Starting phenix.real_space_refine on Sun Aug 24 16:37:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tby_41148/08_2025/8tby_41148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tby_41148/08_2025/8tby_41148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tby_41148/08_2025/8tby_41148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tby_41148/08_2025/8tby_41148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tby_41148/08_2025/8tby_41148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tby_41148/08_2025/8tby_41148.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 13468 2.51 5 N 3738 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21126 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3018 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 17, 'TRANS': 356} Chain breaks: 1 Chain: "B" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3018 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 17, 'TRANS': 356} Chain breaks: 1 Chain: "C" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3018 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 17, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3018 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 17, 'TRANS': 356} Chain breaks: 1 Chain: "E" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3018 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 17, 'TRANS': 356} Chain breaks: 1 Chain: "F" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3018 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 17, 'TRANS': 356} Chain breaks: 1 Chain: "G" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3018 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 17, 'TRANS': 356} Chain breaks: 1 Time building chain proxies: 3.45, per 1000 atoms: 0.16 Number of scatterers: 21126 At special positions: 0 Unit cell: (154.8, 156.52, 116.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3836 8.00 N 3738 7.00 C 13468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 843.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4900 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 22 sheets defined 46.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.706A pdb=" N TRP A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.064A pdb=" N GLN A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 211 through 218 removed outlier: 4.068A pdb=" N TYR A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.023A pdb=" N ALA A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.706A pdb=" N TRP B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.064A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 196 through 210 Processing helix chain 'B' and resid 211 through 218 removed outlier: 4.069A pdb=" N TYR B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 218 " --> pdb=" O TRP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 283 through 290 removed outlier: 4.023A pdb=" N ALA B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.706A pdb=" N TRP C 62 " --> pdb=" O ARG C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.063A pdb=" N GLN C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 196 through 210 Processing helix chain 'C' and resid 211 through 218 removed outlier: 4.069A pdb=" N TYR C 215 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG C 218 " --> pdb=" O TRP C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 247 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 283 through 290 removed outlier: 4.024A pdb=" N ALA C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 317 Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.707A pdb=" N TRP D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 removed outlier: 4.064A pdb=" N GLN D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 211 through 218 removed outlier: 4.069A pdb=" N TYR D 215 " --> pdb=" O ASN D 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 218 " --> pdb=" O TRP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 247 Processing helix chain 'D' and resid 262 through 272 Processing helix chain 'D' and resid 283 through 290 removed outlier: 4.024A pdb=" N ALA D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.706A pdb=" N TRP E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.064A pdb=" N GLN E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 196 through 210 Processing helix chain 'E' and resid 211 through 218 removed outlier: 4.068A pdb=" N TYR E 215 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 218 " --> pdb=" O TRP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 247 Processing helix chain 'E' and resid 262 through 272 Processing helix chain 'E' and resid 283 through 290 removed outlier: 4.023A pdb=" N ALA E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 357 through 369 Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 392 through 403 Processing helix chain 'E' and resid 406 through 413 Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'F' and resid 31 through 47 Processing helix chain 'F' and resid 58 through 71 removed outlier: 3.706A pdb=" N TRP F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 removed outlier: 4.064A pdb=" N GLN F 161 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 196 through 210 Processing helix chain 'F' and resid 211 through 218 removed outlier: 4.068A pdb=" N TYR F 215 " --> pdb=" O ASN F 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG F 218 " --> pdb=" O TRP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 247 Processing helix chain 'F' and resid 262 through 272 Processing helix chain 'F' and resid 283 through 290 removed outlier: 4.023A pdb=" N ALA F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 357 through 369 Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 392 through 403 Processing helix chain 'F' and resid 406 through 413 Processing helix chain 'F' and resid 413 through 418 Processing helix chain 'G' and resid 31 through 47 Processing helix chain 'G' and resid 58 through 71 removed outlier: 3.707A pdb=" N TRP G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 4.063A