Starting phenix.real_space_refine on Tue Jul 23 05:54:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/07_2024/8tby_41148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/07_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_41148/07_2024/8tby_41148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/07_2024/8tby_41148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/07_2024/8tby_41148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tby_41148/07_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 Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.06, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 8.44 Conformation dependent library (CDL) restraints added in 3.7 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: 2.37 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: 6.42 Time building geometry restraints manager: 9.27 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: 99.96 - 106.77: 693 106.77 - 113.58: 11576 113.58 - 120.40: 7671 120.40 - 127.21: 9118 127.21 - 134.02: 286 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 2.440 nonbonded pdb=" OH TYR E 399 " pdb=" O ALA E 410 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR D 399 " pdb=" O ALA D 410 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR C 399 " pdb=" O ALA C 410 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR F 399 " pdb=" O ALA F 410 " model vdw 2.262 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.010 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 54.370 Find NCS groups from input model: 0.790 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.300 ------------------------------------------------------------------------------- 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 : 2.599 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: 0.3757 time to fit residues: 62.6492 Evaluate side-chains 79 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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: 2.9990 chunk 196 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 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 76 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS C 76 HIS ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 383 HIS D 76 HIS D 109 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 ASN D 383 HIS ** E 160 GLN ** 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 211 ASN G 383 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21644 Z= 0.232 Angle : 0.521 7.481 29344 Z= 0.273 Chirality : 0.037 0.171 3185 Planarity : 0.004 0.041 3773 Dihedral : 3.767 14.692 2933 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % 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: 2.17 (0.17), residues: 2590 helix: 3.09 (0.15), residues: 1127 sheet: 0.16 (0.21), residues: 560 loop : 0.18 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 359 HIS 0.006 0.001 HIS G 268 PHE 0.014 0.001 PHE C 97 TYR 0.010 0.001 TYR C 403 ARG 0.006 0.000 ARG G 56 *********************** 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 80 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8739 (mmp) cc_final: 0.8302 (mmm) REVERT: A 123 MET cc_start: 0.7967 (pmm) cc_final: 0.6875 (pmm) REVERT: A 168 MET cc_start: 0.9209 (tpt) cc_final: 0.8242 (tpp) REVERT: B 84 LEU cc_start: 0.9445 (tp) cc_final: 0.9151 (tt) REVERT: B 168 MET cc_start: 0.9137 (tpt) cc_final: 0.8403 (tpp) REVERT: B 408 MET cc_start: 0.9639 (mpp) cc_final: 0.9208 (pmm) REVERT: C 123 MET cc_start: 0.8847 (pmm) cc_final: 0.7799 (pmm) REVERT: C 408 MET cc_start: 0.9695 (mpp) cc_final: 0.9413 (pmm) REVERT: D 48 MET cc_start: 0.8022 (mmp) cc_final: 0.7726 (mmm) REVERT: D 168 MET cc_start: 0.9106 (mmp) cc_final: 0.8793 (mmm) REVERT: D 408 MET cc_start: 0.9653 (mpp) cc_final: 0.9364 (pmm) REVERT: E 48 MET cc_start: 0.8938 (mmp) cc_final: 0.8620 (mmm) REVERT: E 121 MET cc_start: 0.8768 (mmp) cc_final: 0.8248 (tpp) REVERT: F 280 LEU cc_start: 0.9829 (tp) cc_final: 0.9302 (pp) REVERT: F 408 MET cc_start: 0.9674 (mpp) cc_final: 0.9445 (pmm) REVERT: G 123 MET cc_start: 0.7126 (pmm) cc_final: 0.5007 (pmm) REVERT: G 168 MET cc_start: 0.8947 (tpt) cc_final: 0.8653 (tpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.3566 time to fit residues: 45.8615 