Starting phenix.real_space_refine on Wed May 21 11:14:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tby_41148/05_2025/8tby_41148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tby_41148/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tby_41148/05_2025/8tby_41148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tby_41148/05_2025/8tby_41148.map" model { file = "/net/cci-nas-00/data/ceres_data/8tby_41148/05_2025/8tby_41148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tby_41148/05_2025/8tby_41148.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.87, per 1000 atoms: 0.56 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: 5.12 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.24 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: 6.70 Time building geometry restraints manager: 6.01 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.460 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP G 112 HIS 0.010 0.001 HIS C 268 PHE 0.007 0.001 PHE E 95 TYR 0.007 0.001 TYR C 399 ARG 0.002 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.11633 ( 1064) hydrogen bonds : angle 4.41418 ( 3045) covalent geometry : bond 0.00200 (21644) covalent geometry : angle 0.55656 (29344) *********************** 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 : 2.280 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 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 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: 0.6877 (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: 0.9410 (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: 0.3397 time to fit residues: 56.7061 Evaluate side-chains 79 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.2964 r_free = 0.2964 target = 0.030841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.025643 restraints weight = 335986.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.026288 restraints weight = 211881.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.026762 restraints weight = 154858.168| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21644 Z= 0.132 Angle : 0.507 5.575 29344 Z= 0.262 Chirality : 0.037 0.164 3185 Planarity : 0.004 0.044 3773 Dihedral : 3.723 13.785 2933 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2590 helix: 2.98 (0.15), residues: 1127 sheet: 0.36 (0.22), residues: 546 loop : 0.16 (0.22), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 359 HIS 0.005 0.001 HIS G 268 PHE 0.012 0.001 PHE C 97 TYR 0.010 0.001 TYR C 403 ARG 0.008 0.000 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 1064) hydrogen bonds : angle 3.79692 ( 3045) covalent geometry : bond 0.00278 (21644) covalent geometry : angle 0.50694 (29344) *********************** 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 : 2.314 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: 0.8937 (mmp) cc_final: 0.8298 (mmm) REVERT: A 123 MET cc_start: 0.7095 (pmm) cc_final: 0.6072 (pmm) REVERT: A 168 MET cc_start: 0.8714 (tpt) cc_final: 0.7947 (tpp) REVERT: B 48 MET cc_start: 0.7821 (mmm) cc_final: 0.6860 (mmm) REVERT: B 84 LEU cc_start: 0.9375 (tp) cc_final: 0.9116 (tt) REVERT: B 168 MET cc_start: 0.8820 (tpt) cc_final: 0.8064 (tpp) REVERT: B 408 MET cc_start: 0.9728 (mpp) cc_final: 0.9371 (pmm) REVERT: C 48 MET cc_start: 0.9094 (tpt) cc_final: 0.8566 (mmm) REVERT: C 123 MET cc_start: 0.8368 (pmm) cc_final: 0.7431 (pmm) REVERT: C 408 MET cc_start: 0.9725 (mpp) cc_final: 0.9465 (pmm) REVERT: D 48 MET cc_start: 0.8459 (mmp) cc_final: 0.7999 (mmm) REVERT: D 168 MET cc_start: 0.9548 (mmp) cc_final: 0.9013 (mmm) REVERT: D 254 LEU cc_start: 0.9485 (tp) cc_final: 0.9166 (tt) REVERT: D 408 MET cc_start: 0.9730 (mpp) cc_final: 0.9416 (pmm) REVERT: E 48 MET cc_start: 0.9012 (mmp) cc_final: 0.8588 (mmm) REVERT: E 121 MET cc_start: 0.8939 (mmp) cc_final: 0.8340 (tpp) REVERT: F 280 LEU cc_start: 0.9831 (tp) cc_final: 0.9418 (pp) REVERT: F 408 MET cc_start: 0.9670 (mpp) cc_final: 0.9440 (pmm) REVERT: G 123 MET cc_start: 0.6494 (pmm) cc_final: 0.5204 (pmm) REVERT: G 168 MET cc_start: 0.8987 (tpt) cc_final: 0.8657 (tpp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3455 time to fit residues: 45.8965 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 : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 131 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.028051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.022973 restraints weight = 355863.