pdb=" N GLN G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 196 through 210 Processing helix chain 'G' and resid 211 through 218 removed outlier: 4.068A pdb=" N TYR G 215 " --> pdb=" O ASN G 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG G 218 " --> pdb=" O TRP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 247 Processing helix chain 'G' and resid 262 through 272 Processing helix chain 'G' and resid 283 through 290 removed outlier: 4.024A pdb=" N ALA G 287 " --> pdb=" O ASP G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 317 Processing helix chain 'G' and resid 357 through 369 Processing helix chain 'G' and resid 373 through 388 Processing helix chain 'G' and resid 392 through 403 Processing helix chain 'G' and resid 406 through 413 Processing helix chain 'G' and resid 413 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 108 removed outlier: 6.915A pdb=" N TRP A 112 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU A 140 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP A 132 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU G 77 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR A 50 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL G 79 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLU A 52 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N THR G 81 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 13.211A pdb=" N TYR G 83 " --> pdb=" O PRO A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 99 removed outlier: 3.725A pdb=" N LEU A 77 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 52 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N THR A 81 " --> pdb=" O PRO B 54 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 132 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU B 140 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP B 112 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 178 removed outlier: 6.602A pdb=" N TYR A 169 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N SER A 255 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ALA A 171 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER A 250 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 280 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS A 252 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU A 282 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU A 254 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER A 277 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE A 328 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 279 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR A 330 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 281 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP A 348 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY A 225 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS A 350 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A 227 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR A 352 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR A 229 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 99 removed outlier: 3.847A pdb=" N LEU B 77 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 52 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR B 81 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP C 132 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU C 140 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP C 112 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 178 removed outlier: 6.602A pdb=" N TYR B 169 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N SER B 255 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ALA B 171 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER B 250 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU B 280 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS B 252 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU B 282 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU B 254 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER B 277 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE B 328 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 279 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR B 330 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 281 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP B 348 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY B 225 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 350 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 227 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR B 352 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR B 229 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 99 removed outlier: 3.558A pdb=" N LEU C 77 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N THR C 81 " --> pdb=" O PRO D 54 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP D 132 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU D 140 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TRP D 112 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AB1, first strand: chain 'C' and resid 175 through 178 removed outlier: 6.602A pdb=" N TYR C 169 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N SER C 255 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ALA C 171 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 250 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU C 280 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS C 252 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLU C 282 " --> pdb=" O CYS C 252 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU C 254 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER C 277 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE C 328 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 279 " --> pdb=" O PHE C 328 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR C 330 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C 281 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP C 348 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY C 225 