Starting phenix.real_space_refine on Sat Feb 17 07:39:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/02_2024/8p49_17402.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/02_2024/8p49_17402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/02_2024/8p49_17402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/02_2024/8p49_17402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/02_2024/8p49_17402.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/02_2024/8p49_17402.pdb" } resolution = 2.79 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= -0.000 sd= 0.013 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 29 5.16 5 C 11728 2.51 5 N 2870 2.21 5 O 3287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3073 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain: "B" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2931 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 18, 'TRANS': 339} Chain breaks: 4 Chain: "C" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2989 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 18, 'TRANS': 347} Chain breaks: 2 Chain: "D" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2800 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 18, 'TRANS': 322} Chain breaks: 4 Chain: "E" Number of atoms: 3066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3066 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 18, 'TRANS': 357} Chain: "F" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3055 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 18, 'TRANS': 355} Time building chain proxies: 9.08, per 1000 atoms: 0.51 Number of scatterers: 17914 At special positions: 0 Unit cell: (98.77, 141.93, 136.95, 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 29 16.00 O 3287 8.00 N 2870 7.00 C 11728 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: 6.17 Conformation dependent library (CDL) restraints added in 3.3 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4172 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 38 sheets defined 44.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.570A pdb=" N ASN A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 91 Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.629A pdb=" N GLU A 132 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP A 133 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 removed outlier: 3.783A pdb=" N VAL A 145 " --> pdb=" O PHE A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.774A pdb=" N LYS A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.577A pdb=" N LYS A 352 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 371 Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 81 through 91 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.511A pdb=" N VAL B 134 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 145 removed outlier: 3.973A pdb=" N VAL B 145 " --> pdb=" O PHE B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.559A pdb=" N MET B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 3.749A pdb=" N LEU B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 341 through 346 removed outlier: 3.511A pdb=" N ILE B 346 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 353 through 371 Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'C' and resid 38 through 53 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 142 through 145 removed outlier: 3.824A pdb=" N VAL C 145 " --> pdb=" O PHE C 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 148 through 156 removed outlier: 3.799A pdb=" N LYS C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 265 through 279 Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.502A pdb=" N LYS C 352 " --> pdb=" O PRO C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 371 Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'D' and resid 38 through 54 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.615A pdb=" N GLU D 132 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP D 133 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 156 removed outlier: 3.739A pdb=" N LYS D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.620A pdb=" N ASP D 235 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.692A pdb=" N ARG D 307 " --> pdb=" O HIS D 304 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 309 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'D' and resid 353 through 371 Processing helix chain 'D' and resid 375 through 389 Processing helix chain 'E' and resid 38 through 53 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 81 through 92 Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 131 through 135 removed outlier: 3.591A pdb=" N VAL E 134 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 145 Processing helix chain 'E' and