Starting phenix.real_space_refine on Sat May 24 07:45:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyl_36725/05_2025/8jyl_36725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyl_36725/05_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_36725/05_2025/8jyl_36725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyl_36725/05_2025/8jyl_36725.map" model { file = "/net/cci-nas-00/data/ceres_data/8jyl_36725/05_2025/8jyl_36725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyl_36725/05_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-5687/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: 9.99, per 1000 atoms: 0.39 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: 5.75 Conformation dependent library (CDL) restraints added in 2.9 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: 3.51 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: 8.88 Time building geometry restraints manager: 6.69 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: 0.19 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: 1.770 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: 0.030 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 49.250 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.910 ------------------------------------------------------------------------------- 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 : 2.863 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: 1.2746 time to fit residues: 608.1136 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 : 2.748 ------------------------------------------------------------------------------- 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: 3.63 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 2.773 Fit side-chains REVERT: A 119 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8032 (mm-30) REVERT: A 484 GLU cc_start: 0.5278 (OUTLIER) cc_final: 0.4359 (pm20) REVERT: B 61 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7700 (mmtm) REVERT: B 118 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: B 119 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: B 125 ASP cc_start: 0.7546 (m-30) cc_final: 0.7345 (m-30) REVERT: B 286 ASP cc_start: 0.7900 (t0) cc_final: 0.7697 (t0) REVERT: B 309 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: B 338 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6706 (mm-30) REVERT: C 118 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: C 119 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: C 350 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8212 (mttm) REVERT: C 466 TRP cc_start: 0.8410 (m100) cc_final: 0.8139 (m100) REVERT: C 484 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.4544 (pm20) REVERT: D 118 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: D 119 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: D 275 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8195 (mt) REVERT: D 350 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8207 (mttm) REVERT: D 466 TRP cc_start: 0.8412 (m100) cc_final: 0.8140 (m100) REVERT: D 468 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7143 (mt-10) REVERT: D 484 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.4554 (pm20) REVERT: E 119 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: E 484 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4356 (pm20) REVERT: F 61 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7698 (mmtm) REVERT: F 118 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: F 119 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: F 125 ASP cc_start: 0.7540 (m-30) cc_final: 0.7337 (m-30) REVERT: F 286 ASP cc_start: 0.7904 (t0) cc_final: 0.7703 (t0) REVERT: F 309 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: F 338 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6712 (mm-30) REVERT: F 443 LEU cc_start: 0.7642 (mt) cc_final: 0.7417 (mt) outliers start: 91 outliers final: 26 residues processed: 448 average time/residue: 1.2414 time to fit residues: 649.2785 Evaluate side-chains 413 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 366 time to evaluate : 2.837 ------------------------------------------------------------------------------- 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: 5.9990 chunk 257 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 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: 1.3202 ------------------------------------------------------------------------------- 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 F 195 HIS F 226 HIS F 274 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.179687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139698 restraints weight = 20378.584| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.46 r_work: 0.3102 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1230 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= 0.140 Angle : 0.558 5.907 35274 Z= 0.292 Chirality : 0.046 0.217 3978 Planarity : 0.005 0.099 4470 Dihedral : 6.284 55.544 3630 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.13 % Allowed : 15.58 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.14), residues: 3150 helix: 1.11 (0.15), residues: 1104 sheet: -0.36 (0.20), residues: 582 loop : -0.20 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 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 0.04663 ( 996) hydrogen bonds : angle 5.86976 ( 2682) covalent geometry : bond 0.00311 (26010) covalent geometry : angle 0.55849 (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 430 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 371 time to evaluate : 3.099 Fit side-chains REVERT: A 256 ASN cc_start: 0.8142 (t0) cc_final: 0.7916 (t0) REVERT: A 484 GLU cc_start: 0.5071 (OUTLIER) cc_final: 0.4291 (pm20) REVERT: B 61 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7634 (mmtm) REVERT: B 112 ASP cc_start: 0.8610 (m-30) cc_final: 0.8410 (m-30) REVERT: B 119 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: B 309 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: B 338 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6619 (mm-30) REVERT: B 468 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7113 (mt-10) REVERT: C 113 ILE cc_start: 0.8358 (mt) cc_final: 0.8089 (mt) REVERT: C 118 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: C 275 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8197 (mt) REVERT: C 484 GLU cc_start: 0.5495 (OUTLIER) cc_final: 0.4608 (pm20) REVERT: D 113 ILE cc_start: 0.8357 (mt) cc_final: 0.8088 (mt) REVERT: D 118 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8167 (pt0) REVERT: D 275 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8207 (mt) REVERT: D 484 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.4623 (pm20) REVERT: E 256 ASN cc_start: 0.8138 (t0) cc_final: 0.7912 (t0) REVERT: E 484 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.4301 (pm20) REVERT: F 61 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7639 (mmtm) REVERT: F 119 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: F 309 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: F 338 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6619 (mm-30) REVERT: F 443 LEU cc_start: 0.7592 (mt) cc_final: 0.7359 (mt) REVERT: F 468 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7124 (mt-10) outliers start: 59 outliers final: 20 residues processed: 416 average time/residue: 1.2794 time to fit residues: 626.9222 Evaluate side-chains 401 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 367 time to evaluate : 3.115 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 236 optimal weight: 0.0570 chunk 285 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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 206 ASN B 226 HIS C 160 ASN C 195 HIS D 160 ASN D 195 HIS E 160 ASN F 206 ASN F 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.165183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121042 restraints weight = 19986.670| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.43 r_work: 0.3015 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 26010 Z= 0.112 Angle : 0.519 5.716 35274 Z= 0.269 Chirality : 0.045 0.201 3978 Planarity : 0.005 0.092 4470 Dihedral : 5.951 54.055 3630 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.60 % Allowed : 14.97 % Favored : 82.43 % 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: 0.39 (0.15), residues: 3150 helix: 1.20 (0.15), residues: 1122 sheet: -0.23 (0.20), residues: 582 loop : -0.17 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 402 HIS 0.004 0.001 HIS C 414 PHE 0.014 0.002 PHE E 81 TYR 0.012 0.001 TYR C 245 ARG 0.001 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 996) hydrogen bonds : angle 5.55853 ( 2682) covalent geometry : bond 0.00244 (26010) covalent geometry : angle 0.51926 (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 439 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 367 time to evaluate : 2.881 Fit side-chains REVERT: A 256 ASN cc_start: 0.7992 (t0) cc_final: 0.7756 (t0) REVERT: A 441 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7482 (mt) REVERT: A 484 GLU cc_start: 0.4815 (OUTLIER) cc_final: 0.4251 (pm20) REVERT: B 61 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7626 (mmtm) REVERT: B 113 ILE cc_start: 0.8377 (mt) cc_final: 0.8130 (mt) REVERT: B 119 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7722 (mm-30) REVERT: B 309 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 428 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6772 (pttp) REVERT: B 468 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7022 (mt-10) REVERT: C 113 ILE cc_start: 0.8082 (mt) cc_final: 0.7812 (mt) REVERT: C 118 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: C 275 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8095 (mt) REVERT: C 484 GLU cc_start: 0.5294 (OUTLIER) cc_final: 0.4596 (pm20) REVERT: D 113 ILE cc_start: 0.8073 (mt) cc_final: 0.7812 (mt) REVERT: D 118 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: D 275 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8099 (mt) REVERT: D 484 GLU cc_start: 0.5301 (OUTLIER) cc_final: 0.4585 (pm20) REVERT: E 256 ASN cc_start: 0.7989 (t0) cc_final: 0.7751 (t0) REVERT: E 441 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7487 (mt) REVERT: E 484 GLU cc_start: 0.4805 (OUTLIER) cc_final: 0.4239 (pm20) REVERT: F 61 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7643 (mmtm) REVERT: F 113 ILE cc_start: 0.8383 (mt) cc_final: 0.8137 (mt) REVERT: F 119 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7712 (mm-30) REVERT: F 309 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: F 428 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6777 (pttp) REVERT: F 443 LEU cc_start: 0.7539 (mt) cc_final: 0.7312 (mt) REVERT: F 468 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7032 (mt-10) outliers start: 72 outliers final: 18 residues processed: 419 average time/residue: 1.2124 time to fit residues: 595.8760 Evaluate side-chains 394 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 358 time to evaluate : 2.680 ------------------------------------------------------------------------------- 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 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 309 GLU 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 