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS C 350 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU C 227 " --> pdb=" O LYS C 350 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR C 352 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR C 229 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 99 removed outlier: 3.579A pdb=" N LEU D 77 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 52 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 79 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N THR D 81 " --> pdb=" O PRO E 54 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP E 132 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU E 140 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TRP E 112 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AB4, first strand: chain 'D' and resid 175 through 178 removed outlier: 6.602A pdb=" N TYR D 169 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N SER D 255 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ALA D 171 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER D 250 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU D 280 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS D 252 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU D 282 " --> pdb=" O CYS D 252 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU D 254 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER D 277 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE D 328 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 279 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR D 330 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU D 281 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP D 348 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY D 225 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS D 350 " --> pdb=" O GLY D 225 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU D 227 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR D 352 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR D 229 " --> pdb=" O TYR D 352 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 77 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 165 through 166 Processing sheet with id=AB7, first strand: chain 'E' and resid 175 through 178 removed outlier: 6.603A pdb=" N TYR E 169 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N SER E 255 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ALA E 171 " --> pdb=" O SER E 255 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER E 250 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU E 280 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS E 252 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLU E 282 " --> pdb=" O CYS E 252 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU E 254 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER E 277 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE E 328 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL E 279 " --> pdb=" O PHE E 328 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR E 330 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 281 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP E 348 " --> pdb=" O ARG E 223 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY E 225 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS E 350 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU E 227 " --> pdb=" O LYS E 350 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR E 352 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR E 229 " --> pdb=" O TYR E 352 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 48 through 54 removed outlier: 3.974A pdb=" N TRP F 132 " --> pdb=" O ASP F 120 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU F 140 " --> pdb=" O TRP F 112 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP F 112 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 90 through 99 removed outlier: 3.872A pdb=" N LEU F 77 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR F 81 " --> pdb=" O PRO G 54 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP G 132 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU G 140 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP G 112 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AC2, first strand: chain 'F' and resid 175 through 178 removed outlier: 6.602A pdb=" N TYR F 169 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N SER F 255 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ALA F 171 " --> pdb=" O SER F 255 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER F 250 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU F 280 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS F 252 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU F 282 " --> pdb=" O CYS F 252 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU F 254 " --> pdb=" O GLU F 282 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER F 277 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE F 328 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL F 279 " --> pdb=" O PHE F 328 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR F 330 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU F 281 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP F 348 " --> pdb=" O ARG F 223 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY F 225 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS F 350 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU F 227 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR F 352 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR F 229 " --> pdb=" O TYR F 352 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 165 through 166 Processing sheet with id=AC4, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.602A pdb=" N TYR G 169 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N SER G 255 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ALA G 171 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER G 250 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU G 280 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS G 252 " --> pdb=" O LEU G 280 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU G 282 " --> pdb=" O CYS G 252 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU G 254 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER G 277 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE G 328 " --> pdb=" O SER G 277 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL G 279 " --> pdb=" O PHE G 328 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR G 330 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU G 281 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP G 348 " --> pdb=" O ARG G 223 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY G 225 " --> pdb=" O ASP G 348 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS G 350 " --> pdb=" O GLY G 225 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU G 227 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR G 352 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR G 229 " --> pdb=" O TYR G 352 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3045 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6958 1.35 - 1.46: 5318 1.46 - 1.58: 9221 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 21644 Sorted by residual: bond pdb=" CB THR E 138 " pdb=" CG2 THR E 138 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CB THR B 138 " pdb=" CG2 THR B 138 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB THR G 138 " pdb=" CG2 THR G 138 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CB THR D 138 " pdb=" CG2 THR D 138 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CB THR F 138 " pdb=" CG2 THR F 138 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 ... (remaining 21639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 28624 1.47 - 2.95: 574 2.95 - 4.42: 76 4.42 - 5.90: 55 5.90 - 7.37: 15 Bond angle restraints: 29344 Sorted by residual: angle pdb=" CB MET G 48 " pdb=" CG MET G 48 " pdb=" SD MET G 48 " ideal model delta sigma weight residual 112.70 105.33 7.37 3.00e+00 1.11e-01 6.04e+00 angle pdb=" CB MET C 48 " pdb=" CG MET C 48 " pdb=" SD MET C 48 " ideal model delta sigma weight residual 112.70 105.34 7.36 3.00e+00 1.11e-01 6.02e+00 angle pdb=" CB MET D 48 " pdb=" CG MET D 48 " pdb=" SD MET D 48 " ideal model delta sigma weight residual 112.70 105.35 7.35 3.00e+00 1.11e-01 6.00e+00 angle pdb=" CB MET A 48 " pdb=" CG MET A 48 " pdb=" SD MET A 48 " ideal model delta sigma weight residual 112.70 105.37 7.33 3.00e+00 1.11e-01 5.98e+00 angle pdb=" CB MET B 48 " pdb=" CG MET B 48 " pdb=" SD MET B 48 " ideal model delta sigma weight residual 112.70 105.37 7.33 3.00e+00 1.11e-01 5.97e+00 ... (remaining 29339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 11305 16.05 - 32.11: 1211 32.11 - 48.16: 294 48.16 - 64.22: 14 64.22 - 80.27: 49 Dihedral angle restraints: 12873 sinusoidal: 5257 harmonic: 7616 Sorted by residual: dihedral pdb=" CA TYR E 47 " pdb=" C TYR E 47 " pdb=" N MET E 48 " pdb=" CA MET E 48 " ideal model delta harmonic sigma weight residual -180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TYR D 47 " pdb=" C TYR D 47 " pdb=" N MET D 48 " pdb=" CA MET D 48 " ideal model delta harmonic sigma weight residual 180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TYR G 47 " pdb=" C TYR G 47 " pdb=" N MET G 48 " pdb=" CA MET G 48 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 12870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2175 0.032 - 0.065: 707 0.065 - 0.097: 217 0.097 - 0.129: 70 0.129 - 0.162: 16 Chirality restraints: 3185 Sorted by residual: chirality pdb=" CA ILE A 98 " pdb=" N ILE A 98 " pdb=" C ILE A 98 " pdb=" CB ILE A 98 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ILE D 98 " pdb=" N ILE D 98 " pdb=" C ILE D 98 " pdb=" CB ILE D 98 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE F 98 " pdb=" N ILE F 98 " pdb=" C ILE F 98 " pdb=" CB ILE F 98 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 3182 not shown) Planarity restraints: 3773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 220 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO D 221 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 220 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO G 221 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 221 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 221 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 220 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO E 221 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 221 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 221 " -0.023 5.00e-02 4.00e+02 ... (remaining 3770 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4425 2.79 - 3.32: 21151 3.32 - 3.84: 36224 3.84 - 4.37: 38937 4.37 - 4.90: 66648 Nonbonded interactions: 167385 Sorted by model distance: nonbonded pdb=" OH TYR B 399 " pdb=" O ALA B 410 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR E 399 " pdb=" O ALA E 410 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR D 399 " pdb=" O ALA D 410 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR C 399 " pdb=" O ALA C 410 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR F 399 " pdb=" O ALA F 410 " model vdw 2.262 3.040 ... (remaining 167380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.340 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.002 0.036 21644 Z= 0.094 Angle : 0.557 7.373 29344 Z= 0.279 Chirality : 0.038 0.162 3185 Planarity : 0.004 0.042 3773 Dihedral : 14.364 80.270 7973 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.17), residues: 2590 helix: 2.89 (0.15), residues: 1078 sheet: 0.24 (0.22), residues: 567 loop : 0.21 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 69 TYR 0.007 0.001 TYR C 399 PHE 0.007 0.001 PHE E 95 TRP 0.006 0.001 TRP G 112 HIS 0.010 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00200 (21644) covalent geometry : angle 0.55656 (29344) hydrogen bonds : bond 0.11633 ( 1064) hydrogen bonds : angle 4.41418 ( 3045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8272 (pmm) cc_final: 0.6415 (pmm) REVERT: A 168 MET