resid 148 through 156 removed outlier: 3.640A pdb=" N LYS E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 265 through 279 Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 348 through 352 Processing helix chain 'E' and resid 353 through 371 Processing helix chain 'E' and resid 375 through 388 Processing helix chain 'F' and resid 38 through 53 Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 142 through 145 removed outlier: 3.617A pdb=" N VAL F 145 " --> pdb=" O PHE F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 145' Processing helix chain 'F' and resid 148 through 156 Processing helix chain 'F' and resid 157 through 161 removed outlier: 3.515A pdb=" N MET F 161 " --> pdb=" O LEU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 181 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.537A pdb=" N ASP F 235 " --> pdb=" O SER F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 265 through 279 Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.866A pdb=" N ARG F 307 " --> pdb=" O HIS F 304 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR F 308 " --> pdb=" O PRO F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 336 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 348 through 352 Processing helix chain 'F' and resid 353 through 371 Processing helix chain 'F' and resid 375 through 389 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 5.718A pdb=" N VAL A 62 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE A 115 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASP A 30 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.574A pdb=" N LEU A 101 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.509A pdb=" N ILE A 224 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR A 262 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP A 226 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 259 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP A 301 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 261 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 165 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU A 319 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE A 167 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 191 through 194 removed outlier: 3.710A pdb=" N GLU A 242 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 247 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS A 240 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 280 through 285 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.902A pdb=" N PHE B 31 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 115 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL B 62 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.566A pdb=" N ILE B 224 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR B 262 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP B 226 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 259 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP B 301 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 261 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE B 165 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 319 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE B 167 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 189 Processing sheet with id=AB4, first strand: chain 'B' and resid 191 through 194 removed outlier: 6.629A pdb=" N ILE B 247 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS B 240 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 280 through 285 Processing sheet with id=AB6, first strand: chain 'C' and resid 18 through 23 removed outlier: 6.720A pdb=" N VAL C 18 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 34 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET C 20 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C 32 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY C 22 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASP C 30 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C 64 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE C 115 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL C 62 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 139 through 140 Processing sheet with id=AB8, first strand: chain 'C' and resid 223 through 227 removed outlier: 6.455A pdb=" N ILE C 224 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR C 262 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TRP C 226 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU C 259 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP C 301 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU C 261 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 186 through 189 Processing sheet with id=AC1, first strand: chain 'C' and resid 191 