Starting phenix.real_space_refine on Wed Jun 18 14:45:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tby_41148/06_2025/8tby_41148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tby_41148/06_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_41148/06_2025/8tby_41148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tby_41148/06_2025/8tby_41148.map" model { file = "/net/cci-nas-00/data/ceres_data/8tby_41148/06_2025/8tby_41148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tby_41148/06_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-5710/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: 11.70, per 1000 atoms: 0.55 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: 5.13 Conformation dependent library (CDL) restraints added in 2.6 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: 2.54 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: 6.89 Time building geometry restraints manager: 5.95 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: 0.17 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: 0.360 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: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 45.150 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.980 ------------------------------------------------------------------------------- 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 : 2.309 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: 0.3371 time to fit residues: 56.5098 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 : 2.225 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.025662 restraints weight = 335988.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.026294 restraints weight = 211061.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.026770 restraints weight = 154306.502| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 5.577 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 3.79691 ( 3045) covalent geometry : bond 0.00278 (21644) covalent geometry : angle 0.50693 (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 : 2.354 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: 0.8910 (mmp) cc_final: 0.8279 (mmm) REVERT: A 123 MET cc_start: 0.7149 (pmm) cc_final: 0.6098 (pmm) REVERT: A 168 MET cc_start: 0.8734 (tpt) cc_final: 0.7961 (tpp) REVERT: B 48 MET cc_start: 0.7744 (mmm) cc_final: 0.6802 (mmm) REVERT: B 84 LEU cc_start: 0.9381 (tp) cc_final: 0.9120 (tt) REVERT: B 168 MET cc_start: 0.8847 (tpt) cc_final: 0.8083 (tpp) REVERT: B 408 MET cc_start: 0.9721 (mpp) cc_final: 0.9362 (pmm) REVERT: C 48 MET cc_start: 0.9052 (tpt) cc_final: 0.8551 (mmm) REVERT: C 123 MET cc_start: 0.8411 (pmm) cc_final: 0.7458 (pmm) REVERT: C 408 MET cc_start: 0.9713 (mpp) cc_final: 0.9451 (pmm) REVERT: D 48 MET cc_start: 0.8415 (mmp) cc_final: 0.7972 (mmm) REVERT: D 168 MET cc_start: 0.9532 (mmp) cc_final: 0.8999 (mmm) REVERT: D 254 LEU cc_start: 0.9485 (tp) cc_final: 0.9165 (tt) REVERT: D 408 MET cc_start: 0.9720 (mpp) cc_final: 0.9403 (pmm) REVERT: E 48 MET cc_start: 0.8970 (mmp) cc_final: 0.8565 (mmm) REVERT: E 121 MET cc_start: 0.8925 (mmp) cc_final: 0.8329 (tpp) REVERT: F 280 LEU cc_start: 0.9831 (tp) cc_final: 0.9415 (pp) REVERT: F 408 MET cc_start: 0.9657 (mpp) cc_final: 0.9426 (pmm) REVERT: G 123 MET cc_start: 0.6554 (pmm) cc_final: 0.5234 (pmm) REVERT: G 168 MET cc_start: 0.8990 (tpt) cc_final: 0.8660 (tpp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3465 time to fit residues: 45.8913 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 : 2.312 ------------------------------------------------------------------------------- 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: 8.9990 chunk 77 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 165 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- 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 = 0.2876 r_free = 0.2876 target = 0.028382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.023329 restraints weight = 352905.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.023937 restraints weight = 222440.