cc_start: 0.8914 (tpt) cc_final: 0.7876 (mpp) REVERT: B 84 LEU cc_start: 0.9348 (tp) cc_final: 0.9029 (tt) REVERT: B 168 MET cc_start: 0.9040 (tpt) cc_final: 0.8489 (mtt) REVERT: B 401 MET cc_start: 0.8762 (mmp) cc_final: 0.8540 (mmm) REVERT: B 408 MET cc_start: 0.9606 (mpp) cc_final: 0.9177 (pmm) REVERT: C 123 MET cc_start: 0.8789 (pmm) cc_final: 0.8258 (pmm) REVERT: C 408 MET cc_start: 0.9652 (mpp) cc_final: 0.9368 (pmm) REVERT: D 254 LEU cc_start: 0.9340 (tp) cc_final: 0.9049 (tt) REVERT: E 121 MET cc_start: 0.8321 (mmp) cc_final: 0.8057 (mmm) REVERT: E 123 MET cc_start: 0.7187 (pmm) cc_final: 0.6878 (pmm) REVERT: F 280 LEU cc_start: 0.9830 (tp) cc_final: 0.9442 (pp) REVERT: F 408 MET cc_start: 0.9684 (mpp) cc_final: 0.9411 (pmm) REVERT: G 168 MET cc_start: 0.8957 (tpt) cc_final: 0.8694 (tpp) REVERT: G 332 ASN cc_start: 0.8953 (m-40) cc_final: 0.8615 (p0) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1344 time to fit residues: 22.6297 Evaluate side-chains 80 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 40.0000 chunk 258 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS D 76 HIS D 109 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.030792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.025566 restraints weight = 337486.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.026233 restraints weight = 214215.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.026695 restraints weight = 155770.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.027024 restraints weight = 123717.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.027254 restraints weight = 105108.990| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21644 Z= 0.133 Angle : 0.504 7.092 29344 Z= 0.260 Chirality : 0.037 0.165 3185 Planarity : 0.004 0.043 3773 Dihedral : 3.708 12.983 2933 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.17), residues: 2590 helix: 2.97 (0.15), residues: 1127 sheet: 0.37 (0.22), residues: 546 loop : 0.19 (0.22), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 56 TYR 0.011 0.001 TYR C 403 PHE 0.012 0.001 PHE C 97 TRP 0.017 0.001 TRP C 359 HIS 0.005 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00275 (21644) covalent geometry : angle 0.50437 (29344) hydrogen bonds : bond 0.02916 ( 1064) hydrogen bonds : angle 3.78384 ( 3045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8918 (mmp) cc_final: 0.8273 (mmm) REVERT: A 123 MET cc_start: 0.7351 (pmm) cc_final: 0.6193 (pmm) REVERT: A 168 MET cc_start: 0.8767 (tpt) cc_final: 0.7973 (tpp) REVERT: B 48 MET cc_start: 0.7701 (mmm) cc_final: 0.6758 (mmm) REVERT: B 84 LEU cc_start: 0.9378 (tp) cc_final: 0.9100 (tt) REVERT: B 168 MET cc_start: 0.8845 (tpt) cc_final: 0.8074 (tpp) REVERT: B 408 MET cc_start: 0.9714 (mpp) cc_final: 0.9353 (pmm) REVERT: C 48 MET cc_start: 0.9031 (tpt) cc_final: 0.8539 (mmm) REVERT: C 123 MET cc_start: 0.8546 (pmm) cc_final: 0.7548 (pmm) REVERT: C 408 MET cc_start: 0.9712 (mpp) cc_final: 0.9451 (pmm) REVERT: D 48 MET cc_start: 0.8436 (mmp) cc_final: 0.7982 (mmm) REVERT: D 168 MET cc_start: 0.9512 (mmp) cc_final: 0.8984 (mmm) REVERT: D 254 LEU cc_start: 0.9485 (tp) cc_final: 0.9163 (tt) REVERT: D 408 MET cc_start: 0.9717 (mpp) cc_final: 0.9402 (pmm) REVERT: E 48 MET cc_start: 0.8985 (mmp) cc_final: 0.8573 (mmm) REVERT: E 121 MET cc_start: 0.8917 (mmp) cc_final: 0.8294 (tpp) REVERT: F 280 LEU cc_start: 0.9836 (tp) cc_final: 0.9425 (pp) REVERT: F 408 MET cc_start: 0.9654 (mpp) cc_final: 0.9429 (pmm) REVERT: G 123 MET cc_start: 0.6672 (pmm) cc_final: 0.5303 (pmm) REVERT: G 168 MET cc_start: 0.8994 (tpt) cc_final: 0.8660 (tpp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1399 time to fit residues: 18.2778 Evaluate side-chains 76 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 77 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 383 HIS ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS F 149 ASN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.029459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.024338 restraints weight = 347593.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.024971 restraints weight = 218439.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.025424 restraints weight = 159415.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.025746 restraints weight = 127199.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025977 restraints weight = 107615.650| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21644 Z= 0.171 Angle : 0.542 6.866 29344 Z= 0.279 Chirality : 0.037 0.168 3185 Planarity : 0.004 0.053 3773 Dihedral : 3.796 18.112 2933 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.17), residues: 2590 helix: 2.92 (0.15), residues: 1127 sheet: -0.05 (0.21), residues: 588 loop : 0.40 (0.23), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 177 TYR 0.011 0.001 TYR G 60 PHE 0.011 0.001 PHE C 97 TRP 0.010 0.001 TRP C 359 HIS 0.004 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00351 (21644) covalent geometry : angle 0.54163 (29344) hydrogen bonds : bond 0.02873 ( 1064) hydrogen bonds : angle 3.82686 ( 3045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9057 (mmp) cc_final: 0.8579 (mmm) REVERT: A 123 MET cc_start: 0.8272 (pmm) cc_final: 0.7934 (pmm) REVERT: A 168 MET cc_start: 0.8933 (tpt) cc_final: 0.8074 (tpp) REVERT: B 48 MET cc_start: 0.7618 (mmm) cc_final: 0.6599 (mmm) REVERT: B 84 LEU cc_start: 0.9429 (tp) cc_final: 0.9169 (tt) REVERT: B 168 MET cc_start: 0.8926 (tpt) cc_final: 0.8136 (tpp) REVERT: B 401 MET cc_start: 0.8860 (mmp) cc_final: 0.8629 (mmm) REVERT: B 408 MET cc_start: 0.9741 (mpp) cc_final: 0.9377 (pmm) REVERT: C 48 MET cc_start: 0.8943 (tpt) cc_final: 0.8065 (mmm) REVERT: C 408 MET cc_start: 0.9750 (mpp) cc_final: 0.9478 (pmm) REVERT: D 48 MET cc_start: 0.8396 (mmp) cc_final: 0.8009 (mmm) REVERT: D 168 MET cc_start: 0.9500 (mmp) cc_final: 0.8557 (mpp) REVERT: D 408 MET cc_start: 0.9650 (mpp) cc_final: 0.9388 (pmm) REVERT: E 48 MET cc_start: 0.8936 (mmp) cc_final: 0.8648 (mmm) REVERT: E 121 MET cc_start: 0.9147 (mmp) cc_final: 0.8841 (tpp) REVERT: F 408 MET cc_start: 0.9665 (mpp) cc_final: 0.9448 (pmm) REVERT: G 123 MET cc_start: 0.6743 (pmm) cc_final: 0.5347 (pmm) REVERT: G 168 MET cc_start: 0.8953 (tpt) cc_final: 0.8598 (tpt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1395 time to fit residues: 17.5794 Evaluate side-chains 70 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 162 optimal weight: 9.9990 chunk 148 optimal weight: 50.0000 chunk 110 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 240 optimal weight: 0.0010 chunk 53 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 57 optimal weight: 0.0870 chunk 130 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 overall best weight: 3.