVERT: F 61 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7725 (mmtm) REVERT: F 119 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: F 309 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: F 443 LEU cc_start: 0.7627 (mt) cc_final: 0.7388 (mt) outliers start: 58 outliers final: 33 residues processed: 412 average time/residue: 0.6705 time to fit residues: 321.8595 Evaluate side-chains 413 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 362 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 81 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN B 226 HIS C 160 ASN D 160 ASN E 160 ASN F 160 ASN F 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.163006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125631 restraints weight = 19980.444| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 0.85 r_work: 0.3054 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work: 0.2802 rms_B_bonded: 4.77 restraints_weight: 0.1250 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26010 Z= 0.132 Angle : 0.568 10.916 35274 Z= 0.293 Chirality : 0.046 0.213 3978 Planarity : 0.005 0.102 4470 Dihedral : 6.199 54.325 3628 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.91 % Allowed : 16.88 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 3150 helix: 1.20 (0.15), residues: 1104 sheet: -0.37 (0.20), residues: 582 loop : -0.23 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 47 TYR 0.015 0.001 TYR E 245 PHE 0.018 0.002 PHE A 81 TRP 0.015 0.002 TRP D 466 HIS 0.006 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00294 (26010) covalent geometry : angle 0.56790 (35274) hydrogen bonds : bond 0.04181 ( 996) hydrogen bonds : angle 5.63335 ( 2682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11262.82 seconds wall clock time: 192 minutes 44.44 seconds (11564.44 seconds total)