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.024367 restraints weight = 163162.987| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21644 Z= 0.222 Angle : 0.612 7.935 29344 Z= 0.318 Chirality : 0.038 0.171 3185 Planarity : 0.005 0.068 3773 Dihedral : 4.058 19.590 2933 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % 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: 1.90 (0.17), residues: 2590 helix: 2.72 (0.15), residues: 1120 sheet: -0.13 (0.21), residues: 595 loop : 0.45 (0.23), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 359 HIS 0.006 0.001 HIS D 249 PHE 0.017 0.002 PHE C 97 TYR 0.014 0.001 TYR C 108 ARG 0.006 0.001 ARG G 177 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 1064) hydrogen bonds : angle 4.02337 ( 3045) covalent geometry : bond 0.00447 (21644) covalent geometry : angle 0.61164 (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 : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9152 (mmp) cc_final: 0.8625 (mmm) REVERT: A 123 MET cc_start: 0.8394 (pmm) cc_final: 0.8049 (pmm) REVERT: A 168 MET cc_start: 0.9083 (tpt) cc_final: 0.8411 (tpp) REVERT: B 48 MET cc_start: 0.7968 (mmm) cc_final: 0.7071 (mmm) REVERT: B 84 LEU cc_start: 0.9451 (tp) cc_final: 0.9216 (tt) REVERT: B 168 MET cc_start: 0.8877 (tpt) cc_final: 0.8141 (tpt) REVERT: B 401 MET cc_start: 0.8906 (mmp) cc_final: 0.8675 (mmm) REVERT: B 408 MET cc_start: 0.9772 (mpp) cc_final: 0.9420 (pmm) REVERT: C 48 MET cc_start: 0.9105 (tpt) cc_final: 0.8449 (mmm) REVERT: C 123 MET cc_start: 0.7494 (pmm) cc_final: 0.6730 (pmm) REVERT: C 408 MET cc_start: 0.9754 (mpp) cc_final: 0.9471 (pmm) REVERT: D 168 MET cc_start: 0.9514 (mmp) cc_final: 0.8620 (mpp) REVERT: D 408 MET cc_start: 0.9639 (mpp) cc_final: 0.9388 (pmm) REVERT: E 121 MET cc_start: 0.9326 (mmp) cc_final: 0.9014 (tpp) REVERT: F 168 MET cc_start: 0.8427 (mpp) cc_final: 0.8224 (mpp) REVERT: G 123 MET cc_start: 0.6566 (pmm) cc_final: 0.5326 (pmm) REVERT: G 168 MET cc_start: 0.8967 (tpt) cc_final: 0.8575 (tpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3321 time to fit residues: 42.6895 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 : 2.365 ------------------------------------------------------------------------------- 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: 50.0000 chunk 237 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 124 optimal weight: 0.1980 chunk 105 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.029066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.024030 restraints weight = 349957.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.024674 restraints weight = 214875.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.025126 restraints weight = 154893.358| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21644 Z= 0.126 Angle : 0.532 7.198 29344 Z= 0.271 Chirality : 0.038 0.169 3185 Planarity : 0.004 0.045 3773 Dihedral : 3.854 16.540 2933 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: 2.01 (0.17), residues: 2590 helix: 2.84 (0.15), residues: 1127 sheet: -0.11 (0.20), residues: 609 loop : 0.47 (0.24), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 66 HIS 0.010 0.001 HIS A 383 PHE 0.010 0.001 PHE C 380 TYR 0.009 0.001 TYR C 108 ARG 0.010 0.000 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.02617 ( 1064) hydrogen bonds : angle 3.84105 ( 3045) covalent geometry : bond 0.00268 (21644) covalent geometry : angle 0.53176 (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 86 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 2.409 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: 0.9167 (mmp) cc_final: 0.8645 (mmm) REVERT: A 123 MET cc_start: 0.8295 (pmm) cc_final: 0.7747 (pmm) REVERT: B 48 MET cc_start: 0.8068 (mmm) cc_final: 0.7130 (mmm) REVERT: B 84 LEU cc_start: 0.9439 (tp) cc_final: 0.9209 (tt) REVERT: B 168 MET cc_start: 0.8717 (tpt) cc_final: 0.8345 (tpp) REVERT: B 401 MET cc_start: 0.8858 (mmp) cc_final: 0.8596 (mmm) REVERT: B 408 MET cc_start: 0.9766 (mpp) cc_final: 0.9404 (pmm) REVERT: C 48 MET cc_start: 0.9034 (tpt) cc_final: 0.8492 (mmm) REVERT: C 123 MET cc_start: 0.8075 (pmm) cc_final: 0.6277 (pmm) REVERT: C 408 MET cc_start: 0.9767 (mpp) cc_final: 0.9486 (pmm) REVERT: D 48 MET