through 194 removed outlier: 6.264A pdb=" N ILE C 198 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 242 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 247 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS C 240 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 280 through 285 Processing sheet with id=AC3, first strand: chain 'D' and resid 18 through 20 removed outlier: 6.631A pdb=" N GLN D 111 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG D 65 " --> pdb=" O GLN D 111 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR D 113 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 139 through 140 Processing sheet with id=AC5, first strand: chain 'D' and resid 223 through 227 removed outlier: 6.494A pdb=" N ILE D 224 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR D 262 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP D 226 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU D 259 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP D 301 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU D 261 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 165 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU D 319 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE D 167 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 186 through 189 Processing sheet with id=AC7, first strand: chain 'D' and resid 191 through 194 removed outlier: 7.430A pdb=" N ILE D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 241 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 280 through 285 Processing sheet with id=AC9, first strand: chain 'E' and resid 60 through 69 removed outlier: 5.546A pdb=" N VAL E 62 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE E 115 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP E 30 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD2, first strand: chain 'E' and resid 136 through 140 removed outlier: 5.122A pdb=" N LYS E 137 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR E 185 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 223 through 227 removed outlier: 6.245A pdb=" N LEU E 259 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP E 301 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU E 261 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 191 through 194 removed outlier: 6.344A pdb=" N ILE E 198 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 280 through 285 Processing sheet with id=AD6, first strand: chain 'F' and resid 60 through 69 removed outlier: 5.335A pdb=" N VAL F 62 " --> pdb=" O ILE F 115 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE F 115 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASP F 30 " --> pdb=" O SER F 116 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.565A pdb=" N LEU F 101 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 136 through 140 removed outlier: 5.340A pdb=" N LYS F 137 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR F 185 " --> pdb=" O LYS F 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 223 through 227 removed outlier: 6.553A pdb=" N ILE F 224 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR F 262 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TRP F 226 " --> pdb=" O THR F 262 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU F 259 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP F 301 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU F 261 " --> pdb=" O ASP F 301 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE F 165 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU F 319 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE F 167 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 191 through 194 removed outlier: 6.604A pdb=" N ILE F 198 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 280 through 285 856 hydrogen bonds defined for protein. 2187 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: 6.46 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5654 1.34 - 1.46: 2335 1.46 - 1.57: 10198 1.57 - 1.69: 0 1.69 - 1.80: 58 Bond restraints: 18245 Sorted by residual: bond pdb=" CB GLU E 81 " pdb=" CG GLU E 81 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.31e-01 bond pdb=" CA GLU B 126 " pdb=" CB GLU B 126 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.86e-01 bond pdb=" CB PRO A 392 " pdb=" CG PRO A 392 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.76e-01 bond pdb=" N GLY E 257 " pdb=" CA GLY E 257 " ideal model delta sigma weight residual 1.445 1.451 -0.006 8.30e-03 1.45e+04 5.28e-01 bond pdb=" N PRO B 339 " pdb=" CA PRO B 339 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.31e-02 5.83e+03 5.11e-01 ... (remaining 18240 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 505 107.15 - 113.86: 10560 113.86 - 120.58: 7202 