Starting phenix.real_space_refine on Sun Sep 29 04:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/09_2024/8tby_41148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/09_2024/8tby_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/09_2024/8tby_41148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/09_2024/8tby_41148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/09_2024/8tby_41148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/09_2024/8tby_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-5461/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: 11.39, per 1000 atoms: 0.54 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: 4.67 Conformation dependent library (CDL) restraints added in 2.7 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: 2.47 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: 6.78 Time building geometry restraints manager: 5.50 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 43.890 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.740 ------------------------------------------------------------------------------- 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= 0.130 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 3.281 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: 0.3691 time to fit residues: 61.7329 Evaluate side-chains 79 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.608 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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= 0.182 Angle : 0.507 5.575 29344 Z= 0.262 Chirality : 0.037 0.164 3185 Planarity : 0.004 0.044 3773 Dihedral : 3.723 13.785 2933 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2590 helix: 2.98 (0.15), residues: 1127 sheet: 0.36 (0.22), residues: 546 loop : 0.16 (0.22), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 359 HIS 0.005 0.001 HIS G 268 PHE 0.012 0.001 PHE C 97 TYR 0.010 0.001 TYR C 403 ARG 0.008 0.000 ARG D 114 *********************** 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 fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.671 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: 0.8548 (mmp) cc_final: 0.8052 (mmm) REVERT: A 123 MET cc_start: 0.7830 (pmm) cc_final: 0.6533 (pmm) REVERT: A 168 MET cc_start: 0.9010 (tpt) cc_final: 0.8229 (tpp) REVERT: B 48 MET cc_start: 0.7233 (mmm) cc_final: 0.6467 (mmm) REVERT: B 84 LEU cc_start: 0.9416 (tp) cc_final: 0.9114 (tt) REVERT: B 168 MET cc_start: 0.9141 (tpt) cc_final: 0.8376 (tpp) REVERT: B 408 MET cc_start: 0.9595 (mpp) cc_final: 0.9216 (pmm) REVERT: C 123 MET cc_start: 0.8899 (pmm) cc_final: 0.7846 (pmm) REVERT: C 408 MET cc_start: 0.9637 (mpp) cc_final: 0.9373 (pmm) REVERT: D 48 MET cc_start: 0.7823 (mmp) cc_final: 0.7601 (mmm) REVERT: D 168 MET cc_start: 0.9084 (mmp) cc_final: 0.8756 (mmm) REVERT: D 254 LEU cc_start: 0.9440 (tp) cc_final: 0.9094 (tt) REVERT: D 408 MET cc_start: 0.9709 (mpp) cc_final: 0.9374 (pmm) REVERT: E 48 MET cc_start: 0.8825 (mmp) cc_final: 0.8468 (mmm) REVERT: E 121 MET cc_start: 0.8674 (mmp) cc_final: 0.8134 (tpp) REVERT: F 280 LEU cc_start: 0.9831 (tp) cc_final: 0.9369 (pp) REVERT: F 408 MET cc_start: 0.9688 (mpp) cc_final: 0.9462 (pmm) REVERT: G 123 MET cc_start: 0.7219 (pmm) cc_final: 0.5651 (pmm) REVERT: G 168 MET cc_start: 0.9024 (tpt) cc_final: 0.8741 (tpp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3465 time to fit residues: 45.9824 Evaluate side-chains 76 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 383 HIS ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21644 Z= 0.337 Angle : 0.656 8.357 29344 Z= 0.345 Chirality : 0.039 0.173 3185 Planarity : 0.005 0.043 3773 Dihedral : 4.222 19.152 2933 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2590 helix: 2.50 (0.15), residues: 1113 sheet: -0.17 (0.21), residues: 595 loop : 0.36 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 112 HIS 0.008 0.001 HIS D 249 PHE 0.019 0.002 PHE C 97 TYR 0.016 0.002 TYR C 108 ARG 0.010 0.001 ARG D 343 *********************** 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 76 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8910 (mmp) cc_final: 0.8461 (mmm) REVERT: A 123 MET cc_start: 0.8877 (pmm) cc_final: 0.8330 (pmm) REVERT: A 168 MET cc_start: 0.9350 (tpt) cc_final: 0.8572 (tpt) REVERT: B 48 MET cc_start: 0.7647 (mmm) cc_final: 0.6882 (mmm) REVERT: B 408 MET cc_start: 0.9676 (mpp) cc_final: 0.9349 (pmm) REVERT: C 48 MET cc_start: 0.7885 (mmp) cc_final: 0.7553 (mmm) REVERT: C 123 MET cc_start: 0.8056 (pmm) cc_final: 0.7018 (pmm) REVERT: C 408 MET cc_start: 0.9653 (mpp) cc_final: 0.9362 (pmm) REVERT: D 168 MET cc_start: 0.9150 (mmp) cc_final: 0.8623 (mpp) REVERT: E 121 MET cc_start: 0.9274 (mmp) cc_final: 0.9018 (tpp) REVERT: G 123 MET cc_start: 0.7316 (pmm) cc_final: 0.5703 (pmm) REVERT: G 168 MET cc_start: 0.9006 (tpt) cc_final: 0.8679 (tpt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3207 time to fit residues: 41.0539 Evaluate side-chains 68 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 250 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21644 Z= 0.227 Angle : 0.562 8.197 29344 Z= 0.292 Chirality : 0.038 0.167 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.020 17.169 2933 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: 1.77 (0.17), residues: 2590 helix: 2.64 (0.15), residues: 1127 sheet: -0.18 (0.20), residues: 609 loop : 0.33 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 66 HIS 0.012 0.002 HIS A 383 PHE 0.012 0.001 PHE E 97 TYR 0.012 0.001 TYR C 108 ARG 0.005 0.000 ARG C 224 *********************** 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 84 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.468 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: 0.8899 (mmp) cc_final: 0.8491 (mmm) REVERT: A 123 MET cc_start: 0.8861 (pmm) cc_final: 0.8128 (pmm) REVERT: B 48 MET cc_start: 0.7786 (mmm) cc_final: 0.6976 (mmm) REVERT: B 84 LEU cc_start: 0.9507 (tp) cc_final: 0.9244 (tt) REVERT: B 168 MET cc_start: 0.8838 (tpt) cc_final: 0.8578 (tpp) REVERT: B 408 MET cc_start: 0.9674 (mpp) cc_final: 0.9367 (pmm) REVERT: C 123 MET cc_start: 0.8498 (pmm) cc_final: 0.6448 (pmm) REVERT: C 408 MET cc_start: 0.9644 (mpp) cc_final: 0.9335 (pmm) REVERT: D 48 MET cc_start: 0.8074 (mmp) cc_final: 0.7834 (mmm) REVERT: D 168 MET cc_start: 0.9085 (mmp) cc_final: 0.8674 (mpp) REVERT: D 408 MET cc_start: 0.9642 (mpp) cc_final: 0.9440 (pmm) REVERT: G 123 MET cc_start: 0.7586 (pmm) cc_final: 0.6402 (ptp) REVERT: G 168 MET cc_start: 0.8941 (tpt) cc_final: 0.8710 (tpt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3557 time to fit residues: 47.1407 Evaluate side-chains 73 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 5.9990 chunk 142 optimal weight: 0.0870 chunk 3 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 127 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 ASN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21644 Z= 0.190 Angle : 0.546 8.138 29344 Z= 0.279 Chirality : 0.038 0.166 3185 Planarity : 0.004 0.048 3773 Dihedral : 3.952 16.744 2933 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: 1.85 (0.17), residues: 2590 helix: 2.68 (0.15), residues: 1134 sheet: -0.12 (0.21), residues: 609 loop : 0.37 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 66 HIS 0.009 0.001 HIS A 268 PHE 0.016 0.001 PHE C 43 TYR 0.010 0.001 TYR F 222 ARG 0.003 0.000 ARG D 346 *********************** 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 75 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8433 (mmp) cc_final: 0.8063 (mmm) REVERT: A 123 MET cc_start: 0.8547 (pmm) cc_final: 0.7135 (pmm) REVERT: B 48 MET cc_start: 0.7969 (mmm) cc_final: 0.7052 (mmm) REVERT: B 84 LEU cc_start: 0.9498 (tp) cc_final: 0.9237 (tt) REVERT: B 168 MET cc_start: 0.8888 (tpt) cc_final: 0.8544 (tpp) REVERT: B 408 MET cc_start: 0.9680 (mpp) cc_final: 0.9304 (pmm) REVERT: C 48 MET cc_start: 0.7526 (mmp) cc_final: 0.6842 (mmp) REVERT: C 123 MET cc_start: 0.9160 (pmm) cc_final: 0.8924 (pmm) REVERT: C 408 MET cc_start: 0.9677 (mpp) cc_final: 0.9365 (pmm) REVERT: D 48 MET cc_start: 0.8195 (mmp) cc_final: 0.7888 (mmm) REVERT: D 168 MET cc_start: 0.9051 (mmp) cc_final: 0.8707 (mpp) REVERT: D 408 MET cc_start: 0.9655 (mpp) cc_final: 0.9429 (pmm) REVERT: E 48 MET cc_start: 0.8858 (mmp) cc_final: 0.8565 (mmm) REVERT: E 121 MET cc_start: 0.9126 (tpp) cc_final: 0.8820 (tpp) REVERT: G 123 MET cc_start: 0.7718 (pmm) cc_final: 0.6403 (ptp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3405 time to fit residues: 41.7237 Evaluate side-chains 71 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21644 Z= 0.201 Angle : 0.550 9.356 29344 Z= 0.282 Chirality : 0.038 0.168 3185 Planarity : 0.004 0.055 3773 Dihedral : 3.943 17.852 2933 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 1.95 (0.17), residues: 2590 helix: 2.73 (0.15), residues: 1127 sheet: -0.02 (0.21), residues: 595 loop : 0.42 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 66 HIS 0.007 0.001 HIS A 268 PHE 0.012 0.001 PHE G 380 TYR 0.013 0.001 TYR D 169 ARG 0.013 0.000 ARG E 177 *********************** 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 74 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.145 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: 0.8447 (mmp) cc_final: 0.8032 (mmm) REVERT: A 168 MET cc_start: 0.9313 (tpt) cc_final: 0.9056 (tpt) REVERT: B 48 MET cc_start: 0.8065 (mmm) cc_final: 0.7043 (mmm) REVERT: B 84 LEU cc_start: 0.9510 (tp) cc_final: 0.9256 (tt) REVERT: B 408 MET cc_start: 0.9685 (mpp) cc_final: 0.9314 (pmm) REVERT: C 48 MET cc_start: 0.7597 (mmp) cc_final: 0.7079 (mmp) REVERT: C 123 MET cc_start: 0.9036 (pmm) cc_final: 0.8637 (pmm) REVERT: C 408 MET cc_start: 0.9683 (mpp) cc_final: 0.9368 (pmm) REVERT: D 48 MET cc_start: 0.8285 (mmp) cc_final: 0.7963 (mmm) REVERT: D 168 MET cc_start: 0.9159 (mmp) cc_final: 0.8734 (mpp) REVERT: D 408 MET cc_start: 0.9663 (mpp) cc_final: 0.9390 (pmm) REVERT: E 48 MET cc_start: 0.8858 (mmp) cc_final: 0.8572 (mmm) REVERT: G 123 MET cc_start: 0.7891 (pmm) cc_final: 0.6761 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3160 time to fit residues: 38.7941 Evaluate side-chains 71 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 182 optimal weight: 40.0000 chunk 141 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 HIS G 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21644 Z= 0.322 Angle : 0.649 8.617 29344 Z= 0.340 Chirality : 0.039 0.178 3185 Planarity : 0.005 0.042 3773 Dihedral : 4.299 20.527 2933 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 1.46 (0.17), residues: 2590 helix: 2.21 (0.15), residues: 1134 sheet: -0.18 (0.21), residues: 609 loop : 0.27 