Evaluate side-chains 71 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.726 ------------------------------------------------------------------------------- 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: 20.0000 chunk 72 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 383 HIS ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 366 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN E 383 HIS ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN F 383 HIS ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 21644 Z= 0.374 Angle : 0.704 9.885 29344 Z= 0.373 Chirality : 0.040 0.176 3185 Planarity : 0.005 0.070 3773 Dihedral : 4.428 20.670 2933 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 25.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.35 % Allowed : 8.09 % Favored : 91.55 % 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: 1.32 (0.17), residues: 2590 helix: 2.12 (0.15), residues: 1120 sheet: -0.18 (0.20), residues: 595 loop : 0.14 (0.23), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 176 HIS 0.009 0.002 HIS C 383 PHE 0.022 0.002 PHE E 137 TYR 0.019 0.002 TYR C 108 ARG 0.009 0.001 ARG D 346 *********************** 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 82 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8951 (mmp) cc_final: 0.8417 (mmm) REVERT: A 123 MET cc_start: 0.8938 (pmm) cc_final: 0.8085 (pmm) REVERT: A 168 MET cc_start: 0.9247 (tpt) cc_final: 0.8576 (tpt) REVERT: B 48 MET cc_start: 0.8191 (mmm) cc_final: 0.7212 (mmm) REVERT: B 408 MET cc_start: 0.9666 (mpp) cc_final: 0.9297 (pmm) REVERT: C 48 MET cc_start: 0.8128 (mmp) cc_final: 0.7799 (mmm) REVERT: C 123 MET cc_start: 0.7965 (pmm) cc_final: 0.7709 (pmm) REVERT: C 408 MET cc_start: 0.9603 (mpp) cc_final: 0.9271 (pmm) REVERT: D 168 MET cc_start: 0.9101 (mmp) cc_final: 0.8649 (mpp) REVERT: D 408 MET cc_start: 0.9698 (mpp) cc_final: 0.9401 (pmm) REVERT: G 123 MET cc_start: 0.6979 (pmm) cc_final: 0.4226 (pmm) REVERT: G 168 MET cc_start: 0.8997 (tpt) cc_final: 0.8689 (tpt) outliers start: 8 outliers final: 3 residues processed: 81 average time/residue: 0.3260 time to fit residues: 43.4485 Evaluate side-chains 71 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 2.644 ------------------------------------------------------------------------------- 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: 5.9990 chunk 177 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21644 Z= 0.252 Angle : 0.574 9.547 29344 Z= 0.300 Chirality : 0.038 0.163 3185 Planarity : 0.004 0.046 3773 Dihedral : 4.204 19.992 2933 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.17), residues: 2590 helix: 2.43 (0.15), residues: 1127 sheet: -0.14 (0.20), residues: 609 loop : 0.18 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 66 HIS 0.011 0.002 HIS A 383 PHE 0.016 0.002 PHE D 43 TYR 0.013 0.001 TYR C 108 ARG 0.006 0.001 ARG D 346 *********************** 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 76 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8968 (mmp) cc_final: 0.8555 (mmm) REVERT: B 48 MET cc_start: 0.8348 (mmm) cc_final: 0.7352 (mmm) REVERT: B 408 MET cc_start: 0.9681 (mpp) cc_final: 0.9296 (pmm) REVERT: C 48 MET cc_start: 0.7805 (mmp) cc_final: 0.7290 (mmm) REVERT: C 408 MET cc_start: 0.9581 (mpp) cc_final: 0.9210 (pmm) REVERT: D 168 MET cc_start: 0.9095 (mmp) cc_final: 0.8744 (mpp) REVERT: D 408 MET cc_start: 0.9657 (mpp) cc_final: 0.9337 (pmm) REVERT: F 121 MET cc_start: 0.8853 (tpp) cc_final: 0.8567 (tpp) REVERT: G 168 MET cc_start: 0.9067 (tpt) cc_final: 0.8745 (tpt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3395 time to fit residues: 42.6550 Evaluate side-chains 68 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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: 6.9990 chunk 142 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 173 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 127 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 ASN ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21644 Z= 0.169 Angle : 0.531 7.994 29344 Z= 0.271 Chirality : 0.038 0.167 3185 Planarity : 0.004 0.048 3773 Dihedral : 4.030 17.421 2933 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: 1.89 (0.17), residues: 2590 