120.58 - 127.30: 6229 127.30 - 134.02: 124 Bond angle restraints: 24620 Sorted by residual: angle pdb=" N VAL F 241 " pdb=" CA VAL F 241 " pdb=" C VAL F 241 " ideal model delta sigma weight residual 111.45 108.56 2.89 9.30e-01 1.16e+00 9.64e+00 angle pdb=" C GLU A 195 " pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.34e+00 angle pdb=" N VAL A 70 " pdb=" CA VAL A 70 " pdb=" C VAL A 70 " ideal model delta sigma weight residual 111.88 109.14 2.74 1.06e+00 8.90e-01 6.68e+00 angle pdb=" C LYS B 125 " pdb=" N GLU B 126 " pdb=" CA GLU B 126 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" CA GLU B 126 " pdb=" CB GLU B 126 " pdb=" CG GLU B 126 " ideal model delta sigma weight residual 114.10 119.17 -5.07 2.00e+00 2.50e-01 6.42e+00 ... (remaining 24615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 10447 16.62 - 33.25: 579 33.25 - 49.87: 162 49.87 - 66.49: 36 66.49 - 83.11: 5 Dihedral angle restraints: 11229 sinusoidal: 4816 harmonic: 6413 Sorted by residual: dihedral pdb=" CA ARG C 90 " pdb=" CB ARG C 90 " pdb=" CG ARG C 90 " pdb=" CD ARG C 90 " ideal model delta sinusoidal sigma weight residual 60.00 119.11 -59.11 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG F 210 " pdb=" CA ARG F 210 " pdb=" CB ARG F 210 " pdb=" CG ARG F 210 " ideal model delta sinusoidal sigma weight residual -180.00 -121.58 -58.42 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG E 190 " pdb=" CB ARG E 190 " pdb=" CG ARG E 190 " pdb=" CD ARG E 190 " ideal model delta sinusoidal sigma weight residual 60.00 117.99 -57.99 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 11226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1737 0.028 - 0.055: 704 0.055 - 0.083: 195 0.083 - 0.110: 169 0.110 - 0.138: 79 Chirality restraints: 2884 Sorted by residual: chirality pdb=" CA ILE E 223 " pdb=" N ILE E 223 " pdb=" C ILE E 223 " pdb=" CB ILE E 223 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE F 299 " pdb=" N ILE F 299 " pdb=" C ILE F 299 " pdb=" CB ILE F 299 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE B 223 " pdb=" N ILE B 223 " pdb=" C ILE B 223 " pdb=" CB ILE B 223 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 2881 not shown) Planarity restraints: 3083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 56 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO C 57 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 147 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO D 148 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 148 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 148 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 188 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO B 189 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 189 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 189 " 0.015 5.00e-02 4.00e+02 ... (remaining 3080 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2751 2.77 - 3.30: 16071 3.30 - 3.83: 26884 3.83 - 4.37: 31377 4.37 - 4.90: 56775 Nonbonded interactions: 133858 Sorted by model distance: nonbonded pdb=" O PRO A 264 " pdb=" OH TYR A 308 " model vdw 2.233 2.440 nonbonded pdb=" OE1 GLU D 136 " pdb=" OG1 THR D 185 " model vdw 2.256 2.440 nonbonded pdb=" NH1 ARG A 65 " pdb=" OH TYR A 110 " model vdw 2.267 2.520 nonbonded pdb=" O PRO D 264 " pdb=" OH TYR D 308 " model vdw 2.305 2.440 nonbonded pdb=" O LYS F 73 " pdb=" OG1 THR F 103 " model vdw 2.324 2.440 ... (remaining 133853 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' and (resid 17 through 20 or resid 31 through 54 or resid 57 through 6 \ 7 or resid 77 through 95 or resid 109 through 389)) selection = (chain 'B' and (resid 17 through 20 or resid 31 through 54 or resid 57 through 6 \ 7 or resid 77 through 95 or resid 109 through 389)) selection = (chain 'C' and (resid 17 through 20 or resid 31 through 54 or resid 57 through 6 \ 7 or resid 77 through 95 or resid 109 through 389)) selection = (chain 'D' and resid 17 through 389) selection = (chain 'E' and (resid 17 through 20 or resid 31 through 54 or resid 57 through 6 \ 7 or resid 77 through 95 or resid 109 through 389)) selection = (chain 'F' and (resid 17 through 20 or resid 31 through 54 or resid 57 through 6 \ 7 or resid 77 through 95 or resid 109 through 389)) } 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 individual isotropic 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.210 Check model and map are aligned: 0.230 Set scattering table: 0.190 Process input model: 48.920 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 0.038 18245 Z= 0.139 Angle : 0.441 7.190 24620 Z= 0.238 Chirality : 0.042 0.138 2884 Planarity : 0.003 0.033 3083 Dihedral : 11.691 83.113 7057 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.95 % Allowed : 7.49 % Favored : 91.57 % 