cc_start: 0.8501 (mmp) cc_final: 0.7971 (mmm) REVERT: D 168 MET cc_start: 0.9527 (mmp) cc_final: 0.8692 (mpp) REVERT: D 408 MET cc_start: 0.9690 (mpp) cc_final: 0.9415 (pmm) REVERT: E 48 MET cc_start: 0.9030 (mmp) cc_final: 0.8640 (mmm) REVERT: E 121 MET cc_start: 0.9330 (mmp) cc_final: 0.9094 (tpp) REVERT: G 123 MET cc_start: 0.6732 (pmm) cc_final: 0.5546 (ptp) REVERT: G 168 MET cc_start: 0.8898 (tpt) cc_final: 0.8630 (tpt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3682 time to fit residues: 49.5672 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 : 2.237 ------------------------------------------------------------------------------- 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: 0.7980 chunk 59 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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** ** 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** ** 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 = 0.2798 r_free = 0.2798 target = 0.025950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.020175 restraints weight = 331377.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.020707 restraints weight = 233138.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.021095 restraints weight = 182504.731| |-----------------------------------------------------------------------------| r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21644 Z= 0.205 Angle : 0.592 8.690 29344 Z= 0.309 Chirality : 0.038 0.170 3185 Planarity : 0.004 0.051 3773 Dihedral : 4.022 18.036 2933 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: 1.81 (0.17), residues: 2590 helix: 2.64 (0.15), residues: 1127 sheet: -0.16 (0.20), residues: 609 loop : 0.40 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 66 HIS 0.006 0.001 HIS A 383 PHE 0.014 0.002 PHE C 368 TYR 0.012 0.001 TYR A 169 ARG 0.005 0.001 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 1064) hydrogen bonds : angle 3.99917 ( 3045) covalent geometry : bond 0.00412 (21644) covalent geometry : angle 0.59235 (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 77 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9034 (mmp) cc_final: 0.8531 (mmm) REVERT: A 123 MET cc_start: 0.7673 (pmm) cc_final: 0.6732 (pmm) REVERT: B 48 MET cc_start: 0.8596 (mmm) cc_final: 0.7510 (mmm) REVERT: B 84 LEU cc_start: 0.9422 (tp) cc_final: 0.9213 (tt) REVERT: B 401 MET cc_start: 0.8917 (mmp) cc_final: 0.8653 (mmm) REVERT: B 408 MET cc_start: 0.9832 (mpp) cc_final: 0.9511 (pmm) REVERT: C 48 MET cc_start: 0.9169 (tpt) cc_final: 0.8605 (mmm) REVERT: C 408 MET cc_start: 0.9828 (mpp) cc_final: 0.9585 (pmm) REVERT: D 48 MET cc_start: 0.8891 (mmp) cc_final: 0.8354 (mmm) REVERT: D 168 MET cc_start: 0.9534 (mmp) cc_final: 0.8797 (mpp) REVERT: D 408 MET cc_start: 0.9704 (mpp) cc_final: 0.9464 (pmm) REVERT: E 48 MET cc_start: 0.9100 (mmp) cc_final: 0.8703 (mmm) REVERT: G 123 MET cc_start: 0.6906 (pmm) cc_final: 0.5267 (ptp) REVERT: G 168 MET cc_start: 0.9022 (tpt) cc_final: 0.8818 (tpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3216 time to fit residues: 40.9099 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 : 2.256 ------------------------------------------------------------------------------- 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: 6.9990 chunk 188 optimal weight: 9.9990 chunk 116 optimal weight: 40.0000 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 123 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 G 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.025448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.019791 restraints weight = 335239.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.020315 restraints weight = 235573.