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.023572 restraints weight = 225959.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.024004 restraints weight = 165958.711| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 21644 Z= 0.242 Angle : 0.640 9.406 29344 Z= 0.334 Chirality : 0.039 0.174 3185 Planarity : 0.005 0.088 3773 Dihedral : 4.163 20.246 2933 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2590 helix: 2.61 (0.15), residues: 1113 sheet: -0.16 (0.21), residues: 595 loop : 0.42 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 112 HIS 0.008 0.001 HIS D 249 PHE 0.018 0.002 PHE C 97 TYR 0.015 0.002 TYR G 60 ARG 0.013 0.001 ARG G 177 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 1064) hydrogen bonds : angle 4.10310 ( 3045) covalent geometry : bond 0.00488 (21644) covalent geometry : angle 0.64050 (29344) *********************** 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 77 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9142 (mmp) cc_final: 0.8487 (mmm) REVERT: A 123 MET cc_start: 0.8380 (pmm) cc_final: 0.8037 (pmm) REVERT: A 168 MET cc_start: 0.9051 (tpt) cc_final: 0.8357 (tpt) REVERT: B 48 MET cc_start: 0.8090 (mmm) cc_final: 0.7154 (mmm) REVERT: B 84 LEU cc_start: 0.9457 (tp) cc_final: 0.9228 (tt) REVERT: B 401 MET cc_start: 0.8906 (mmp) cc_final: 0.8698 (mmm) REVERT: B 408 MET cc_start: 0.9774 (mpp) cc_final: 0.9490 (pmm) REVERT: C 48 MET cc_start: 0.9086 (tpt) cc_final: 0.8437 (mmm) REVERT: C 123 MET cc_start: 0.7444 (pmm) cc_final: 0.6670 (pmm) REVERT: C 408 MET cc_start: 0.9726 (mpp) cc_final: 0.9445 (pmm) REVERT: D 168 MET cc_start: 0.9523 (mmp) cc_final: 0.8660 (mpp) REVERT: G 123 MET cc_start: 0.6445 (pmm) cc_final: 0.5269 (pmm) REVERT: G 168 MET cc_start: 0.8965 (tpt) cc_final: 0.8583 (tpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3050 time to fit residues: 39.8038 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 : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 148 optimal weight: 30.0000 chunk 237 optimal weight: 0.4980 chunk 99 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 379 ASN ** C 86 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** E 379 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.026523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.020678 restraints weight = 330817.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.021225 restraints weight = 233925.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.021615 restraints weight = 183039.474| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21644 Z= 0.127 Angle : 0.539 7.533 29344 Z= 0.274 Chirality : 0.038 0.169 3185 Planarity : 0.004 0.045 3773 Dihedral : 3.907 16.837 2933 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2590 helix: 2.77 (0.15), residues: 1127 sheet: -0.12 (0.20), residues: 609 loop : 0.45 (0.24), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 66 HIS 0.010 0.001 HIS A 383 PHE 0.010 0.001 PHE C 380 TYR 0.010 0.001 TYR C 108 ARG 0.004 0.000 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.02661 ( 1064) hydrogen bonds : angle 3.87546 ( 3045) covalent geometry : bond 0.00265 (21644) covalent geometry : angle 0.53880 (29344) *********************** 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 85 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 2.484 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 48 MET cc_start: 0.9247 (mmp) cc_final: 0.8717 (mmm) REVERT: A 123 MET cc_start: 0.8204 (pmm) cc_final: 0.7695 (pmm) REVERT: B 48 MET cc_start: 0.8281 (mmm) cc_final: 0.7302 (mmm) REVERT: B 84 LEU cc_start: 0.9416 (tp) cc_final: 0.9207 (tt) REVERT: B 168 MET cc_start: 0.8660 (tpt) cc_final: 0.8317 (tpp) REVERT: B 401 MET cc_start: 0.8900 (mmp) cc_final: 0.8627 (mmm) REVERT: B 408 MET cc_start: 0.9817 (mpp) cc_final: 0.9478 (pmm) REVERT: C 48 MET cc_start: 0.9073 (tpt) cc_final: 0.8511 (mmm) REVERT: C 123 MET cc_start: 0.7987 (pmm) cc_final: 0.6365 (pmm) REVERT: C 408 MET cc_start: 