Starting phenix.real_space_refine on Sat Jun 21 20:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyl_36725/06_2025/8jyl_36725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyl_36725/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jyl_36725/06_2025/8jyl_36725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyl_36725/06_2025/8jyl_36725.map" model { file = "/net/cci-nas-00/data/ceres_data/8jyl_36725/06_2025/8jyl_36725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyl_36725/06_2025/8jyl_36725.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 10.84, per 1000 atoms: 0.43 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: 6.13 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.41 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: 9.87 Time building geometry restraints manager: 6.92 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 52.760 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (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 TRP 0.009 0.002 TRP C 402 HIS 0.007 0.001 HIS E 228 PHE 0.017 0.002 PHE F 287 TYR 0.021 0.002 TYR D 245 ARG 0.003 0.000 ARG C 383 Details of bonding type rmsd hydrogen bonds : bond 0.22428 ( 996) hydrogen bonds : angle 8.05245 ( 2682) covalent geometry : bond 0.00877 (26010) covalent geometry : angle 0.71006 (35274) *********************** 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 : 2.733 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: 1.2992 time to fit residues: 618.0376 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 : 2.823 ------------------------------------------------------------------------------- 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 263 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 283 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS B 274 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 274 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 274 HIS D 344 GLN D 390 ASN E 29 GLN E 108 HIS E 160 ASN E 195 HIS E 267 HIS E 274 HIS E 390 ASN F 17 ASN F 29 GLN F 108 HIS F 160 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 267 HIS F 390 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137417 restraints weight = 20315.373| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.45 r_work: 0.2947 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0998 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= 0.230 Angle : 0.655 7.173 35274 Z= 0.346 Chirality : 0.051 0.255 3978 Planarity : 0.006 0.101 4470 Dihedral : 7.123 61.015 3644 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.28 % Allowed : 14.39 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3150 helix: 0.83 (0.15), residues: 1104 sheet: -0.54 (0.19), residues: 582 loop : -0.19 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 402 HIS 0.008 0.002 HIS F 274 PHE 0.026 0.003 PHE C 187 TYR 0.025 0.002 TYR D 245 ARG 0.004 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.06060 ( 996) hydrogen bonds : angle 6.31600 ( 2682) covalent geometry : bond 0.00520 (26010) covalent geometry : angle 0.65512 (35274) *********************** 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 476 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 385 time to evaluate : 2.643 Fit side-chains REVERT: A 119 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: A 484 GLU cc_start: 0.5279 (OUTLIER) cc_final: 0.4360 (pm20) REVERT: B 61 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7697 (mmtm) REVERT: B 118 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: B 119 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: B 286 ASP cc_start: 0.7895 (t0) cc_final: 0.7691 (t0) REVERT: B 309 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: B 338 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6701 (mm-30) REVERT: C 118 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: C 119 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: C 350 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8206 (mttm) REVERT: C 466 TRP cc_start: 0.8406 (m100) cc_final: 0.8134 (m100) REVERT: C 484 GLU cc_start: 0.5521 (OUTLIER) cc_final: 0.4544 (pm20) REVERT: D 118 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: D 119 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: D 275 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8185 (mt) REVERT: D 350 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8201 (mttm) REVERT: D 466 TRP cc_start: 0.8410 (m100) cc_final: 0.8137 (m100) REVERT: D 468 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7144 (mt-10) REVERT: D 484 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.4555 (pm20) REVERT: E 119 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: E 484 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4357 (pm20) REVERT: F 61 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7694 (mmtm) REVERT: F 118 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: F 119 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: F 125 ASP cc_start: 0.7533 (m-30) cc_final: 0.7332 (m-30) REVERT: F 286 ASP cc_start: 0.7898 (t0) cc_final: 0.7696 (t0) REVERT: F 309 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: F 338 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6704 (mm-30) REVERT: F 443 LEU cc_start: 0.7649 (mt) cc_final: 0.7422 (mt) outliers start: 91 outliers final: 26 residues processed: 448 average time/residue: 1.3212 time to fit residues: 686.7990 Evaluate side-chains 414 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 367 time to evaluate : 2.999 ------------------------------------------------------------------------------- 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 296 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 277 optimal weight: 0.0070 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.3404 ------------------------------------------------------------------------------- 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 A 274 HIS B 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 195 HIS F 226 HIS F 274 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139453 restraints weight = 20366.340| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.46 