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 309 GLU 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: 4.9990 chunk 225 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 287 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 103 optimal weight: 40.0000 chunk 78 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 39 HIS 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** D 344 GLN E 160 ASN F 39 HIS F 226 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.161205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123361 restraints weight = 19878.613| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 0.85 r_work: 0.3014 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26010 Z= 0.195 Angle : 0.609 6.319 35274 Z= 0.317 Chirality : 0.049 0.224 3978 Planarity : 0.006 0.100 4470 Dihedral : 6.512 59.200 3630 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.67 % Allowed : 15.15 % Favored : 82.18 % 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: 0.30 (0.14), residues: 3150 helix: 1.16 (0.15), residues: 1104 sheet: -0.30 (0.20), residues: 582 loop : -0.22 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 402 HIS 0.005 0.001 HIS B 274 PHE 0.021 0.003 PHE C 81 TYR 0.023 0.002 TYR D 245 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 996) hydrogen bonds : angle 5.84361 ( 2682) covalent geometry : bond 0.00441 (26010) covalent geometry : angle 0.60916 (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 447 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 373 time to evaluate : 2.799 Fit side-chains REVERT: A 256 ASN cc_start: 0.8098 (t0) cc_final: 0.7874 (t0) REVERT: A 484 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4358 (pm20) REVERT: B 61 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7782 (mmtm) REVERT: B 118 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: B 119 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: B 309 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: B 338 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6560 (mm-30) REVERT: C 113 ILE cc_start: 0.8493 (mt) cc_final: 0.8229 (mt) REVERT: C 118 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8064 (pt0) REVERT: C 275 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8252 (mt) REVERT: C 350 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8222 (mttm) REVERT: C 484 GLU cc_start: 0.5494 (OUTLIER) cc_final: 0.4694 (pm20) REVERT: D 113 ILE cc_start: 0.8488 (mt) cc_final: 0.8226 (mt) REVERT: D 118 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8079 (pt0) REVERT: D 275 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8262 (mt) REVERT: D 350 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8222 (mttm) REVERT: D 484 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4694 (pm20) REVERT: E 256 ASN cc_start: 0.8083 (t0) cc_final: 0.7860 (t0) REVERT: E 484 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.4368 (pm20) REVERT: F 61 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7779 (mmtm) REVERT: F 118 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: F 119 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: F 309 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: F 338 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6565 (mm-30) REVERT: F 443 LEU cc_start: 0.7781 (mt) cc_final: 0.7544 (mt) outliers start: 74 outliers final: 30 residues processed: 429 average time/residue: 1.2255 time to fit residues: 613.9651 Evaluate side-chains 415 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 367 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 484 GLU Chi-restraints excluded: chain D residue 520 VAL 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 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: 9.9990 chunk 219 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 226 HIS C 36 HIS C 160 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN D 36 HIS D 160 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.158882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120150 restraints weight = 19714.977| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 0.85 r_work: 0.2970 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 26010 Z= 0.314 Angle : 0.735 7.766 35274 Z= 0.383 Chirality : 0.056 0.262 3978 Planarity : 0.007 0.106 4470 Dihedral : 7.089 65.244 3630 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.21 % Allowed : 14.83 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.07 % 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: 0.03 (0.14), residues: 3150 helix: 0.86 (0.15), residues: 1104 sheet: -0.51 (0.19), residues: 582 loop : -0.28 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 402 HIS 0.007 0.002 HIS E 274 PHE 0.029 0.003 PHE C 187 TYR 0.031 0.003 TYR C 245 ARG 0.004 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.05986 ( 996) hydrogen bonds : angle 6.15618 ( 2682) covalent geometry : bond 0.00720 (26010) covalent geometry : angle 0.73453 (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 465 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 376 time to evaluate : 2.899 Fit side-chains REVERT: A 119 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: A 350 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8548 (mttm) REVERT: A 484 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4371 (pm20) REVERT: B 61 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7900 (mmtm) REVERT: B 118 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: B 119 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: B 309 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: B 338 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6921 (mt-10) REVERT: B 468 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: C 118 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: C 275 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8284 (mt) REVERT: C 350 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8257 (mttm) REVERT: C 484 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.4668 (pm20) REVERT: D 118 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: D 119 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: D 275 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8277 (mt) REVERT: D 350 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8258 (mttm) REVERT: D 484 GLU cc_start: 0.5552 (OUTLIER) cc_final: 0.4672 (pm20) REVERT: E 119 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: E 350 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8545 (mttm) REVERT: E 484 GLU cc_start: 0.5131 (OUTLIER) cc_final: 0.4376 (pm20) REVERT: F 61 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7896 (mmtm) REVERT: F 118 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: F 119 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: F 309 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: F 338 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6926 (mt-10) REVERT: F 443 LEU cc_start: 0.7902 (mt) cc_final: 0.7667 (mt) REVERT: F 468 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6889 (mt-10) outliers start: 89 outliers final: 37 residues processed: 438 average time/residue: 1.2511 time to fit residues: 641.8837 Evaluate side-chains 437 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 375 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 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 434 SER Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 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 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: 1.9990 chunk 154 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 251 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 ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.160330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112038 restraints weight = 19826.427| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.52 r_work: 0.2944 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26010 Z= 0.207 Angle : 0.633 6.885 35274 Z= 0.330 Chirality : 0.050 0.241 3978 Planarity : 0.006 0.108 4470 Dihedral : 6.736 58.758 3630 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.45 % Allowed : 16.16 % Favored : 81.39 % 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: 0.11 (0.14), residues: 3150 helix: 0.99 (0.15), residues: 1104 sheet: -0.50 (0.19), residues: 582 loop : -0.27 (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 A 195 PHE 0.022 0.003 PHE A 81 TYR 0.024 0.002 TYR D 245 ARG 0.003 0.001 ARG D 47 Details of bonding type rmsd hydrogen bonds : bond 0.05123 ( 996) hydrogen bonds : angle 5.96182 ( 2682) covalent geometry : bond 0.00470 (26010) covalent geometry : angle 0.63312 (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 445 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 377 time to evaluate : 3.173 Fit side-chains REVERT: A 119 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: A 256 ASN cc_start: 0.8071 (t0) cc_final: 0.7834 (t0) REVERT: A 484 GLU cc_start: 0.5001 (OUTLIER) cc_final: 0.4287 (pm20) REVERT: B 61 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7791 (mmtm) REVERT: B 118 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: B 119 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: B 309 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: B 338 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6878 (mt-10) REVERT: B 468 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6996 (mt-10) REVERT: C 118 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: C 275 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8241 (mt) REVERT: C 484 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.4649 (pm20) REVERT: D 118 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8197 (pt0) REVERT: D 275 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8227 (mt) REVERT: D 484 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.4659 (pm20) REVERT: E 119 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: E 256 ASN cc_start: 0.8070 (t0) cc_final: 0.7835 (t0) REVERT: E 350 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8613 (mttm) REVERT: E 484 GLU cc_start: 0.5007 (OUTLIER) cc_final: 0.4289 (pm20) REVERT: F 61 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7786 (mmtm) REVERT: F 112 ASP cc_start: 0.8555 (m-30) cc_final: 0.8328 (m-30) REVERT: F 118 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: F 119 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: F 309 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: F 338 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6890 (mt-10) REVERT: F 443 LEU cc_start: 0.7918 (mt) cc_final: 0.7693 (mt) REVERT: F 468 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7007 (mt-10) outliers start: 68 outliers final: 34 residues processed: 428 average time/residue: 1.2272 time to fit residues: 617.7021 Evaluate side-chains 426 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 373 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 434 SER 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 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 E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 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 434 SER 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: 8.9990 chunk 122 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 