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.020661 restraints weight = 183259.611| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21644 Z= 0.222 Angle : 0.616 8.052 29344 Z= 0.324 Chirality : 0.039 0.170 3185 Planarity : 0.005 0.049 3773 Dihedral : 4.194 20.018 2933 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 1.52 (0.17), residues: 2590 helix: 2.27 (0.15), residues: 1134 sheet: -0.19 (0.21), residues: 609 loop : 0.34 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 66 HIS 0.006 0.001 HIS C 86 PHE 0.016 0.002 PHE G 97 TYR 0.018 0.002 TYR D 169 ARG 0.005 0.001 ARG D 343 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 1064) hydrogen bonds : angle 4.17299 ( 3045) covalent geometry : bond 0.00444 (21644) covalent geometry : angle 0.61591 (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 76 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.305 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: 0.9007 (mmp) cc_final: 0.8444 (mmm) REVERT: B 48 MET cc_start: 0.8553 (mmm) cc_final: 0.7426 (mmm) REVERT: B 408 MET cc_start: 0.9812 (mpp) cc_final: 0.9550 (pmm) REVERT: C 48 MET cc_start: 0.9137 (tpt) cc_final: 0.8573 (mmm) REVERT: C 123 MET cc_start: 0.8620 (pmm) cc_final: 0.7618 (pmm) REVERT: C 408 MET cc_start: 0.9804 (mpp) cc_final: 0.9545 (pmm) REVERT: D 48 MET cc_start: 0.8905 (mmp) cc_final: 0.8459 (mmm) REVERT: D 168 MET cc_start: 0.9441 (mmp) cc_final: 0.8771 (mpp) REVERT: D 408 MET cc_start: 0.9677 (mpp) cc_final: 0.9438 (pmm) REVERT: E 48 MET cc_start: 0.8907 (mmp) cc_final: 0.8690 (mmm) REVERT: E 121 MET cc_start: 0.9211 (mmm) cc_final: 0.8372 (mmm) REVERT: G 123 MET cc_start: 0.7605 (pmm) cc_final: 0.6558 (pmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3183 time to fit residues: 39.9645 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 : 2.242 ------------------------------------------------------------------------------- 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: 6.9990 chunk 8 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 216 optimal weight: 0.5980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 HIS ** F 86 HIS ** 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 = 0.2798 r_free = 0.2798 target = 0.025858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.020055 restraints weight = 326111.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.020586 restraints weight = 229509.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.020977 restraints weight = 179441.141| |-----------------------------------------------------------------------------| r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21644 Z= 0.110 Angle : 0.554 9.936 29344 Z= 0.279 Chirality : 0.039 0.177 3185 Planarity : 0.004 0.046 3773 Dihedral : 3.967 16.625 2933 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 1.93 (0.17), residues: 2590 helix: 2.73 (0.15), residues: 1127 sheet: -0.07 (0.21), residues: 609 loop : 0.46 (0.24), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 66 HIS 0.003 0.001 HIS D 46 PHE 0.021 0.001 PHE D 288 TYR 0.009 0.001 TYR E 222 ARG 0.008 0.000 ARG F 44 Details of bonding type rmsd hydrogen bonds : bond 0.02539 ( 1064) hydrogen bonds : angle 3.90856 ( 3045) covalent geometry : bond 0.00236 (21644) covalent geometry : angle 0.55449 (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 76 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.264 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: 0.9120 (mmp) cc_final: 0.8443 (mmp) REVERT: A 123 MET cc_start: 0.8758 (pmm) cc_final: 0.8035 (pmm) REVERT: B 48 MET cc_start: 0.8811 (mmm) cc_final: 0.7732 (mmm) REVERT: B 84 LEU cc_start: 0.9412 (tp) cc_final: 0.9208 (tt) REVERT: B 401 MET cc_start: 0.8865 (mmp) cc_final: 0.8624 (mmm) REVERT: B 408 MET cc_start: 0.9828 (mpp) cc_final: 0.9503 (pmm) REVERT: C 48 MET cc_start: 0.9237 (tpt) cc_final: 0.8553 (mmm) REVERT: C 408 MET cc_start: 0.9798 (mpp) cc_final: 0.9543 (pmm) REVERT: D 168 MET cc_start: 0.9603 (mmp) cc_final: 0.8950 (mpp) REVERT: D 408 MET cc_start: 0.9705 (mpp) cc_final: 0.9461 (pmm) REVERT: E 48 MET cc_start: 0.9027 (mmp) cc_final: 0.8686 (mmm) REVERT: E 168 MET cc_start: 0.9360 (tpt) cc_final: 0.9023 (tpt) REVERT: G 123 MET cc_start: 0.7372 (pmm) cc_final: 0.5928 (ptp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3165 time to fit residues: 39.7626 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 : 2.272 ------------------------------------------------------------------------------- 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: 5.9990 chunk 69 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 45 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.019396 restraints weight = 342440.