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 66 HIS 0.007 0.002 HIS D 412 PHE 0.018 0.002 PHE G 97 TYR 0.027 0.002 TYR A 229 ARG 0.007 0.001 ARG E 177 *********************** 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 73 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.553 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: 0.8779 (mmp) cc_final: 0.8090 (mmp) REVERT: A 123 MET cc_start: 0.8942 (pmm) cc_final: 0.7708 (pmm) REVERT: B 48 MET cc_start: 0.8448 (mmm) cc_final: 0.7362 (mmm) REVERT: B 408 MET cc_start: 0.9708 (mpp) cc_final: 0.9426 (pmm) REVERT: C 48 MET cc_start: 0.8038 (mmp) cc_final: 0.7427 (mmp) REVERT: C 123 MET cc_start: 0.9511 (pmm) cc_final: 0.9089 (pmm) REVERT: C 408 MET cc_start: 0.9687 (mpp) cc_final: 0.9369 (pmm) REVERT: E 48 MET cc_start: 0.8967 (mmp) cc_final: 0.8733 (mmm) REVERT: E 329 MET cc_start: 0.8328 (tpt) cc_final: 0.8047 (tpt) REVERT: G 123 MET cc_start: 0.7646 (pmm) cc_final: 0.6765 (ptp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3244 time to fit residues: 39.0658 Evaluate side-chains 71 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 0.0170 chunk 196 optimal weight: 8.9990 overall best weight: 3.1824 ------------------------------------------------------------------------------- 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** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21644 Z= 0.186 Angle : 0.567 9.357 29344 Z= 0.286 Chirality : 0.039 0.171 3185 Planarity : 0.004 0.044 3773 Dihedral : 4.085 17.689 2933 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 1.78 (0.17), residues: 2590 helix: 2.52 (0.15), residues: 1134 sheet: -0.06 (0.21), residues: 609 loop : 0.41 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP F 66 HIS 0.006 0.001 HIS A 268 PHE 0.023 0.001 PHE D 288 TYR 0.010 0.001 TYR A 169 ARG 0.006 0.000 ARG E 177 *********************** 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 fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.435 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: 0.8713 (mmp) cc_final: 0.8121 (mmm) REVERT: A 123 MET cc_start: 0.9071 (pmm) cc_final: 0.8234 (pmm) REVERT: B 48 MET cc_start: 0.8453 (mmm) cc_final: 0.7438 (mmm) REVERT: B 408 MET cc_start: 0.9682 (mpp) cc_final: 0.9388 (pmm) REVERT: C 48 MET cc_start: 0.8027 (mmp) cc_final: 0.7335 (mmp) REVERT: C 123 MET cc_start: 0.9500 (pmm) cc_final: 0.9074 (pmm) REVERT: C 408 MET cc_start: 0.9692 (mpp) cc_final: 0.9367 (pmm) REVERT: E 48 MET cc_start: 0.8863 (mmp) cc_final: 0.8658 (mmm) REVERT: E 123 MET cc_start: 0.7522 (pmm) cc_final: 0.7219 (pmm) REVERT: G 123 MET cc_start: 0.7978 (pmm) cc_final: 0.6588 (pmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3254 time to fit residues: 39.4979 Evaluate side-chains 70 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 231 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21644 Z= 0.155 Angle : 0.555 8.636 29344 Z= 0.277 Chirality : 0.039 0.168 3185 Planarity : 0.004 0.045 3773 Dihedral : 3.961 16.705 2933 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.98 (0.17), residues: 2590 helix: 2.70 (0.15), residues: 1134 sheet: 0.03 (0.21), residues: 609 loop : 0.48 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP D 66 HIS 0.006 0.001 HIS A 268 PHE 0.021 0.001 PHE E 288 TYR 0.031 0.001 TYR D 169 ARG 0.005 0.000 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.564 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: 0.8626 (mmp) cc_final: 0.8028 (mmm) REVERT: A 123 MET cc_start: 0.9239 (pmm) cc_final: 0.8386 (pmm) REVERT: B 48 MET cc_start: 0.8346 (mmm) cc_final: 0.7326 (mmm) REVERT: B 408 MET cc_start: 0.9677 (mpp) cc_final: 0.9315 (pmm) REVERT: C 48 MET cc_start: 0.7979 (mmp) cc_final: 0.7299 (mmp) REVERT: C 123 MET cc_start: 0.9549 (pmm) cc_final: 0.8645 (pmm) REVERT: C 408 MET cc_start: 0.9651 (mpp) cc_final: 0.9362 (pmm) REVERT: D 168 MET cc_start: 0.9378 (mmp) cc_final: 0.9063 (mmp) REVERT: E 48 MET cc_start: 0.8785 (mmp) cc_final: 0.8567 (mmm) REVERT: E 123 MET cc_start: 0.7703 (pmm) cc_final: 0.7109 (pmm) REVERT: E 329 MET cc_start: 0.8226 (tpt) cc_final: 0.7716 (tpt) REVERT: G 123 MET cc_start: 0.8321 (pmm) cc_final: 0.6912 (pmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3291 time to fit residues: 41.7444 Evaluate side-chains 71 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 150 optimal weight: 0.2980 chunk 116 optimal weight: 0.5980 chunk 171 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21644 Z= 0.187 Angle : 0.559 8.404 29344 Z= 0.282 Chirality : 0.038 0.169 3185 Planarity : 0.004 0.045 3773 Dihedral : 3.974 19.816 2933 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 2.71 (0.15), residues: 1134 sheet: 0.04 (0.21), residues: 609 loop : 0.49 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 66 HIS 0.006 0.001 HIS A 268 PHE 0.035 0.001 PHE G 43 TYR 0.013 0.001 TYR D 169 ARG 0.004 0.000 ARG F 185 ********************** 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 fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8663 (mmp) cc_final: 0.8014 (mmp) REVERT: A 123 MET cc_start: 0.9463 (pmm) cc_final: 0.8209 (pmm) REVERT: B 48 MET cc_start: 0.8433 (mmm) cc_final: 0.7309 (mmm) REVERT: B 408 MET cc_start: 0.9685 (mpp) cc_final: 0.9323 (pmm) REVERT: C 48 MET cc_start: 0.8070 (mmp) cc_final: 0.7378 (mmp) REVERT: C 123 MET cc_start: 0.9579 (pmm) cc_final: 0.8765 (pmm) REVERT: C 408 MET cc_start: 0.9607 (mpp) cc_final: 0.9325 (pmm) REVERT: D 168 MET cc_start: 0.9397 (mmp) cc_final: 0.9156 (mmm) REVERT: E 123 MET cc_start: 0.7314 (pmm) cc_final: 0.6972 (pmm) REVERT: E 168 MET cc_start: 0.9400 (tpt) cc_final: 0.9199 (tpt) REVERT: E 329 MET cc_start: 0.8290 (tpt) cc_final: 0.7756 (tpt) REVERT: F 121 MET cc_start: 0.9241 (tpt) cc_final: 0.9039 (tpt) REVERT: G 123 MET cc_start: 0.8066 (pmm) cc_final: 0.7174 (pmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3278 time to fit residues: 40.0187 Evaluate side-chains 72 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 189 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN G 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.024973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.019428 restraints weight = 339094.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.019954 restraints weight = 235235.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.020340 restraints weight = 182580.864| |-----------------------------------------------------------------------------| r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4366 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= 0.229 Angle : 0.583 8.279 29344 Z= 0.297 Chirality : 0.038 0.171 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.086 19.512 2933 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2590 helix: 2.55 (0.15), residues: 1134 sheet: -0.09 (0.20), residues: 623 loop : 0.43 (0.24), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 66 HIS 0.006 0.001 HIS A 268 PHE 0.020 0.002 PHE G 43 TYR 0.013 0.001 TYR D 169 ARG 0.005 0.000 ARG E 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.17 seconds wall clock time: 48 minutes 31.70 seconds (2911.70 seconds total)