r_work: 0.3193 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1213 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= 0.143 Angle : 0.562 5.922 35274 Z= 0.294 Chirality : 0.046 0.218 3978 Planarity : 0.005 0.099 4470 Dihedral : 6.310 55.872 3630 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.16 % Allowed : 15.58 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3150 helix: 1.10 (0.15), residues: 1104 sheet: -0.37 (0.20), residues: 582 loop : -0.20 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 402 HIS 0.006 0.001 HIS F 274 PHE 0.017 0.002 PHE A 81 TYR 0.016 0.001 TYR E 245 ARG 0.002 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 996) hydrogen bonds : angle 5.89085 ( 2682) covalent geometry : bond 0.00318 (26010) covalent geometry : angle 0.56161 (35274) *********************** 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 431 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 371 time to evaluate : 3.120 Fit side-chains REVERT: A 256 ASN cc_start: 0.8161 (t0) cc_final: 0.7933 (t0) REVERT: A 484 GLU cc_start: 0.5080 (OUTLIER) cc_final: 0.4293 (pm20) REVERT: B 61 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7644 (mmtm) REVERT: B 119 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: B 125 ASP cc_start: 0.7572 (m-30) cc_final: 0.7368 (m-30) REVERT: B 309 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: B 338 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6626 (mm-30) REVERT: B 468 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7115 (mt-10) REVERT: C 113 ILE cc_start: 0.8365 (mt) cc_final: 0.8092 (mt) REVERT: C 118 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: C 275 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (mt) REVERT: C 484 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.4612 (pm20) REVERT: D 113 ILE cc_start: 0.8365 (mt) cc_final: 0.8092 (mt) REVERT: D 118 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: D 275 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8206 (mt) REVERT: D 484 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.4625 (pm20) REVERT: E 256 ASN cc_start: 0.8150 (t0) cc_final: 0.7922 (t0) REVERT: E 484 GLU cc_start: 0.5084 (OUTLIER) cc_final: 0.4298 (pm20) REVERT: F 61 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7650 (mmtm) REVERT: F 119 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: F 309 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: F 338 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6625 (mm-30) REVERT: F 443 LEU cc_start: 0.7589 (mt) cc_final: 0.7356 (mt) REVERT: F 468 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7133 (mt-10) outliers start: 60 outliers final: 22 residues processed: 417 average time/residue: 1.6537 time to fit residues: 815.8748 Evaluate side-chains 402 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 366 time to evaluate : 3.501 ------------------------------------------------------------------------------- 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 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 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 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 520 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 285 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 195 HIS B 206 ASN B 226 HIS C 160 ASN C 195 HIS D 160 ASN D 195 HIS E 160 ASN E 195 HIS F 206 ASN F 226 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.163374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125702 restraints weight = 19910.893| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 0.85 r_work: 0.3051 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26010 Z= 0.133 Angle : 0.544 5.712 35274 Z= 0.283 Chirality : 0.046 0.210 3978 Planarity : 0.005 0.096 4470 Dihedral : 6.176 55.973 3630 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.45 % Allowed : 15.30 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3150 helix: 1.23 (0.15), residues: 1104 sheet: -0.28 (0.20), residues: 582 loop : -0.21 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 402 HIS 0.004 0.001 HIS D 414 PHE 0.017 0.002 PHE E 81 TYR 0.015 0.001 TYR C 245 ARG 0.002 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 996) hydrogen bonds : angle 5.71434 ( 2682) covalent geometry : bond 0.00293 (26010) covalent geometry : angle 0.54420 (35274) *********************** 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 436 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 368 time to evaluate : 4.285 Fit side-chains REVERT: A 256 ASN cc_start: 0.8091 (t0) cc_final: 0.7865 (t0) REVERT: A 484 GLU cc_start: 0.4946 (OUTLIER) cc_final: 0.4351 (pm20) REVERT: B 61 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7742 (mmtm) REVERT: B 119 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: B 309 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: B 338 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6510 (mm-30) REVERT: B 428 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6965 (pttp) REVERT: B 468 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7091 (mt-10) REVERT: C 113 ILE cc_start: 0.8214 (mt) cc_final: 0.7932 (mt) REVERT: C 118 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: C 275 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8242 (mt) REVERT: C 484 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.4665 (pm20) REVERT: D 113 ILE cc_start: 0.8208 (mt) cc_final: 0.7929 (mt) REVERT: D 118 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: D 275 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8250 (mt) REVERT: D 484 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.4657 (pm20) REVERT: E 256 ASN cc_start: 0.8083 (t0) cc_final: 0.7858 (t0) REVERT: E 484 GLU cc_start: 0.4946 (OUTLIER) cc_final: 0.4349 (pm20) REVERT: F 61 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7731 (mmtm) REVERT: F 119 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: F 309 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: F 338 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6510 (mm-30) REVERT: F 428 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6970 (pttp) REVERT: F 443 LEU cc_start: 0.7794 (mt) cc_final: 0.7553 (mt) REVERT: F 468 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7104 (mt-10) outliers start: 68 outliers final: 24 residues processed: 416 average time/residue: 1.7277 time to fit residues: 838.0018 Evaluate side-chains 395 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 355 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 453 VAL 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 428 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 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 453 VAL 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 453 VAL 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 453 VAL 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 428 LYS Chi-restraints excluded: chain F residue 482 VAL 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 221 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 78 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS C 160 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 226 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.160555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122631 restraints weight = 19836.593| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.84 r_work: 0.3004 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26010 Z= 0.214 Angle : 0.628 6.604 35274 Z= 0.327 Chirality : 0.050 0.230 3978 Planarity : 0.006 0.102 4470 Dihedral : 6.646 60.970 3630 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.78 % Allowed : 15.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3150 helix: 1.10 (0.15), residues: 1104 sheet: -0.38 (0.19), residues: 582 loop : -0.23 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 402 HIS 0.005 0.001 HIS B 274 PHE 0.022 0.003 PHE C 187 TYR 0.024 0.002 TYR C 245 ARG 0.003 0.001 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.05186 ( 996) hydrogen bonds : angle 5.93080 ( 2682) covalent geometry : bond 0.00484 (26010) covalent geometry : angle 0.62756 (35274) *********************** 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 450 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 373 time to evaluate : 2.638 Fit side-chains REVERT: A 256 ASN cc_start: 0.8064 (t0) cc_final: 0.7833 (t0) REVERT: A 350 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8590 (mttm) REVERT: A 484 GLU cc_start: 0.5040 (OUTLIER) cc_final: 0.4360 (pm20) REVERT: B 61 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7800 (mmtm) REVERT: B 118 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: B 119 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: B 309 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: B 338 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6560 (mm-30) REVERT: C 113 ILE cc_start: 0.8573 (mt) cc_final: 0.8308 (mt) REVERT: C 118 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: C 275 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8280 (mt) REVERT: C 350 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8251 (mttm) REVERT: C 484 GLU cc_start: 0.5513 (OUTLIER) cc_final: 0.4681 (pm20) REVERT: D 113 ILE cc_start: 0.8569 (mt) cc_final: 0.8305 (mt) REVERT: D 118 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: D 275 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8269 (mt) REVERT: D 350 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8251 (mttm) REVERT: D 484 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.4680 (pm20) REVERT: E 256 ASN cc_start: 0.8064 (t0) cc_final: 0.7833 (t0) REVERT: E 350 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8583 (mttm) REVERT: E 484 GLU cc_start: 0.5046 (OUTLIER) cc_final: 0.4364 (pm20) REVERT: F 61 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7791 (mmtm) REVERT: F 118 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8257 (pt0) REVERT: F 119 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: F 309 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: F 338 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6563 (mm-30) REVERT: F 443 LEU cc_start: 0.7844 (mt) cc_final: 0.7599 (mt) outliers start: 77 outliers final: 32 residues processed: 431 average time/residue: 1.2434 time to fit residues: 624.3184 Evaluate side-chains 422 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 370 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 482 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 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 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 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 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 482 VAL 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 235 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 214 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 279 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 195 HIS B 226 HIS C 160 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN D 160 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN E 160 ASN F 226 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.160826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114356 restraints weight = 19659.871| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.55 r_work: 0.2920 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1308 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= 0.212 Angle : 0.628 6.721 35274 Z= 0.327 Chirality : 0.050 0.231 3978 Planarity : 0.006 0.104 4470 Dihedral : 6.678 59.912 3630 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.85 % Allowed : 15.