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 (0.19), residues: 2160 helix: 2.12 (0.19), residues: 746 sheet: 0.99 (0.26), residues: 433 loop : 0.33 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 226 HIS 0.003 0.001 HIS E 56 PHE 0.008 0.001 PHE E 120 TYR 0.009 0.001 TYR C 35 ARG 0.002 0.000 ARG F 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8733 (tp) cc_final: 0.8467 (tp) REVERT: A 60 PHE cc_start: 0.8692 (m-80) cc_final: 0.8365 (m-80) REVERT: A 87 MET cc_start: 0.7305 (tpp) cc_final: 0.6748 (ttm) REVERT: A 111 GLN cc_start: 0.8001 (pp30) cc_final: 0.7761 (pp30) REVERT: A 121 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8703 (mp0) REVERT: B 23 MET cc_start: 0.3918 (mmm) cc_final: 0.3057 (mpp) REVERT: B 87 MET cc_start: 0.8359 (mmm) cc_final: 0.8049 (mmp) REVERT: B 125 LYS cc_start: 0.9289 (pttm) cc_final: 0.9053 (ptpp) REVERT: B 169 MET cc_start: 0.8500 (mmm) cc_final: 0.8232 (mmm) REVERT: C 20 MET cc_start: 0.7599 (mpp) cc_final: 0.7337 (mpp) REVERT: C 51 LYS cc_start: 0.9258 (tppt) cc_final: 0.9044 (tmmt) REVERT: C 111 GLN cc_start: 0.6402 (pm20) cc_final: 0.5972 (pm20) REVERT: C 135 GLN cc_start: 0.7982 (mt0) cc_final: 0.7775 (mt0) REVERT: D 33 LYS cc_start: 0.6200 (tptm) cc_final: 0.5889 (tptt) REVERT: D 290 ILE cc_start: 0.8663 (mt) cc_final: 0.8391 (mp) REVERT: E 56 HIS cc_start: 0.8597 (t-90) cc_final: 0.8352 (t-90) REVERT: E 329 LYS cc_start: 0.8602 (tptp) cc_final: 0.8259 (ttmt) REVERT: E 387 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7660 (mp) REVERT: F 23 MET cc_start: 0.8259 (pmm) cc_final: 0.7888 (pmm) REVERT: F 111 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8580 (pp30) outliers start: 19 outliers final: 5 residues processed: 225 average time/residue: 1.3228 time to fit residues: 331.9825 Evaluate side-chains 169 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 343 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 135 GLN C 56 HIS C 135 GLN D 141 ASN E 124 GLN F 111 GLN F 124 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18245 Z= 0.159 Angle : 0.489 9.243 24620 Z= 0.256 Chirality : 0.042 0.137 2884 Planarity : 0.004 0.035 3083 Dihedral : 4.441 47.418 2372 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.30 % Allowed : 11.83 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2160 helix: 1.88 (0.19), residues: 788 sheet: 1.00 (0.26), residues: 438 loop : 0.30 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.004 0.001 HIS F 56 PHE 0.025 0.001 PHE E 17 TYR 0.013 0.001 TYR F 110 ARG 0.006 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8699 (m-80) cc_final: 0.8376 (m-80) REVERT: A 111 GLN cc_start: 0.7988 (pp30) cc_final: 0.7733 (pp30) REVERT: A 121 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8735 (mp0) REVERT: A 185 THR cc_start: 0.8418 (p) cc_final: 0.8204 (p) REVERT: B 23 MET cc_start: 0.3998 (mmm) cc_final: 0.3064 (mpp) REVERT: B 87 MET cc_start: 0.8422 (mmm) cc_final: 0.8091 (mmp) REVERT: B 169 MET cc_start: 0.8534 (mmm) cc_final: 0.8246 (mmm) REVERT: B 176 ASN cc_start: 0.8113 (m110) cc_final: 0.7753 (p0) REVERT: C 20 MET cc_start: 0.7610 (mpp) cc_final: 0.7394 (mpp) REVERT: C 111 GLN cc_start: 0.6504 (pm20) cc_final: 0.6275 (pm20) REVERT: D 290 ILE cc_start: 0.8684 (mt) cc_final: 0.8396 (mp) REVERT: E 56 HIS cc_start: 0.8648 (t-90) cc_final: 0.8375 (t-90) REVERT: E 149 GLU cc_start: 0.8375 (tp30) cc_final: 0.8055 (pt0) REVERT: E 329 LYS cc_start: 0.8584 (tptp) cc_final: 0.8252 (ttmt) REVERT: F 23 MET cc_start: 0.8257 (pmm) cc_final: 0.7878 (pmm) outliers start: 26 outliers final: 8 residues processed: 187 average time/residue: 1.2697 time to fit residues: 266.8654 Evaluate side-chains 171 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 163 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 56 HIS C 135 GLN F 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18245 Z= 0.190 Angle : 0.482 6.909 24620 Z= 0.253 Chirality : 0.043 0.148 2884 Planarity : 0.004 0.039 3083 Dihedral : 4.166 49.604 2360 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.55 % Allowed : 12.92 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.19), residues: 2160 helix: 1.96 (0.19), residues: 781 sheet: 1.00 (0.26), residues: 442 loop : 0.26 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.006 0.001 HIS F 56 PHE 0.025 0.001 PHE E 17 TYR 0.010 0.001 TYR E 35 ARG 0.004 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8674 (m-80) cc_final: 0.8329 (m-80) REVERT: A 111 GLN cc_start: 0.8004 (pp30) cc_final: 0.7728 (pp30) REVERT: A 121 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8747 (mp0) REVERT: A 185 THR cc_start: 0.8448 (p) cc_final: 0.8231 (p) REVERT: B 23 MET cc_start: 0.3951 (mmm) cc_final: 0.3102 (mpp) REVERT: B 87 MET cc_start: 0.8428 (mmm) cc_final: 0.8094 (mmp) REVERT: B 169 MET cc_start: 0.8560 (mmm) cc_final: 0.8247 (mmm) REVERT: B 176 ASN cc_start: 0.8124 (m110) cc_final: 0.7753 (p0) REVERT: C 20 MET cc_start: 0.7520 (mpp) cc_final: 0.7121 (mpp) REVERT: C 111 GLN cc_start: 0.6514 (pm20) cc_final: 0.6268 (pm20) REVERT: C 374 LYS cc_start: 0.7269 (mptt) cc_final: 0.7022 (mppt) REVERT: D 290 ILE cc_start: 0.8678 (mt) cc_final: 0.8373 (mp) REVERT: E 56 HIS cc_start: 0.8652 (t-90) cc_final: 0.8375 (t-90) REVERT: E 111 GLN cc_start: 0.7971 (pp30) cc_final: 0.7719 (pp30) REVERT: E 124 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: E 149 GLU cc_start: 0.8369 (tp30) cc_final: 0.8085 (pt0) REVERT: E 329 LYS cc_start: 0.8588 (tptp) cc_final: 0.8263 (ttmt) REVERT: F 23 MET cc_start: 0.8269 (pmm) cc_final: 0.7876 (pmm) outliers start: 31 outliers final: 10 residues processed: 194 average time/residue: 1.1994 time to fit residues: 262.6616 Evaluate side-chains 168 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 56 HIS F 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18245 Z= 0.287 Angle : 0.523 8.427 24620 Z= 0.272 Chirality : 0.044 0.322 2884 Planarity : 0.004 0.043 3083 Dihedral : 4.305 48.542 2360 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.75 % Allowed : 13.37 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 2160 helix: 1.87 (0.19), residues: 781 sheet: 0.96 (0.25), residues: 439 loop : 0.15 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 226 HIS 0.007 0.001 HIS F 56 PHE 0.026 0.001 PHE E 17 TYR 0.012 0.001 TYR F 110 ARG 0.009 0.000 ARG F 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8004 (pp30) cc_final: 0.7734 (pp30) REVERT: A 121 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8769 (mp0) REVERT: A 185 THR cc_start: 0.8499 (p) cc_final: 0.8291 (p) REVERT: A 195 GLU cc_start: 0.6924 (mp0) cc_final: 0.6630 (pm20) REVERT: B 23 MET cc_start: 0.3916 (mmm) cc_final: 0.3059 (mpp) REVERT: B 87 MET cc_start: 0.8437 (mmm) cc_final: 0.8076 (mmp) REVERT: B 169 MET cc_start: 0.8572 (mmm) cc_final: 0.8274 (mmm) REVERT: B 176 ASN cc_start: 0.8181 (m110) cc_final: 0.7781 (p0) REVERT: B 195 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7519 (mp0) REVERT: C 20 MET cc_start: 0.7533 (mpp) cc_final: 0.7233 (mpp) REVERT: C 87 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7231 (mpp) REVERT: C 111 GLN cc_start: 0.6691 (pm20) cc_final: 0.6237 (pm20) REVERT: E 56 HIS cc_start: 0.8675 (t-90) cc_final: 0.8409 (t-90) REVERT: E 111 GLN cc_start: 0.8124 (pp30) cc_final: 0.7858 (pp30) REVERT: E 149 GLU cc_start: 0.8422 (tp30) cc_final: 0.8185 (pt0) REVERT: E 329 LYS cc_start: 0.8593 (tptp) cc_final: 0.8266 (ttmt) REVERT: E 387 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7987 (mt) REVERT: F 23 MET cc_start: 0.8275 (pmm) cc_final: 0.7874 (pmm) outliers start: 35 outliers final: 15 residues processed: 190 average time/residue: 1.2166 time to fit residues: 260.8726 Evaluate side-chains 172 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 380 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 135 GLN C 56 HIS C 135 GLN F 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18245 Z= 0.163 Angle : 0.486 10.120 24620 Z= 0.252 Chirality : 0.042 0.157 2884 Planarity : 0.004 0.039 3083 Dihedral : 4.050 37.723 2360 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.80 % Allowed : 13.97 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 2160 helix: 1.97 (0.19), residues: 777 sheet: 0.96 (0.26), residues: 439 loop : 0.21 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.004 0.001 HIS F 56 PHE 0.026 0.001 PHE E 17 TYR 0.010 0.001 TYR F 209 ARG 0.004 0.000 ARG F 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8028 (pp30) cc_final: 0.7748 (pp30) REVERT: A 121 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8781 (mp0) REVERT: A 185 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8240 (p) REVERT: B 23 MET cc_start: 0.3930 (mmm) cc_final: 0.3078 (mpp) REVERT: B 87 MET cc_start: 0.8416 (mmm) cc_final: 0.8052 (mmp) REVERT: B 169 MET cc_start: 0.8582 (mmm) cc_final: 0.8265 (mmm) REVERT: B 176 ASN cc_start: 0.8133 (m110) cc_final: 0.7751 (p0) REVERT: B 195 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7560 (mp0) REVERT: C 111 GLN cc_start: 0.6771 (pm20) cc_final: 0.6277 (pm20) REVERT: E 56 HIS cc_start: 0.8679 (t-90) cc_final: 0.8414 (t-90) REVERT: E 111 GLN cc_start: 0.8210 (pp30) cc_final: 0.7914 (pp30) REVERT: E 149 GLU cc_start: 0.8310 (tp30) cc_final: 0.8082 (pt0) REVERT: F 23 MET cc_start: 0.8312 (pmm) cc_final: 0.8051 (pmm) REVERT: F 109 LEU cc_start: 0.8684 (tp) cc_final: 0.8428 (tm) REVERT: F 110 TYR cc_start: 0.8580 (t80) cc_final: 0.8358 (t80) outliers start: 36 outliers final: 14 residues processed: 190 average time/residue: 1.1962 time to fit residues: 256.8640 Evaluate side-chains 167 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 