0.9836 (mpp) cc_final: 0.9586 (pmm) REVERT: D 48 MET cc_start: 0.8636 (mmp) cc_final: 0.8108 (mmm) REVERT: D 168 MET cc_start: 0.9574 (mmp) cc_final: 0.8778 (mpp) REVERT: D 408 MET cc_start: 0.9728 (mpp) cc_final: 0.9494 (pmm) REVERT: E 48 MET cc_start: 0.9103 (mmp) cc_final: 0.8673 (mmm) REVERT: E 121 MET cc_start: 0.9119 (tpp) cc_final: 0.8613 (tpp) REVERT: G 123 MET cc_start: 0.6555 (pmm) cc_final: 0.5385 (ptp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3671 time to fit residues: 48.8466 Evaluate side-chains 71 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN ** 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** E 379 ASN ** E 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.025578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.019927 restraints weight = 337874.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.020449 restraints weight = 237170.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.020821 restraints weight = 185353.418| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21644 Z= 0.236 Angle : 0.624 8.965 29344 Z= 0.329 Chirality : 0.039 0.197 3185 Planarity : 0.005 0.047 3773 Dihedral : 4.163 19.472 2933 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.17), residues: 2590 helix: 2.45 (0.15), residues: 1127 sheet: -0.17 (0.21), residues: 595 loop : 0.26 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 66 HIS 0.006 0.002 HIS A 383 PHE 0.021 0.002 PHE E 179 TYR 0.013 0.002 TYR C 108 ARG 0.011 0.001 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 1064) hydrogen bonds : angle 4.14854 ( 3045) covalent geometry : bond 0.00468 (21644) covalent geometry : angle 0.62379 (29344) *********************** 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 73 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.382 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 48 MET cc_start: 0.9002 (mmp) cc_final: 0.8490 (mmm) REVERT: A 123 MET cc_start: 0.7751 (pmm) cc_final: 0.6763 (pmm) REVERT: B 48 MET cc_start: 0.8511 (mmm) cc_final: 0.7362 (mmm) REVERT: B 401 MET cc_start: 0.8910 (mmp) cc_final: 0.8668 (mmm) REVERT: B 408 MET cc_start: 0.9815 (mpp) cc_final: 0.9549 (pmm) REVERT: C 48 MET cc_start: 0.9116 (tpt) cc_final: 0.8510 (mmm) REVERT: C 408 MET cc_start: 0.9789 (mpp) cc_final: 0.9525 (pmm) REVERT: D 48 MET cc_start: 0.8880 (mmp) cc_final: 0.8402 (mmm) REVERT: D 168 MET cc_start: 0.9494 (mmp) cc_final: 0.9121 (mmp) REVERT: E 48 MET cc_start: 0.9005 (mmp) cc_final: 0.8744 (mmm) REVERT: F 121 MET cc_start: 0.9236 (mmm) cc_final: 0.8959 (tpp) REVERT: F 280 LEU cc_start: 0.9780 (tp) cc_final: 0.9454 (pp) REVERT: G 123 MET cc_start: 0.7513 (pmm) cc_final: 0.5483 (pmm) REVERT: G 168 MET cc_start: 0.9036 (tpt) cc_final: 0.8832 (tpt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3186 time to fit residues: 38.6422 Evaluate side-chains 71 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 91 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 182 optimal weight: 30.0000 chunk 123 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 ** 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.025310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.019643 restraints weight = 336884.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.020175 restraints weight = 234611.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.020570 restraints weight = 183000.948| |-----------------------------------------------------------------------------| r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21644 Z= 0.202 Angle : 0.586 7.985 29344 Z= 0.307 Chirality : 0.038 0.170 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.161 19.316 2933 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.17), residues: 2590 helix: 2.36 (0.15), residues: 1134 sheet: -0.18 (0.21), residues: 609 loop : 0.32 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 66 HIS 0.005 0.001 HIS F 412 PHE 0.014 0.002 PHE G 97 TYR 0.017 0.002 TYR D 169 ARG 0.006 0.000 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 1064) hydrogen bonds : angle 4.12619 ( 3045) covalent geometry : bond 0.00405 (21644) covalent geometry : angle 0.58595 (29344) *********************** 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 : 2.483 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: 0.9071 (mmp) cc_final: 0.8489 (mmm) REVERT: A 123 MET cc_start: 0.8361 (pmm) cc_final: 0.7004 (pmm) REVERT: B 48 MET cc_start: 0.8781 (mmm) cc_final: 0.7597 (mmm) REVERT: B 408 MET cc_start: 0.9829 (mpp) cc_final: 0.9580 (pmm) REVERT: C 48 MET cc_start: 0.9249 (tpt) cc_final: 0.8677 (mmm) REVERT: C 123 MET cc_start: 0.8969 (pmm) cc_final: 0.7899 (pmm) REVERT: C 408 MET cc_start: 0.9812 (mpp) cc_final: 0.9556 (pmm) REVERT: D 48 MET cc_start: 0.9008 (mmp) cc_final: 0.8536 (mmm) REVERT: D 168 MET cc_start: 0.9400 (mmp) cc_final: 0.8745 (mpp) REVERT: E 48 MET cc_start: 0.9072 (mmp) cc_final: 0.8776 (mmm) REVERT: G 123 MET cc_start: 0.7902 (pmm) cc_final: 0.6535 (ptp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3299 time to fit residues: 40.7574 Evaluate side-chains 71 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 59 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 HIS ** 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 = 0.2797 r_free = 0.2797 target = 0.025843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.020086 restraints weight = 327764.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.020624 restraints weight = 230890.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.021018 restraints weight = 180540.701| |-----------------------------------------------------------------------------| r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21644 Z= 0.105 Angle : 0.558 9.225 29344 Z= 0.278 Chirality : 0.039 0.169 3185 Planarity : 0.004 0.047 3773 Dihedral : 3.965 17.875 2933 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2590 helix: 2.72 (0.15), residues: 1127 sheet: -0.05 (0.21), residues: 609 loop : 0.46 (0.24), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 66 HIS 0.004 0.001 HIS A 383 PHE 0.021 0.001 PHE D 288 TYR 0.010 0.001 TYR A 229 ARG 0.007 0.000 ARG F 44 Details of bonding type rmsd hydrogen bonds : bond 0.02544 ( 1064) hydrogen bonds : angle 3.90000 ( 3045) covalent geometry : bond 0.00229 (21644) covalent geometry : angle 0.55770 (29344) *********************** 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 75 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.380 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 48 MET cc_start: 0.9096 (mmp) cc_final: 0.8421 (mmp) REVERT: A 123 MET cc_start: 0.8820 (pmm) cc_final: 0.8613 (pmm) REVERT: B 48 MET cc_start: 0.8846 (mmm) cc_final: 0.7741 (mmm) REVERT: B 84 LEU cc_start: 0.9406 (tp) cc_final: 0.9205 (tt) REVERT: B 401 MET cc_start: 0.8807 (mmp) cc_final: 0.8600 (mmm) REVERT: B 408 MET cc_start: 0.9828 (mpp) cc_final: 0.9505 (pmm) REVERT: C 48 MET cc_start: 0.8856 (tpt) cc_final: 0.8108 (mmm) REVERT: C 123 MET cc_start: 0.8989 (pmm) cc_final: 0.8363 (pmm) REVERT: C 168 MET cc_start: 0.9407 (mtt) cc_final: 0.9190 (mtt) REVERT: C 408 MET cc_start: 0.9796 (mpp) cc_final: 0.9540 (pmm) REVERT: D 168 MET cc_start: 0.9608 (mmp) cc_final: 0.8947 (mpp) REVERT: E 48 MET cc_start: 0.9045 (mmp) cc_final: 0.8702 (mmm) REVERT: E 121 MET cc_start: 0.9041 (tpp) cc_final: 0.8770 (tpp) REVERT: F 123 MET cc_start: 0.8929 (pmm) cc_final: 0.8450 (pmm) REVERT: G 123 MET cc_start: 0.7318 (pmm) cc_final: 0.5687 (ptp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3401 time to fit residues: 41.8465 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 : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 238 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 37 optimal weight: 40.0000 chunk 45 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 210 optimal weight: 0.1980 chunk 92 optimal weight: 4.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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** ** D 249 HIS ** 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** G 149 ASN ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.025205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.019570 restraints weight = 339473.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.020105 restraints weight = 235635.