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.029212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.024128 restraints weight = 348852.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.024765 restraints weight = 216998.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.025216 restraints weight = 157566.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.025534 restraints weight = 125249.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.025759 restraints weight = 105889.840| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21644 Z= 0.142 Angle : 0.526 6.746 29344 Z= 0.270 Chirality : 0.038 0.168 3185 Planarity : 0.004 0.050 3773 Dihedral : 3.772 16.200 2933 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.17), residues: 2590 helix: 2.94 (0.15), residues: 1127 sheet: 0.01 (0.21), residues: 595 loop : 0.51 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 177 TYR 0.013 0.001 TYR A 169 PHE 0.011 0.001 PHE A 97 TRP 0.006 0.001 TRP F 112 HIS 0.008 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00294 (21644) covalent geometry : angle 0.52594 (29344) hydrogen bonds : bond 0.02597 ( 1064) hydrogen bonds : angle 3.77409 ( 3045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9066 (mmp) cc_final: 0.8569 (mmm) REVERT: A 123 MET cc_start: 0.8521 (pmm) cc_final: 0.7684 (pmm) REVERT: B 48 MET cc_start: 0.7916 (mmm) cc_final: 0.7007 (mmm) REVERT: B 84 LEU cc_start: 0.9443 (tp) cc_final: 0.9190 (tt) REVERT: B 168 MET cc_start: 0.8637 (tpt) cc_final: 0.8219 (tpp) REVERT: B 401 MET cc_start: 0.8840 (mmp) cc_final: 0.8592 (mmm) REVERT: B 408 MET cc_start: 0.9755 (mpp) cc_final: 0.9392 (pmm) REVERT: C 48 MET cc_start: 0.9007 (tpt) cc_final: 0.8509 (mmm) REVERT: C 408 MET cc_start: 0.9764 (mpp) cc_final: 0.9485 (pmm) REVERT: D 48 MET cc_start: 0.8442 (mmp) cc_final: 0.7971 (mmm) REVERT: D 168 MET cc_start: 0.9502 (mmp) cc_final: 0.9076 (mmp) REVERT: D 408 MET cc_start: 0.9676 (mpp) cc_final: 0.9402 (pmm) REVERT: E 48 MET cc_start: 0.8963 (mmp) cc_final: 0.8642 (mmm) REVERT: E 121 MET cc_start: 0.9271 (mmp) cc_final: 0.8835 (tpp) REVERT: E 329 MET cc_start: 0.8374 (tpt) cc_final: 0.8165 (tpt) REVERT: G 123 MET cc_start: 0.6874 (pmm) cc_final: 0.5341 (pmm) REVERT: G 168 MET cc_start: 0.8875 (tpt) cc_final: 0.8493 (tpt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1569 time to fit residues: 20.3503 Evaluate side-chains 73 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 222 optimal weight: 50.0000 chunk 251 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 185 optimal weight: 50.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS G 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.025743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.020067 restraints weight = 334623.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.020590 restraints weight = 235163.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.020971 restraints weight = 184440.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.021245 restraints weight = 154064.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.021452 restraints weight = 135539.418| |-----------------------------------------------------------------------------| r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21644 Z= 0.220 Angle : 0.628 8.007 29344 Z= 0.329 Chirality : 0.039 0.230 3185 Planarity : 0.005 0.068 3773 Dihedral : 4.130 17.305 2933 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.17), residues: 2590 helix: 2.52 (0.15), residues: 1127 sheet: -0.10 (0.21), residues: 595 loop : 0.33 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 224 TYR 0.014 0.002 TYR G 108 PHE 0.022 0.002 PHE C 365 TRP 0.011 0.001 TRP C 62 HIS 0.007 0.001 HIS F 412 Details of bonding type rmsd covalent geometry : bond 0.00435 (21644) covalent geometry : angle 0.62775 (29344) hydrogen bonds : bond 0.03099 ( 1064) hydrogen bonds : angle 4.07253 ( 3045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9127 (mmp) cc_final: 0.8571 (mmp) REVERT: A 123 MET cc_start: 0.7707 (pmm) cc_final: 0.6747 (pmm) REVERT: A 168 MET cc_start: 0.9065 (tpt) cc_final: 0.8654 (tpt) REVERT: B 48 MET cc_start: 0.8416 (mmm) cc_final: 0.7385 (mmm) REVERT: B 408 MET cc_start: 0.9806 (mpp) cc_final: 0.9539 (pmm) REVERT: C 48 MET cc_start: 0.9080 (tpt) cc_final: 0.8584 (mmm) REVERT: C 408 MET cc_start: 0.9786 (mpp) cc_final: 0.9515 (pmm) REVERT: D 48 MET cc_start: 0.8824 (mmp) cc_final: 0.8409 (mmm) REVERT: D 168 MET cc_start: 0.9418 (mmp) cc_final: 0.8753 (mpp) REVERT: D 408 MET cc_start: 0.9666 (mpp) cc_final: 0.9427 (pmm) REVERT: E 48 MET cc_start: 0.8916 (mmp) cc_final: 0.8647 (mmm) REVERT: G 123 MET cc_start: 0.7069 (pmm) cc_final: 0.5686 (ptp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1332 time to fit residues: 16.5087 Evaluate side-chains 69 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 51 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.025437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.019828 restraints weight = 334994.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.020349 restraints weight = 236068.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.020721 restraints weight = 184276.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.021007 restraints weight = 154079.