helix: 2.73 (0.15), residues: 1127 sheet: 0.01 (0.21), residues: 595 loop : 0.28 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 66 HIS 0.008 0.001 HIS A 383 PHE 0.015 0.001 PHE A 43 TYR 0.010 0.001 TYR C 108 ARG 0.004 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 73 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8491 (mmp) cc_final: 0.8149 (mmm) REVERT: A 123 MET cc_start: 0.8736 (pmm) cc_final: 0.8030 (pmm) REVERT: B 48 MET cc_start: 0.8255 (mmm) cc_final: 0.7224 (mmm) REVERT: B 84 LEU cc_start: 0.9502 (tp) cc_final: 0.9252 (tt) REVERT: B 408 MET cc_start: 0.9682 (mpp) cc_final: 0.9329 (pmm) REVERT: C 48 MET cc_start: 0.7703 (mmp) cc_final: 0.7065 (mmp) REVERT: C 408 MET cc_start: 0.9580 (mpp) cc_final: 0.9253 (pmm) REVERT: D 168 MET cc_start: 0.9123 (mmp) cc_final: 0.8670 (mpp) REVERT: D 408 MET cc_start: 0.9671 (mpp) cc_final: 0.9351 (pmm) REVERT: E 121 MET cc_start: 0.9083 (tpp) cc_final: 0.8733 (tpp) REVERT: E 168 MET cc_start: 0.9390 (tpt) cc_final: 0.9007 (tpt) REVERT: E 329 MET cc_start: 0.8165 (tpt) cc_final: 0.7944 (tpt) REVERT: G 168 MET cc_start: 0.9070 (tpt) cc_final: 0.8722 (tpt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3140 time to fit residues: 38.5653 Evaluate side-chains 70 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.360 ------------------------------------------------------------------------------- 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: 9.9990 chunk 225 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 250 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 314 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 379 ASN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 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 : 0.004 0.042 21644 Z= 0.284 Angle : 0.614 8.374 29344 Z= 0.322 Chirality : 0.039 0.177 3185 Planarity : 0.004 0.041 3773 Dihedral : 4.289 21.057 2933 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.36 (0.15), residues: 1127 sheet: -0.09 (0.21), residues: 609 loop : 0.27 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP F 66 HIS 0.008 0.002 HIS E 383 PHE 0.016 0.002 PHE E 97 TYR 0.013 0.002 TYR G 226 ARG 0.006 0.001 ARG D 224 *********************** 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 71 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8719 (mmp) cc_final: 0.8155 (mmp) REVERT: A 123 MET cc_start: 0.8773 (pmm) cc_final: 0.7569 (pmm) REVERT: B 48 MET cc_start: 0.8419 (mmm) cc_final: 0.7263 (mmm) REVERT: B 408 MET cc_start: 0.9678 (mpp) cc_final: 0.9311 (pmm) REVERT: C 48 MET cc_start: 0.8089 (mmp) cc_final: 0.7367 (mmp) REVERT: C 408 MET cc_start: 0.9642 (mpp) cc_final: 0.9290 (pmm) REVERT: D 168 MET cc_start: 0.9089 (mmp) cc_final: 0.8680 (mpp) REVERT: D 408 MET cc_start: 0.9675 (mpp) cc_final: 0.9366 (pmm) REVERT: E 168 MET cc_start: 0.9309 (tpt) cc_final: 0.9022 (tpt) REVERT: E 329 MET cc_start: 0.8159 (tpt) cc_final: 0.7878 (tpt) REVERT: G 123 MET cc_start: 0.7633 (pmm) cc_final: 0.7402 (pmm) REVERT: G 168 MET cc_start: 0.9003 (tpt) cc_final: 0.8733 (tpt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3164 time to fit residues: 37.8246 Evaluate side-chains 69 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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: 20.0000 chunk 28 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 0.0370 chunk 115 optimal weight: 20.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** E 379 ASN ** 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 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.003 0.027 21644 Z= 0.173 Angle : 0.543 8.552 29344 Z= 0.274 Chirality : 0.038 0.168 3185 Planarity : 0.004 0.044 3773 Dihedral : 4.075 17.413 2933 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 1.88 (0.17), residues: 2590 helix: 2.65 (0.15), residues: 1134 sheet: 0.00 (0.21), residues: 609 loop : 0.38 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 66 HIS 0.006 0.001 HIS A 383 PHE 0.022 0.001 PHE B 288 TYR 0.011 0.001 TYR F 229 ARG 0.005 0.000 ARG D 346 *********************** 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 fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8701 (mmp) cc_final: 0.8136 (mmp) REVERT: A 123 MET cc_start: 0.9127 (pmm) cc_final: 0.8883 (pmm) REVERT: B 408 MET cc_start: 0.9697 (mpp) cc_final: 0.9279 (pmm) REVERT: C 48 MET cc_start: 0.8088 (mmp) cc_final: 0.7420 (mmp) REVERT: C 123 MET cc_start: 0.8616 (pmm) cc_final: 0.7894 (pmm) REVERT: C 408 MET cc_start: 0.9595 (mpp) cc_final: 0.9239 (pmm) REVERT: D 168 MET cc_start: 0.9154 (mmp) cc_final: 0.8809 (mpp) REVERT: D 408 MET cc_start: 0.9676 (mpp) cc_final: 0.9374 (pmm) REVERT: E 123 MET cc_start: 0.7530 (pmm) cc_final: 0.7291 (pmm) REVERT: G 168 MET cc_start: 0.8991 (tpt) cc_final: 0.8697 (tpt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3341 time to fit residues: 42.8966 Evaluate side-chains 70 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.725 ------------------------------------------------------------------------------- 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: 9.9990 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 170 optimal weight: 0.3980 chunk 123 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN B 149 ASN B 314 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 ASN ** 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 ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21644 Z= 0.170 Angle : 0.534 7.222 29344 Z= 0.270 Chirality : 0.038 0.166 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.004 17.277 2933 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: 2.72 (0.15), residues: 1134 sheet: 0.12 (0.21), residues: 595 loop : 0.40 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 66 HIS 0.005 0.001 HIS E 383 PHE 0.029 0.001 PHE G 43 TYR 0.011 0.001 TYR B 169 ARG 0.004 0.000 ARG D 346 *********************** 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 : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8673 (mmp) cc_final: 0.8086 (mmp) REVERT: A 168 MET cc_start: 0.9064 (tpt) cc_final: 0.8698 (tpp) REVERT: B 48 MET cc_start: 0.8128 (mmm) cc_final: 0.7147 (mmm) REVERT: B 84 LEU cc_start: 0.9513 (tp) cc_final: 0.9272 (tt) REVERT: B 408 MET cc_start: 0.9701 (mpp) cc_final: 0.9276 (pmm) REVERT: C 48 MET cc_start: 0.8140 (mmp) cc_final: 0.7471 (mmp) REVERT: C 123 MET cc_start: 0.8594 (pmm) cc_final: 0.7846 (pmm) REVERT: C 408 MET cc_start: 0.9606 (mpp) cc_final: 0.9278 (pmm) REVERT: D 48 MET cc_start: 0.8289 (mmp) cc_final: 0.7969 (mmm) REVERT: D 408 MET cc_start: 0.9680 (mpp) cc_final: 0.9373 (pmm) REVERT: E 121 MET cc_start: 0.9198 (tpp) cc_final: 0.8909 (tpp) REVERT: E 123 MET cc_start: 0.7349 (pmm) cc_final: 0.6978 (pmm) REVERT: G 168 MET cc_start: 0.9008 (tpt) cc_final: 0.8702 (tpt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3550 time to fit residues: 43.6314 Evaluate side-chains 70 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.604 ------------------------------------------------------------------------------- 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: 0.3980 chunk 239 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 140 optimal weight: 0.4980 chunk 101 optimal weight: 40.0000 chunk 182 optimal weight: 0.0980 chunk 71 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 379 ASN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN F 379 ASN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21644 Z= 0.152 Angle : 0.534 8.753 29344 Z= 0.267 Chirality : 0.038 0.173 3185 Planarity : 0.004 0.045 3773 Dihedral : 3.931 17.999 2933 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: 2.08 (0.17), residues: 2590 helix: 2.78 (0.16), residues: 1134 sheet: 0.19 (0.21), residues: 595 loop : 0.45 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 66 HIS 0.005 0.001 HIS F 383 PHE 0.026 0.001 PHE G 43 TYR 0.012 0.001 TYR D 169 ARG 0.004 0.000 ARG D 346 *********************** 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 72 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8606 (mmp) cc_final: 0.8272 (mmm) REVERT: A 168 MET cc_start: 0.9070 (tpt) cc_final: 0.8685 (tpp) REVERT: B 48 MET cc_start: 0.8090 (mmm) cc_final: 0.7086 (mmm) REVERT: B 84 LEU cc_start: 0.9508 (tp) cc_final: 0.9267 (tt) REVERT: B 408 MET cc_start: 0.9692 (mpp) cc_final: 0.9257 (pmm) REVERT: C 31 MET cc_start: 0.8843 (pmm) cc_final: 0.8510 (mmm) REVERT: C 48 MET cc_start: 0.8094 (mmp) cc_final: 0.7415 (mmp) REVERT: C 123 MET cc_start: 0.8595 (pmm) cc_final: 0.8097 (pmm) REVERT: C 408 MET cc_start: 0.9601 (mpp) cc_final: 0.9263 (pmm) REVERT: D 48 MET cc_start: 0.8320 (mmp) cc_final: 0.7921 (mmm) REVERT: D 168 MET cc_start: 0.9342 (mmp) cc_final: 0.8871 (mpp) REVERT: D 408 MET cc_start: 0.9671 (mpp) cc_final: 0.9358 (pmm) REVERT: E 121 MET cc_start: 0.9209 (tpp) cc_final: 0.8966 (tpp) REVERT: E 123 MET cc_start: 0.7443 (pmm) cc_final: 0.7099 (pmm) REVERT: G 168 MET cc_start: 0.9016 (tpt) cc_final: 0.8782 (tpt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.3283 time to fit residues: 39.7109 Evaluate side-chains 70 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.492 ------------------------------------------------------------------------------- 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: 0.8980 chunk 150 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 379 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4236 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= 0.208 Angle : 0.556 10.897 29344 Z= 0.283 Chirality : 0.038 0.168 3185 Planarity : 0.004 0.045 3773 Dihedral : 4.009 17.403 2933 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 1.96 (0.17), residues: 2590 helix: 2.74 (0.15), residues: 1127 sheet: 0.12 (0.21), residues: 609 loop : 0.34 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 66 HIS 0.005 0.001 HIS B 383 PHE 0.027 0.002 PHE E 288 TYR 0.010 0.001 TYR C 108 ARG 0.004 0.000 ARG D 346 ********************** 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 69 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8612 (mmp) cc_final: 0.8227 (mmp) REVERT: A 168 MET cc_start: 0.9007 (tpt) cc_final: 0.8611 (tpp) REVERT: B 48 MET cc_start: 0.8220 (mmm) cc_final: 0.7167 (mmm) REVERT: B 408 MET cc_start: 0.9690 (mpp) cc_final: 0.9270 (pmm) REVERT: C 31 MET cc_start: 0.9038 (pmm) cc_final: 0.8670 (mmm) REVERT: C 48 MET cc_start: 0.8224 (mmp) cc_final: 0.7543 (mmp) REVERT: C 123 MET cc_start: 0.8378 (pmm) cc_final: 0.7782 (pmm) REVERT: C 408 MET cc_start: 0.9617 (mpp) cc_final: 0.9286 (pmm) REVERT: D 48 MET cc_start: 0.8358 (mmp) cc_final: 0.8064 (mmm) REVERT: D 168 MET cc_start: 0.9350 (mmp) cc_final: 0.9077 (mmt) REVERT: D 408 MET cc_start: 0.9687 (mpp) cc_final: 0.9385 (pmm) REVERT: E 121 MET cc_start: 0.9245 (tpp) cc_final: 0.9032 (tpp) REVERT: E 123 MET cc_start: 0.7235 (pmm) cc_final: 0.6837 (pmm) REVERT: E 168 MET cc_start: 0.9288 (tpt) cc_final: 0.8973 (tpt) REVERT: E 329 MET cc_start: 0.8121 (tpt) cc_final: 0.7587 (tpt) REVERT: F 121 MET cc_start: 0.8844 (tpp) cc_final: 0.8627 (tpp) REVERT: G 168 MET cc_start: 0.9027 (tpt) cc_final: 0.8788 (tpt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3126 time to fit residues: 36.9881 Evaluate side-chains 67 residues out of total 2261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.638 ------------------------------------------------------------------------------- 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: 0.2980 chunk 218 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 40.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 379 ASN B 379 ASN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 379 ASN ** 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 314 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 ASN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.025114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.019570 restraints weight = 341516.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.020099 restraints weight = 236706.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.020488 restraints weight = 183474.637| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.4562 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= 0.214 Angle : 0.563 9.491 29344 Z= 0.287 Chirality : 0.038 0.168 3185 Planarity : 0.004 0.044 3773 Dihedral : 4.098 17.441 2933 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: 1.86 (0.17), residues: 2590 helix: 2.61 (0.15), residues: 1127 sheet: 0.13 (0.21), residues: 609 loop : 0.29 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 66 HIS 0.006 0.001 HIS C 383 PHE 0.019 0.002 PHE G 43 TYR 0.012 0.001 TYR C 108 ARG 0.004 0.000 ARG F 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.18 seconds wall clock time: 48 minutes 38.88 seconds (2918.88 seconds total)