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.019904 restraints weight = 240008.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.020274 restraints weight = 187510.194| |-----------------------------------------------------------------------------| r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21644 Z= 0.241 Angle : 0.639 7.837 29344 Z= 0.333 Chirality : 0.039 0.172 3185 Planarity : 0.005 0.043 3773 Dihedral : 4.207 20.073 2933 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 1.55 (0.17), residues: 2590 helix: 2.30 (0.15), residues: 1134 sheet: -0.16 (0.20), residues: 609 loop : 0.33 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 66 HIS 0.006 0.001 HIS D 412 PHE 0.021 0.002 PHE F 208 TYR 0.020 0.002 TYR A 169 ARG 0.006 0.001 ARG C 367 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 1064) hydrogen bonds : angle 4.18411 ( 3045) covalent geometry : bond 0.00484 (21644) covalent geometry : angle 0.63918 (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 73 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.424 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: 0.9221 (mmp) cc_final: 0.8596 (mmm) REVERT: B 48 MET cc_start: 0.8946 (mmm) cc_final: 0.7779 (mmm) REVERT: B 408 MET cc_start: 0.9837 (mpp) cc_final: 0.9592 (pmm) REVERT: C 48 MET cc_start: 0.9297 (tpt) cc_final: 0.8621 (mmm) REVERT: C 408 MET cc_start: 0.9783 (mpp) cc_final: 0.9494 (pmm) REVERT: D 168 MET cc_start: 0.9510 (mmp) cc_final: 0.8807 (mpp) REVERT: D 408 MET cc_start: 0.9697 (mpp) cc_final: 0.9484 (pmm) REVERT: E 48 MET cc_start: 0.9057 (mmp) cc_final: 0.8796 (mmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3268 time to fit residues: 39.7382 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 : 2.403 ------------------------------------------------------------------------------- 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: 5.9990 chunk 92 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 160 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 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** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.025071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.019535 restraints weight = 340442.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.020056 restraints weight = 237203.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.020442 restraints weight = 183856.654| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21644 Z= 0.181 Angle : 0.592 7.894 29344 Z= 0.304 Chirality : 0.038 0.169 3185 Planarity : 0.004 0.044 3773 Dihedral : 4.178 18.786 2933 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 1.59 (0.17), residues: 2590 helix: 2.34 (0.15), residues: 1134 sheet: -0.13 (0.21), residues: 609 loop : 0.33 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 66 HIS 0.004 0.001 HIS C 86 PHE 0.016 0.002 PHE D 43 TYR 0.031 0.001 TYR D 169 ARG 0.008 0.000 ARG D 155 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 1064) hydrogen bonds : angle 4.14140 ( 3045) covalent geometry : bond 0.00366 (21644) covalent geometry : angle 0.59242 (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 74 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 2.673 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: 0.9221 (mmp) cc_final: 0.8566 (mmm) REVERT: A 123 MET cc_start: 0.8886 (pmm) cc_final: 0.8492 (pmm) REVERT: B 48 MET cc_start: 0.8935 (mmm) cc_final: 0.7765 (mmm) REVERT: B 408 MET cc_start: 0.9828 (mpp) cc_final: 0.9584 (pmm) REVERT: C 31 MET cc_start: 0.8961 (pmm) cc_final: 0.8634 (mmm) REVERT: C 48 MET cc_start: 0.9009 (tpt) cc_final: 0.8243 (mmm) REVERT: C 408 MET cc_start: 0.9808 (mpp) cc_final: 0.9541 (pmm) REVERT: D 168 MET cc_start: 0.9560 (mmp) cc_final: 0.9093 (mmt) REVERT: D 408 MET cc_start: 0.9699 (mpp) cc_final: 0.9476 (pmm) REVERT: E 48 MET cc_start: 0.9020 (mmp) cc_final: 0.8782 (mmm) REVERT: G 123 MET cc_start: 0.7588 (pmm) cc_final: 0.6008 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3338 time to fit residues: 41.2290 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 : 2.445 ------------------------------------------------------------------------------- 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: 4.9990 chunk 157 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 242 optimal weight: 0.0970 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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** A 195 GLN ** 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.025102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.019546 restraints weight = 344824.