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3150 helix: 1.05 (0.15), residues: 1104 sheet: -0.44 (0.19), residues: 582 loop : -0.25 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 402 HIS 0.005 0.001 HIS C 274 PHE 0.022 0.003 PHE D 187 TYR 0.024 0.002 TYR C 245 ARG 0.003 0.001 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 996) hydrogen bonds : angle 5.93404 ( 2682) covalent geometry : bond 0.00480 (26010) covalent geometry : angle 0.62775 (35274) *********************** 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 447 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 368 time to evaluate : 2.779 Fit side-chains REVERT: A 119 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: A 256 ASN cc_start: 0.7902 (t0) cc_final: 0.7660 (t0) REVERT: A 484 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.4273 (pm20) REVERT: B 61 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7742 (mmtm) REVERT: B 118 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8123 (pt0) REVERT: B 119 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: B 309 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: B 338 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6698 (mt-10) REVERT: C 113 ILE cc_start: 0.8550 (mt) cc_final: 0.8310 (mt) REVERT: C 118 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: C 119 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: C 275 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8047 (mt) REVERT: C 350 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8141 (mttm) REVERT: C 484 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4577 (pm20) REVERT: D 113 ILE cc_start: 0.8551 (mt) cc_final: 0.8308 (mt) REVERT: D 118 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: D 275 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8070 (mt) REVERT: D 350 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8141 (mttm) REVERT: D 484 GLU cc_start: 0.5437 (OUTLIER) cc_final: 0.4581 (pm20) REVERT: E 119 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: E 256 ASN cc_start: 0.7899 (t0) cc_final: 0.7656 (t0) REVERT: E 484 GLU cc_start: 0.4959 (OUTLIER) cc_final: 0.4268 (pm20) REVERT: F 61 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7732 (mmtm) REVERT: F 119 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: F 309 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: F 338 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6715 (mt-10) REVERT: F 443 LEU cc_start: 0.7608 (mt) cc_final: 0.7393 (mt) outliers start: 79 outliers final: 36 residues processed: 425 average time/residue: 1.5844 time to fit residues: 785.5633 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 : 3.386 ------------------------------------------------------------------------------- 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 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 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 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 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 269 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 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 = 0.3735 r_free = 0.3735 target = 0.160308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.122339 restraints weight = 19824.552| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 0.83 r_work: 0.3003 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1326 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= 0.217 Angle : 0.640 8.011 35274 Z= 0.333 Chirality : 0.050 0.235 3978 Planarity : 0.006 0.105 4470 Dihedral : 6.729 59.734 3630 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.89 % Allowed : 15.26 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3150 helix: 1.02 (0.15), residues: 1104 sheet: -0.46 (0.19), residues: 582 loop : -0.26 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 402 HIS 0.005 0.001 HIS B 274 PHE 0.022 0.003 PHE D 187 TYR 0.025 0.002 TYR C 245 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.05192 ( 996) hydrogen bonds : angle 5.94848 ( 2682) covalent geometry : bond 0.00492 (26010) covalent geometry : angle 0.63971 (35274) *********************** 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 455 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 375 time to evaluate : 2.906 Fit side-chains REVERT: A 119 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: A 163 ASP cc_start: 0.8377 (m-30) cc_final: 0.8107 (t70) REVERT: A 256 ASN cc_start: 0.8064 (t0) cc_final: 0.7755 (t0) REVERT: A 281 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7282 (tttt) REVERT: A 350 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8598 (mttm) REVERT: A 484 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.4387 (pm20) REVERT: B 61 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7825 (mmtm) REVERT: B 118 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (pt0) REVERT: B 119 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: B 309 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: B 338 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6925 (mt-10) REVERT: C 118 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: C 119 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: C 275 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8274 (mt) REVERT: C 350 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8239 (mttm) REVERT: C 484 GLU cc_start: 0.5551 (OUTLIER) cc_final: 0.4732 (pm20) REVERT: D 118 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8149 (pt0) REVERT: D 275 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8281 (mt) REVERT: D 350 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8239 (mttm) REVERT: D 484 GLU cc_start: 0.5534 (OUTLIER) cc_final: 0.4712 (pm20) REVERT: E 119 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: E 163 ASP cc_start: 0.8371 (m-30) cc_final: 0.8102 (t70) REVERT: E 256 ASN cc_start: 0.8070 (t0) cc_final: 0.7761 (t0) REVERT: E 281 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7287 (tttt) REVERT: E 350 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8599 (mttm) REVERT: E 484 GLU cc_start: 0.5060 (OUTLIER) cc_final: 0.4398 (pm20) REVERT: F 61 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7820 (mmtm) REVERT: F 119 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: F 309 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: F 338 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6927 (mt-10) REVERT: F 443 LEU cc_start: 0.7940 (mt) cc_final: 0.7719 (mt) outliers start: 80 outliers final: 38 residues processed: 430 average time/residue: 1.2820 time to fit residues: 642.5167 Evaluate side-chains 435 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 