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.021212 restraints weight = 134575.796| |-----------------------------------------------------------------------------| r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21644 Z= 0.213 Angle : 0.607 9.543 29344 Z= 0.316 Chirality : 0.039 0.169 3185 Planarity : 0.005 0.043 3773 Dihedral : 4.142 19.203 2933 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.17), residues: 2590 helix: 2.39 (0.15), residues: 1127 sheet: -0.12 (0.21), residues: 609 loop : 0.29 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 224 TYR 0.014 0.002 TYR C 108 PHE 0.015 0.002 PHE E 97 TRP 0.055 0.002 TRP B 66 HIS 0.010 0.002 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00427 (21644) covalent geometry : angle 0.60731 (29344) hydrogen bonds : bond 0.02969 ( 1064) hydrogen bonds : angle 4.13744 ( 3045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8978 (mmp) cc_final: 0.8330 (mmp) REVERT: A 168 MET cc_start: 0.9103 (tpt) cc_final: 0.8789 (tpt) REVERT: B 48 MET cc_start: 0.8467 (mmm) cc_final: 0.7366 (mmm) REVERT: B 408 MET cc_start: 0.9809 (mpp) cc_final: 0.9544 (pmm) REVERT: C 48 MET cc_start: 0.9108 (tpt) cc_final: 0.8584 (mmm) REVERT: C 408 MET cc_start: 0.9783 (mpp) cc_final: 0.9507 (pmm) REVERT: D 48 MET cc_start: 0.8867 (mmp) cc_final: 0.8478 (mmm) REVERT: D 168 MET cc_start: 0.9455 (mmp) cc_final: 0.8787 (mpp) REVERT: D 408 MET cc_start: 0.9669 (mpp) cc_final: 0.9425 (pmm) REVERT: E 48 MET cc_start: 0.8912 (mmp) cc_final: 0.8666 (mmm) REVERT: E 168 MET cc_start: 0.9377 (tpt) cc_final: 0.8975 (tpt) REVERT: G 123 MET cc_start: 0.7311 (pmm) cc_final: 0.5810 (ptp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1142 time to fit residues: 14.5003 Evaluate side-chains 69 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 251 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 86 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 HIS ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.025577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.019838 restraints weight = 329600.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.020364 restraints weight = 232160.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.020758 restraints weight = 181124.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.021042 restraints weight = 151156.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.021256 restraints weight = 132504.009| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21644 Z= 0.150 Angle : 0.561 9.335 29344 Z= 0.286 Chirality : 0.039 0.220 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.031 17.179 2933 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.17), residues: 2590 helix: 2.60 (0.15), residues: 1127 sheet: -0.06 (0.21), residues: 609 loop : 0.35 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 346 TYR 0.018 0.001 TYR D 47 PHE 0.019 0.001 PHE B 288 TRP 0.042 0.002 TRP F 66 HIS 0.007 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00307 (21644) covalent geometry : angle 0.56113 (29344) hydrogen bonds : bond 0.02668 ( 1064) hydrogen bonds : angle 4.00259 ( 3045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9043 (mmp) cc_final: 0.8301 (mmp) REVERT: A 123 MET cc_start: 0.8730 (pmm) cc_final: 0.8178 (pmm) REVERT: A 168 MET cc_start: 0.8963 (tpt) cc_final: 0.8712 (tpt) REVERT: B 48 MET cc_start: 0.8782 (mmm) cc_final: 0.7726 (mmm) REVERT: B 401 MET cc_start: 0.8825 (mmp) cc_final: 0.8616 (mmm) REVERT: B 408 MET cc_start: 0.9822 (mpp) cc_final: 0.9499 (pmm) REVERT: C 48 MET cc_start: 0.9234 (tpt) cc_final: 0.8580 (mmm) REVERT: C 123 MET cc_start: 0.8348 (pmm) cc_final: 0.8087 (pmm) REVERT: C 408 MET cc_start: 0.9800 (mpp) cc_final: 0.9542 (pmm) REVERT: D 48 MET cc_start: 0.8948 (mmp) cc_final: 0.8667 (mmm) REVERT: D 168 MET cc_start: 0.9502 (mmp) cc_final: 0.8771 (mpp) REVERT: D 408 MET cc_start: 0.9695 (mpp) cc_final: 0.9452 (pmm) REVERT: E 48 MET cc_start: 0.9015 (mmp) cc_final: 0.8739 (mmm) REVERT: F 121 MET cc_start: 0.9254 (mmm) cc_final: 0.8979 (tpp) REVERT: G 123 MET cc_start: 0.7252 (pmm) cc_final: 0.5222 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1183 time to fit residues: 14.4467 Evaluate side-chains 70 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 257 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.025125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.019553 restraints weight = 339587.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.020071 restraints weight = 238528.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.020440 restraints weight = 186122.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.020724 restraints weight = 155356.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.020900 restraints weight = 135822.945| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21644 Z= 0.208 Angle : 0.601 8.643 29344 Z= 0.310 Chirality : 0.038 0.170 3185 Planarity : 0.004 0.044 3773 Dihedral : 4.118 18.815 2933 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.17), residues: 2590 helix: 2.38 (0.15), residues: 1134 sheet: -0.10 (0.21), residues: 609 loop : 0.34 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 346 TYR 0.014 0.002 TYR A 169 PHE 0.021 0.002 PHE E 288 TRP 0.051 0.002 TRP F 66 HIS 0.007 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00419 (21644) covalent geometry : angle 0.60082 (29344) hydrogen bonds : bond 0.02884 ( 1064) hydrogen bonds : angle 4.12572 ( 3045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9167 (mmp) cc_final: 0.8534 (mmm) REVERT: A 123 MET cc_start: 0.8348 (pmm) cc_final: 0.7225 (pmm) REVERT: B 48 MET cc_start: 0.8799 (mmm) cc_final: 0.7642 (mmm) REVERT: B 408 MET cc_start: 0.9827 (mpp) cc_final: 0.9576 (pmm) REVERT: C 48 MET cc_start: 0.8983 (tpt) cc_final: 0.8275 (mmm) REVERT: C 408 MET cc_start: 0.9813 (mpp) cc_final: 0.9545 (pmm) REVERT: D 168 MET cc_start: 0.9484 (mmp) cc_final: 0.9180 (mmp) REVERT: D 408 MET cc_start: 0.9703 (mpp) cc_final: 0.9474 (pmm) REVERT: E 121 MET cc_start: 0.9205 (tpp) cc_final: 0.8982 (tpp) REVERT: E 168 MET cc_start: 0.9288 (tpt) cc_final: 0.8995 (tpt) REVERT: G 123 MET cc_start: 0.7434 (pmm) cc_final: 0.5409 (pmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1232 time to fit residues: 15.0201 Evaluate side-chains 69 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 211 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.025462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.019867 restraints weight = 339661.