311 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.161296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114718 restraints weight = 19560.084| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.47 r_work: 0.2930 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26010 Z= 0.194 Angle : 0.622 7.716 35274 Z= 0.323 Chirality : 0.049 0.234 3978 Planarity : 0.006 0.105 4470 Dihedral : 6.647 58.615 3628 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.45 % Allowed : 16.20 % Favored : 81.35 % 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: 0.14 (0.14), residues: 3150 helix: 1.04 (0.15), residues: 1104 sheet: -0.49 (0.19), residues: 582 loop : -0.27 (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 C 274 PHE 0.021 0.003 PHE A 81 TYR 0.023 0.002 TYR D 245 ARG 0.003 0.000 ARG E 426 Details of bonding type rmsd hydrogen bonds : bond 0.04972 ( 996) hydrogen bonds : angle 5.89876 ( 2682) covalent geometry : bond 0.00437 (26010) covalent geometry : angle 0.62166 (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 437 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 369 time to evaluate : 2.962 Fit side-chains REVERT: A 119 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: A 256 ASN cc_start: 0.7964 (t0) cc_final: 0.7728 (t0) REVERT: A 484 GLU cc_start: 0.4943 (OUTLIER) cc_final: 0.4282 (pm20) REVERT: B 61 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7715 (mmtm) REVERT: B 119 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: B 309 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: B 468 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6772 (mt-10) REVERT: C 118 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: C 275 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8080 (mt) REVERT: C 350 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8163 (mttm) REVERT: C 484 GLU cc_start: 0.5455 (OUTLIER) cc_final: 0.4607 (pm20) REVERT: D 118 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: D 275 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8082 (mt) REVERT: D 350 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8163 (mttm) REVERT: D 484 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.4615 (pm20) REVERT: E 119 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: E 256 ASN cc_start: 0.7967 (t0) cc_final: 0.7729 (t0) REVERT: E 350 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8555 (mttm) REVERT: E 484 GLU cc_start: 0.4936 (OUTLIER) cc_final: 0.4277 (pm20) REVERT: F 61 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7711 (mmtm) REVERT: F 119 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: F 309 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: F 338 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6741 (mt-10) REVERT: F 443 LEU cc_start: 0.7676 (mt) cc_final: 0.7459 (mt) REVERT: F 468 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6786 (mt-10) outliers start: 68 outliers final: 35 residues processed: 421 average time/residue: 1.2770 time to fit residues: 632.2815 Evaluate side-chains 423 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 369 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 350 LYS Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 520 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 219 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 304 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.162736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114291 restraints weight = 19903.456| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.62 r_work: 0.2992 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26010 Z= 0.145 Angle : 0.576 7.833 35274 Z= 0.298 Chirality : 0.047 0.219 3978 Planarity : 0.006 0.106 4470 Dihedral : 6.327 55.595 3628 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.95 % Allowed : 16.92 % Favored : 81.13 % 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: 1.15 (0.15), residues: 1104 sheet: -0.41 (0.19), residues: 582 loop : -0.26 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 466 HIS 0.004 0.001 HIS A 39 PHE 0.020 0.002 PHE A 81 TYR 0.017 0.001 TYR A 245 ARG 0.006 0.000 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 996) hydrogen bonds : angle 5.72027 ( 2682) covalent geometry : bond 0.00326 (26010) covalent geometry : angle 0.57642 (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 412 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 358 time to evaluate : 2.770 Fit side-chains REVERT: A 119 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: A 256 ASN cc_start: 0.8080 (t0) cc_final: 0.7877 (t0) REVERT: A 484 GLU cc_start: 0.4876 (OUTLIER) cc_final: 0.4294 (pm20) REVERT: B 61 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7730 (mmtm) REVERT: B 119 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: B 309 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: B 338 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6770 (mm-30) REVERT: B 499 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7517 (mt) REVERT: C 118 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8107 (pt0) REVERT: C 275 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8227 (mt) REVERT: C 350 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8247 (mttm) REVERT: C 484 GLU cc_start: 0.5334 (OUTLIER) cc_final: 0.4631 (pm20) REVERT: D 118 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: D 275 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8229 (mt) REVERT: D 350 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8253 (mttm) REVERT: D 484 GLU cc_start: 0.5345 (OUTLIER) cc_final: 0.4631 (pm20) REVERT: E 119 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: E 256 ASN