373 time to evaluate : 2.732 ------------------------------------------------------------------------------- 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 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 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 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 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 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 34 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 311 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 176 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 C 195 HIS D 160 ASN D 195 HIS E 160 ASN F 160 ASN F 226 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.162677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.125266 restraints weight = 19914.851| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 0.84 r_work: 0.3047 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26010 Z= 0.136 Angle : 0.560 7.616 35274 Z= 0.290 Chirality : 0.046 0.214 3978 Planarity : 0.005 0.102 4470 Dihedral : 6.288 55.133 3630 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.56 % Allowed : 15.80 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3150 helix: 1.19 (0.15), residues: 1104 sheet: -0.36 (0.20), residues: 582 loop : -0.23 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 402 HIS 0.004 0.001 HIS F 414 PHE 0.018 0.002 PHE A 81 TYR 0.016 0.001 TYR A 245 ARG 0.003 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 996) hydrogen bonds : angle 5.68899 ( 2682) covalent geometry : bond 0.00302 (26010) covalent geometry : angle 0.56038 (35274) *********************** 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 435 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 364 time to evaluate : 4.879 Fit side-chains REVERT: A 119 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: A 256 ASN cc_start: 0.8095 (t0) cc_final: 0.7802 (t0) REVERT: A 281 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7250 (tttt) REVERT: A 484 GLU cc_start: 0.4904 (OUTLIER) cc_final: 0.4322 (pm20) REVERT: B 61 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7766 (mmtm) REVERT: B 119 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: B 309 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: B 338 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6694 (mt-10) REVERT: C 118 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: C 275 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8263 (mt) REVERT: C 484 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.4751 (pm20) REVERT: D 118 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: D 275 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8265 (mt) REVERT: D 484 GLU cc_start: 0.5382 (OUTLIER) cc_final: 0.4727 (pm20) REVERT: E 119 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: E 256 ASN cc_start: 0.8092 (t0) cc_final: 0.7797 (t0) REVERT: E 281 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7256 (tttt) REVERT: E 484 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.4336 (pm20) REVERT: F 61 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7759 (mmtm) REVERT: F 118 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: F 119 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: F 309 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: F 338 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6685 (mt-10) REVERT: F 443 LEU cc_start: 0.7863 (mt) cc_final: 0.7631 (mt) outliers start: 71 outliers final: 30 residues processed: 418 average time/residue: 2.2161 time to fit residues: 1103.3773 Evaluate side-chains 412 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 363 time to evaluate : 6.612 ------------------------------------------------------------------------------- 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 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 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 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 281 LYS 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 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 219 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 304 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.160987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125209 restraints weight = 19903.064| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 0.77 r_work: 0.3052 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 26010 Z= 0.205 Angle : 0.632 11.333 35274 Z= 0.328 Chirality : 0.050 0.231 3978 Planarity : 0.006 0.104 4470 Dihedral : 6.637 59.232 3630 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.16 % Allowed : 16.59 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3150 helix: 1.10 (0.15), residues: 1104 sheet: -0.42 (0.19), residues: 582 loop : -0.25 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 402 HIS 0.005 0.001 HIS B 274 PHE 0.021 0.003 PHE E 81 TYR 0.024 0.002 TYR C 245 ARG 0.006 0.001 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 996) hydrogen bonds : angle 5.86291 ( 2682) covalent geometry : bond 0.00464 (26010) covalent geometry : angle 0.63233 (35274) *********************** 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 424 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 364 time to evaluate : 3.123 Fit side-chains REVERT: A 119 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7901 (mm-30) REVERT: A 163 ASP cc_start: 0.8335 (m-30) cc_final: 0.8081 (t70) REVERT: A 256 ASN cc_start: 0.8091 (t0) cc_final: 0.7787 (t0) REVERT: A 281 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7258 (tttt) REVERT: A 484 GLU cc_start: 0.4995 (OUTLIER) cc_final: 0.4363 (pm20) REVERT: B 61 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7801 (mmtm) REVERT: B 119 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: B 309 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: B 338 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6862 (mt-10) REVERT: B 493 ASP cc_start: 0.7162 (t70) cc_final: 0.6960 (t70) REVERT: C 118 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: C 119 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: C 275 