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.020403 restraints weight = 235529.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.020793 restraints weight = 182798.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.021085 restraints weight = 151631.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.021267 restraints weight = 132009.116| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21644 Z= 0.136 Angle : 0.565 8.800 29344 Z= 0.286 Chirality : 0.038 0.169 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.049 17.512 2933 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.17), residues: 2590 helix: 2.49 (0.15), residues: 1134 sheet: -0.04 (0.21), residues: 609 loop : 0.42 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 155 TYR 0.016 0.001 TYR D 169 PHE 0.030 0.002 PHE G 43 TRP 0.059 0.002 TRP D 66 HIS 0.006 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00285 (21644) covalent geometry : angle 0.56518 (29344) hydrogen bonds : bond 0.02636 ( 1064) hydrogen bonds : angle 4.03412 ( 3045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9124 (mmp) cc_final: 0.8460 (mmp) REVERT: A 123 MET cc_start: 0.8690 (pmm) cc_final: 0.7819 (pmm) REVERT: B 48 MET cc_start: 0.8864 (mmm) cc_final: 0.7811 (mmm) REVERT: B 123 MET cc_start: 0.6746 (ptp) cc_final: 0.6055 (ptm) REVERT: B 408 MET cc_start: 0.9822 (mpp) cc_final: 0.9503 (pmm) REVERT: C 31 MET cc_start: 0.8775 (pmm) cc_final: 0.8464 (mmm) REVERT: C 48 MET cc_start: 0.8927 (tpt) cc_final: 0.8179 (mmm) REVERT: C 123 MET cc_start: 0.8293 (pmm) cc_final: 0.7464 (pmm) REVERT: C 408 MET cc_start: 0.9794 (mpp) cc_final: 0.9531 (pmm) REVERT: D 48 MET cc_start: 0.8540 (mmp) cc_final: 0.8306 (mmm) REVERT: D 168 MET cc_start: 0.9536 (mmp) cc_final: 0.9206 (mmp) REVERT: D 408 MET cc_start: 0.9697 (mpp) cc_final: 0.9459 (pmm) REVERT: E 121 MET cc_start: 0.9194 (tpp) cc_final: 0.8982 (tpp) REVERT: E 329 MET cc_start: 0.8330 (tpt) cc_final: 0.8022 (tpt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1229 time to fit residues: 15.4784 Evaluate side-chains 70 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 62 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN G 195 GLN G 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.024514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.019046 restraints weight = 352603.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.019570 restraints weight = 242465.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.019944 restraints weight = 187222.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.020236 restraints weight = 156122.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.020448 restraints weight = 135172.832| |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21644 Z= 0.245 Angle : 0.662 8.458 29344 Z= 0.344 Chirality : 0.039 0.177 3185 Planarity : 0.005 0.046 3773 Dihedral : 4.382 20.194 2933 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.17), residues: 2590 helix: 1.97 (0.15), residues: 1134 sheet: 0.16 (0.21), residues: 567 loop : 0.07 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 155 TYR 0.016 0.002 TYR A 108 PHE 0.021 0.002 PHE G 43 TRP 0.070 0.003 TRP F 66 HIS 0.007 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00491 (21644) covalent geometry : angle 0.66233 (29344) hydrogen bonds : bond 0.03184 ( 1064) hydrogen bonds : angle 4.34185 ( 3045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9115 (mmp) cc_final: 0.8600 (mmm) REVERT: A 123 MET cc_start: 0.8863 (pmm) cc_final: 0.7712 (pmm) REVERT: A 401 MET cc_start: 0.9082 (mmp) cc_final: 0.8881 (mmm) REVERT: B 48 MET cc_start: 0.9003 (mmm) cc_final: 0.7853 (mmm) REVERT: B 408 MET cc_start: 0.9839 (mpp) cc_final: 0.9608 (pmm) REVERT: C 48 MET cc_start: 0.9019 (tpt) cc_final: 0.8384 (mmm) REVERT: C 123 MET cc_start: 0.8027 (pmm) cc_final: 0.7446 (pmm) REVERT: C 408 MET cc_start: 0.9780 (mpp) cc_final: 0.9483 (pmm) REVERT: D 168 MET cc_start: 0.9420 (mmp) cc_final: 0.9050 (mmt) REVERT: D 408 MET cc_start: 0.9704 (mpp) cc_final: 0.9497 (pmm) REVERT: E 168 MET cc_start: 0.9271 (tpt) cc_final: 0.8989 (tpt) REVERT: E 329 MET cc_start: 0.8263 (tpt) cc_final: 0.7951 (tpt) REVERT: F 121 MET cc_start: 0.9066 (tpp) cc_final: 0.8731 (tpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1272 time to fit residues: 15.6148 Evaluate side-chains 68 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 194 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 246 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.025028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.019446 restraints weight = 340700.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.019972 restraints weight = 236944.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.020353 restraints weight = 184393.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.020639 restraints weight = 153355.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.020835 restraints weight = 133779.310| |-----------------------------------------------------------------------------| r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21644 Z= 0.136 Angle : 0.579 9.122 29344 Z= 0.292 Chirality : 0.038 0.168 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.187 18.268 2933 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.17), residues: 2590 helix: 2.40 (0.15), residues: 1127 sheet: -0.06 (0.21), residues: 609 loop : 0.26 (0.24), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 346 TYR 0.012 0.001 TYR D 169 PHE 0.034 0.002 PHE A 288 TRP 0.061 0.002 TRP F 66 HIS 0.009 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00287 (21644) covalent geometry : angle 0.57921 (29344) hydrogen bonds : bond 0.02663 ( 1064) hydrogen bonds : angle 4.09081 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.02 seconds wall clock time: 38 minutes 1.08 seconds (2281.08 seconds total)