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.020500 restraints weight = 183137.071| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21644 Z= 0.171 Angle : 0.573 8.154 29344 Z= 0.293 Chirality : 0.038 0.172 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.014 18.200 2933 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2590 helix: 2.65 (0.15), residues: 1134 sheet: -0.08 (0.20), residues: 609 loop : 0.45 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 66 HIS 0.004 0.001 HIS A 383 PHE 0.017 0.002 PHE F 208 TYR 0.010 0.001 TYR F 229 ARG 0.005 0.000 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.02679 ( 1064) hydrogen bonds : angle 3.95747 ( 3045) covalent geometry : bond 0.00350 (21644) covalent geometry : angle 0.57330 (29344) *********************** 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 75 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.505 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: 0.9195 (mmp) cc_final: 0.8563 (mmm) REVERT: A 123 MET cc_start: 0.8854 (pmm) cc_final: 0.8378 (pmm) REVERT: B 48 MET cc_start: 0.8976 (mmm) cc_final: 0.7771 (mmm) REVERT: B 401 MET cc_start: 0.8795 (mmp) cc_final: 0.8593 (mmm) REVERT: B 408 MET cc_start: 0.9855 (mpp) cc_final: 0.9556 (pmm) REVERT: C 48 MET cc_start: 0.9032 (tpt) cc_final: 0.8248 (mmm) REVERT: C 123 MET cc_start: 0.9364 (pmm) cc_final: 0.8946 (pmm) REVERT: C 408 MET cc_start: 0.9821 (mpp) cc_final: 0.9568 (pmm) REVERT: D 48 MET cc_start: 0.9072 (mmp) cc_final: 0.8792 (mmm) REVERT: D 168 MET cc_start: 0.9490 (mmp) cc_final: 0.9154 (mmp) REVERT: E 48 MET cc_start: 0.9163 (mmp) cc_final: 0.8870 (mmm) REVERT: F 121 MET cc_start: 0.9232 (mmm) cc_final: 0.8967 (tpt) REVERT: G 123 MET cc_start: 0.7903 (pmm) cc_final: 0.5728 (pmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3416 time to fit residues: 41.7178 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 : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 6 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 27 optimal weight: 30.0000 chunk 160 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 182 optimal weight: 40.0000 chunk 73 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 195 GLN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 249 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** D 412 HIS ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** 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** G 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.025150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.019582 restraints weight = 339448.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.020096 restraints weight = 237283.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.020483 restraints weight = 184865.507| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21644 Z= 0.178 Angle : 0.590 8.839 29344 Z= 0.302 Chirality : 0.038 0.170 3185 Planarity : 0.004 0.051 3773 Dihedral : 4.137 18.721 2933 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2590 helix: 2.47 (0.15), residues: 1134 sheet: -0.07 (0.21), residues: 609 loop : 0.39 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 66 HIS 0.004 0.001 HIS C 86 PHE 0.016 0.002 PHE F 208 TYR 0.028 0.002 TYR D 169 ARG 0.005 0.000 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.02764 ( 1064) hydrogen bonds : angle 4.06035 ( 3045) covalent geometry : bond 0.00361 (21644) covalent geometry : angle 0.59017 (29344) *********************** 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 77 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.297 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 48 MET cc_start: 0.9181 (mmp) cc_final: 0.8507 (mmm) REVERT: A 123 MET cc_start: 0.8444 (pmm) cc_final: 0.7439 (pmm) REVERT: B 48 MET cc_start: 0.8849 (mmm) cc_final: 0.7654 (mmm) REVERT: B 408 MET cc_start: 0.9822 (mpp) cc_final: 0.9569 (pmm) REVERT: C 31 MET cc_start: 0.8959 (pmm) cc_final: 0.8651 (mmm) REVERT: C 48 MET cc_start: 0.8981 (tpt) cc_final: 0.8184 (mmm) REVERT: C 123 MET cc_start: 0.9268 (pmm) cc_final: 0.8904 (pmm) REVERT: C 408 MET cc_start: 0.9798 (mpp) cc_final: 0.9525 (pmm) REVERT: D 48 MET cc_start: 0.8587 (mmp) cc_final: 0.8362 (mmm) REVERT: D 168 MET cc_start: 0.9527 (mmp) cc_final: 0.9047 (mmt) REVERT: E 48 MET cc_start: 0.8977 (mmp) cc_final: 0.8769 (mmm) REVERT: G 123 MET cc_start: 0.7641 (pmm) cc_final: 0.5538 (pmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3106 time to fit residues: 39.6274 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 : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 234 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 149 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.019800 restraints weight = 337825.