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8263 (mt) REVERT: C 484 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.4673 (pm20) REVERT: D 118 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: D 275 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8259 (mt) REVERT: D 484 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4727 (pm20) REVERT: E 119 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: E 256 ASN cc_start: 0.8082 (t0) cc_final: 0.7776 (t0) REVERT: E 281 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7257 (tttt) REVERT: E 484 GLU cc_start: 0.5015 (OUTLIER) cc_final: 0.4375 (pm20) REVERT: F 61 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7798 (mmtm) REVERT: F 118 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: F 119 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: F 309 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: F 338 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6865 (mt-10) REVERT: F 443 LEU cc_start: 0.7813 (mt) cc_final: 0.7578 (mt) outliers start: 60 outliers final: 34 residues processed: 410 average time/residue: 1.4838 time to fit residues: 707.1388 Evaluate side-chains 419 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 365 time to evaluate : 3.044 ------------------------------------------------------------------------------- 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 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 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 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 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 281 LYS 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 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 229 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 308 optimal weight: 7.9990 chunk 149 optimal weight: 30.0000 chunk 283 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.163692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3216 r_free = 0.3216 target = 0.115011 restraints weight = 19851.293| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.64 r_work: 0.3013 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26010 Z= 0.133 Angle : 0.564 9.998 35274 Z= 0.292 Chirality : 0.046 0.212 3978 Planarity : 0.005 0.101 4470 Dihedral : 6.215 54.406 3630 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.88 % Allowed : 17.03 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3150 helix: 1.19 (0.15), residues: 1110 sheet: -0.33 (0.20), residues: 582 loop : -0.22 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 466 HIS 0.004 0.001 HIS F 414 PHE 0.019 0.002 PHE E 81 TYR 0.014 0.001 TYR A 245 ARG 0.006 0.000 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 996) hydrogen bonds : angle 5.63159 ( 2682) covalent geometry : bond 0.00295 (26010) covalent geometry : angle 0.56444 (35274) ********************** 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 404 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 352 time to evaluate : 2.603 Fit side-chains REVERT: A 256 ASN cc_start: 0.8115 (t0) cc_final: 0.7910 (t0) REVERT: A 484 GLU cc_start: 0.4889 (OUTLIER) cc_final: 0.4322 (pm20) REVERT: B 61 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7766 (mmtm) REVERT: B 118 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: B 119 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: B 309 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: B 338 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6745 (mt-10) REVERT: C 118 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: C 275 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8252 (mt) REVERT: D 118 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: D 275 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8257 (mt) REVERT: E 256 ASN cc_start: 0.8110 (t0) cc_final: 0.7905 (t0) REVERT: E 484 GLU cc_start: 0.4899 (OUTLIER) cc_final: 0.4331 (pm20) REVERT: F 61 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7741 (mmtm) REVERT: F 118 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: F 119 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7736 (mm-30) REVERT: F 309 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: F 338 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6752 (mt-10) REVERT: F 443 LEU cc_start: 0.7861 (mt) cc_final: 0.7636 (mt) outliers start: 52 outliers final: 29 residues processed: 395 average time/residue: 1.3189 time to fit residues: 606.2990 Evaluate side-chains 396 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 353 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE 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 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 309 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 453 VAL 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 520 VAL Chi-restraints excluded: chain E residue 221 ILE 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 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 309 GLU 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 228 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.162666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129575 restraints weight = 19888.803| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 0.78 r_work: 0.3096 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26010 Z= 0.156 Angle : 0.590 13.211 35274 Z= 0.304 Chirality : 0.047 0.220 3978 Planarity : 0.005 0.102 4470 Dihedral : 6.340 56.683 3630 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.88 % Allowed : 17.28 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3150 helix: 1.17 (0.15), residues: 1110 sheet: -0.33 (0.20), residues: 582 loop : -0.22 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 402 HIS 0.004 0.001 HIS B 414 PHE 0.020 0.002 PHE E 81 TYR 0.019 0.002 TYR D 245 ARG 0.006 0.000 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 996) hydrogen bonds : angle 5.68678 ( 2682) covalent geometry : bond 0.00350 (26010) covalent geometry : angle 0.58962 (35274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24759.57 seconds wall clock time: 437 minutes 44.25 seconds (26264.25 seconds total)