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.020078 restraints weight = 239257.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.020467 restraints weight = 185452.042| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21644 Z= 0.153 Angle : 0.578 8.867 29344 Z= 0.293 Chirality : 0.038 0.169 3185 Planarity : 0.004 0.044 3773 Dihedral : 4.145 18.464 2933 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 1.67 (0.17), residues: 2590 helix: 2.44 (0.15), residues: 1134 sheet: -0.13 (0.20), residues: 623 loop : 0.36 (0.24), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 66 HIS 0.003 0.001 HIS A 383 PHE 0.018 0.002 PHE C 288 TYR 0.011 0.001 TYR D 169 ARG 0.004 0.000 ARG F 185 Details of bonding type rmsd hydrogen bonds : bond 0.02703 ( 1064) hydrogen bonds : angle 4.07308 ( 3045) covalent geometry : bond 0.00316 (21644) covalent geometry : angle 0.57823 (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 73 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.9091 (mmp) cc_final: 0.8611 (mmm) REVERT: A 123 MET cc_start: 0.8717 (pmm) cc_final: 0.8145 (pmm) REVERT: B 48 MET cc_start: 0.8914 (mmm) cc_final: 0.7749 (mmm) REVERT: B 408 MET cc_start: 0.9836 (mpp) cc_final: 0.9532 (pmm) REVERT: C 31 MET cc_start: 0.9037 (pmm) cc_final: 0.8675 (mmm) REVERT: C 48 MET cc_start: 0.9008 (tpt) cc_final: 0.8212 (mmm) REVERT: C 408 MET cc_start: 0.9768 (mpp) cc_final: 0.9466 (pmm) REVERT: D 48 MET cc_start: 0.8731 (mmp) cc_final: 0.8412 (mmm) REVERT: D 168 MET cc_start: 0.9545 (mmp) cc_final: 0.9253 (mmp) REVERT: D 408 MET cc_start: 0.9697 (mpp) cc_final: 0.9473 (pmm) REVERT: E 48 MET cc_start: 0.8976 (mmp) cc_final: 0.8753 (mmm) REVERT: E 123 MET cc_start: 0.6241 (pmm) cc_final: 0.6019 (pmm) REVERT: G 123 MET cc_start: 0.7875 (pmm) cc_final: 0.6782 (pmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3091 time to fit residues: 38.2353 Evaluate side-chains 68 residues out of total 2261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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: 0.8980 chunk 43 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 68 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 1 optimal weight: 0.0570 chunk 243 optimal weight: 0.9990 chunk 111 optimal weight: 40.0000 chunk 254 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 149 ASN ** 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** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.020028 restraints weight = 334543.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.020583 restraints weight = 230513.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.020991 restraints weight = 177214.935| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4150 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 : 0.569 8.343 29344 Z= 0.281 Chirality : 0.039 0.164 3185 Planarity : 0.004 0.046 3773 Dihedral : 3.918 16.322 2933 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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 (0.18), residues: 2590 helix: 2.69 (0.16), residues: 1134 sheet: 0.12 (0.21), residues: 609 loop : 0.46 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 66 HIS 0.003 0.001 HIS D 268 PHE 0.014 0.001 PHE D 43 TYR 0.014 0.001 TYR D 169 ARG 0.005 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.02404 ( 1064) hydrogen bonds : angle 3.82709 ( 3045) covalent geometry : bond 0.00211 (21644) covalent geometry : angle 0.56924 (29344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4474.62 seconds wall clock time: 80 minutes 7.02 seconds (4807.02 seconds total)