cc_start: 0.8074 (t0) cc_final: 0.7868 (t0) REVERT: E 484 GLU cc_start: 0.4873 (OUTLIER) cc_final: 0.4295 (pm20) REVERT: F 61 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7721 (mmtm) REVERT: F 119 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: F 309 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: F 338 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6710 (mt-10) REVERT: F 443 LEU cc_start: 0.7832 (mt) cc_final: 0.7597 (mt) REVERT: F 499 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7498 (mt) outliers start: 54 outliers final: 30 residues processed: 404 average time/residue: 1.2017 time to fit residues: 568.5798 Evaluate side-chains 405 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 355 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 499 ILE 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: 2.9990 chunk 197 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 308 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN 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 = 0.3755 r_free = 0.3755 target = 0.162051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113676 restraints weight = 19853.746| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.72 r_work: 0.2989 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26010 Z= 0.166 Angle : 0.601 10.880 35274 Z= 0.311 Chirality : 0.048 0.222 3978 Planarity : 0.006 0.104 4470 Dihedral : 6.426 57.376 3628 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.13 % Allowed : 16.92 % Favored : 80.95 % 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: 1.15 (0.15), residues: 1104 sheet: -0.40 (0.20), residues: 582 loop : -0.27 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 466 HIS 0.004 0.001 HIS D 274 PHE 0.020 0.002 PHE A 81 TYR 0.020 0.002 TYR D 245 ARG 0.006 0.000 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 996) hydrogen bonds : angle 5.76040 ( 2682) covalent geometry : bond 0.00374 (26010) covalent geometry : angle 0.60062 (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 416 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 357 time to evaluate : 2.685 Fit side-chains REVERT: A 119 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: A 256 ASN cc_start: 0.7957 (t0) cc_final: 0.7733 (t0) REVERT: A 484 GLU cc_start: 0.4873 (OUTLIER) cc_final: 0.4269 (pm20) REVERT: B 61 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7639 (mmtm) REVERT: B 118 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: B 119 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: B 309 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: B 338 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6651 (mm-30) REVERT: B 499 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7430 (mt) REVERT: C 118 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: C 275 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8069 (mt) REVERT: C 350 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8132 (mttm) REVERT: C 484 GLU cc_start: 0.5301 (OUTLIER) cc_final: 0.4634 (pm20) REVERT: D 118 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7931 (pt0) REVERT: D 275 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8068 (mt) REVERT: D 350 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8131 (mttm) REVERT: D 484 GLU cc_start: 0.5334 (OUTLIER) cc_final: 0.4636 (pm20) REVERT: E 119 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: E 256 ASN cc_start: 0.7954 (t0) cc_final: 0.7727 (t0) REVERT: E 484 GLU cc_start: 0.4870 (OUTLIER) cc_final: 0.4268 (pm20) REVERT: F 61 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7634 (mmtm) REVERT: F 118 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: F 119 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7560 (mm-30) REVERT: F 309 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: F 338 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6591 (mt-10) REVERT: F 443 LEU cc_start: 0.7569 (mt) cc_final: 0.7342 (mt) REVERT: F 499 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7443 (mt) outliers start: 59 outliers final: 32 residues processed: 404 average time/residue: 1.2243 time to fit residues: 580.9587 Evaluate side-chains 411 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 3.144 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 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 499 ILE 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: 2.9990 chunk 33 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 285 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 206 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.163075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121536 restraints weight = 19857.573| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.97 r_work: 0.3017 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26010 Z= 0.143 Angle : 0.577 10.460 35274 Z= 0.298 Chirality : 0.047 0.214 3978 Planarity : 0.005 0.104 4470 Dihedral : 6.262 55.412 3628 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.06 % Allowed : 16.96 % Favored : 80.99 % 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 (0.15), residues: 3150 helix: 1.20 (0.15), residues: 1104 sheet: -0.35 (0.20), residues: 582 loop : -0.26 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 466 HIS 0.004 0.001 HIS B 414 PHE 0.019 0.002 PHE A 81 TYR 0.016 0.001 TYR D 245 ARG 0.006 0.000 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 996) hydrogen bonds : angle 5.66401 ( 2682) covalent geometry : bond 0.00322 (26010) covalent geometry : angle 0.57732 (35274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21377.18 seconds wall clock time: 370 minutes 0.54 seconds (22200.54 seconds total)