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.020337 restraints weight = 234704.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.020732 restraints weight = 182284.386| |-----------------------------------------------------------------------------| r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21644 Z= 0.124 Angle : 0.565 8.850 29344 Z= 0.284 Chirality : 0.038 0.169 3185 Planarity : 0.004 0.047 3773 Dihedral : 4.061 23.018 2933 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2590 helix: 2.60 (0.15), residues: 1134 sheet: 0.00 (0.21), residues: 609 loop : 0.46 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP D 66 HIS 0.006 0.001 HIS D 412 PHE 0.033 0.002 PHE G 43 TYR 0.013 0.001 TYR G 229 ARG 0.005 0.000 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.02558 ( 1064) hydrogen bonds : angle 3.95545 ( 3045) covalent geometry : bond 0.00263 (21644) covalent geometry : angle 0.56536 (29344) ********************** 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 74 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9116 (mmp) cc_final: 0.8661 (mmm) REVERT: A 123 MET cc_start: 0.8448 (pmm) cc_final: 0.8133 (pmm) REVERT: B 48 MET cc_start: 0.8923 (mmm) cc_final: 0.7840 (mmm) REVERT: B 123 MET cc_start: 0.7567 (ttp) cc_final: 0.7291 (ttt) REVERT: B 408 MET cc_start: 0.9819 (mpp) cc_final: 0.9496 (pmm) REVERT: C 31 MET cc_start: 0.9031 (pmm) cc_final: 0.8681 (mmm) REVERT: C 48 MET cc_start: 0.8926 (tpt) cc_final: 0.8124 (mmm) REVERT: C 123 MET cc_start: 0.9303 (pmm) cc_final: 0.8962 (pmm) REVERT: C 408 MET cc_start: 0.9789 (mpp) cc_final: 0.9544 (pmm) REVERT: D 48 MET cc_start: 0.8552 (mmp) cc_final: 0.8291 (mmm) REVERT: D 168 MET cc_start: 0.9515 (mmp) cc_final: 0.9218 (mmp) REVERT: E 48 MET cc_start: 0.8916 (mmp) cc_final: 0.8710 (mmm) REVERT: E 123 MET cc_start: 0.6583 (pmm) cc_final: 0.6339 (pmm) REVERT: E 329 MET cc_start: 0.8253 (tpt) cc_final: 0.7885 (tpt) REVERT: F 121 MET cc_start: 0.9143 (tpp) cc_final: 0.8939 (tpt) REVERT: G 123 MET cc_start: 0.7998 (pmm) cc_final: 0.7098 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3183 time to fit residues: 39.2232 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 : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 242 optimal weight: 0.0030 chunk 43 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 111 optimal weight: 50.0000 chunk 254 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.4994 ------------------------------------------------------------------------------- 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.2788 r_free = 0.2788 target = 0.025592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.019915 restraints weight = 334781.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.020465 restraints weight = 232640.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.020870 restraints weight = 180058.895| |-----------------------------------------------------------------------------| r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21644 Z= 0.099 Angle : 0.556 8.421 29344 Z= 0.274 Chirality : 0.038 0.167 3185 Planarity : 0.004 0.047 3773 Dihedral : 3.950 20.409 2933 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.18), residues: 2590 helix: 2.78 (0.15), residues: 1127 sheet: 0.10 (0.21), residues: 609 loop : 0.44 (0.24), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP D 66 HIS 0.006 0.001 HIS D 412 PHE 0.029 0.001 PHE A 288 TYR 0.013 0.001 TYR D 169 ARG 0.004 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.02405 ( 1064) hydrogen bonds : angle 3.85818 ( 3045) covalent geometry : bond 0.00217 (21644) covalent geometry : angle 0.55563 (29344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4368.75 seconds wall clock time: 78 minutes 38.60 seconds (4718.60 seconds total)