109 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 135 GLN C 56 HIS D 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18245 Z= 0.312 Angle : 0.552 10.002 24620 Z= 0.284 Chirality : 0.045 0.280 2884 Planarity : 0.004 0.044 3083 Dihedral : 4.159 37.380 2358 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.15 % Allowed : 14.52 % Favored : 83.33 % 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 (0.19), residues: 2160 helix: 1.83 (0.19), residues: 780 sheet: 0.92 (0.25), residues: 445 loop : 0.12 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 226 HIS 0.003 0.001 HIS A 56 PHE 0.028 0.001 PHE E 17 TYR 0.012 0.001 TYR D 246 ARG 0.007 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8681 (m-80) cc_final: 0.8329 (m-80) REVERT: A 111 GLN cc_start: 0.7985 (pp30) cc_final: 0.7724 (pp30) REVERT: A 121 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8764 (mp0) REVERT: A 185 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 23 MET cc_start: 0.4024 (mmm) cc_final: 0.3157 (mpp) REVERT: B 87 MET cc_start: 0.8441 (mmm) cc_final: 0.8083 (mmp) REVERT: B 169 MET cc_start: 0.8572 (mmm) cc_final: 0.8235 (mmm) REVERT: B 176 ASN cc_start: 0.8134 (m110) cc_final: 0.7794 (p0) REVERT: B 195 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7573 (mp0) REVERT: C 87 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7256 (mpp) REVERT: C 111 GLN cc_start: 0.6765 (pm20) cc_final: 0.6459 (pm20) REVERT: D 173 GLU cc_start: 0.7822 (mp0) cc_final: 0.7613 (pm20) REVERT: D 185 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.6907 (t) REVERT: E 56 HIS cc_start: 0.8685 (t-90) cc_final: 0.8404 (t-90) REVERT: E 111 GLN cc_start: 0.8290 (pp30) cc_final: 0.7993 (pp30) REVERT: E 149 GLU cc_start: 0.8414 (tp30) cc_final: 0.8179 (pt0) REVERT: F 23 MET cc_start: 0.8248 (pmm) cc_final: 0.7821 (pmm) outliers start: 43 outliers final: 24 residues processed: 197 average time/residue: 1.2261 time to fit residues: 272.5161 Evaluate side-chains 176 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 208 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN C 56 HIS E 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18245 Z= 0.150 Angle : 0.513 11.453 24620 Z= 0.263 Chirality : 0.043 0.158 2884 Planarity : 0.004 0.039 3083 Dihedral : 3.991 38.212 2358 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.75 % Allowed : 14.87 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 2160 helix: 1.97 (0.19), residues: 775 sheet: 1.00 (0.26), residues: 434 loop : 0.21 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.003 0.000 HIS F 56 PHE 0.028 0.001 PHE E 17 TYR 0.012 0.001 TYR F 209 ARG 0.003 0.000 ARG F 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8066 (pp30) cc_final: 0.7776 (pp30) REVERT: A 121 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8801 (mp0) REVERT: A 185 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8259 (p) REVERT: B 23 MET cc_start: 0.4005 (mmm) cc_final: 0.3147 (mpp) REVERT: B 87 MET cc_start: 0.8428 (mmm) cc_final: 0.8054 (mmp) REVERT: B 169 MET cc_start: 0.8574 (mmm) cc_final: 0.8247 (mmm) REVERT: B 176 ASN cc_start: 0.8135 (m110) cc_final: 0.7749 (p0) REVERT: B 195 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7532 (mp0) REVERT: C 111 GLN cc_start: 0.6770 (pm20) cc_final: 0.6331 (pm20) REVERT: D 185 THR cc_start: 0.7532 (OUTLIER) cc_final: 0.6950 (t) REVERT: E 40 LYS cc_start: 0.8963 (pptt) cc_final: 0.8676 (tmmm) REVERT: E 56 HIS cc_start: 0.8647 (t-90) cc_final: 0.8370 (t-90) REVERT: E 111 GLN cc_start: 0.8297 (pp30) cc_final: 0.8000 (pp30) REVERT: F 23 MET cc_start: 0.8265 (pmm) cc_final: 0.7989 (pmm) REVERT: F 109 LEU cc_start: 0.8699 (tp) cc_final: 0.8452 (tm) REVERT: F 110 TYR cc_start: 0.8579 (t80) cc_final: 0.8369 (t80) REVERT: F 118 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8736 (pm20) outliers start: 35 outliers final: 16 residues processed: 187 average time/residue: 1.2420 time to fit residues: 262.1841 Evaluate side-chains 169 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN C 56 HIS C 135 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18245 Z= 0.271 Angle : 0.559 13.525 24620 Z= 0.284 Chirality : 0.044 0.176 2884 Planarity : 0.004 0.042 3083 Dihedral : 4.114 38.008 2358 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.60 % Allowed : 15.77 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 2160 helix: 1.89 (0.19), residues: 775 sheet: 0.95 (0.25), residues: 436 loop : 0.18 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 226 HIS 0.003 0.001 HIS F 56 PHE 0.028 0.001 PHE E 17 TYR 0.011 0.001 TYR D 246 ARG 0.002 0.000 ARG F 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7958 (pp30) cc_final: 0.7718 (pp30) REVERT: A 121 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: A 185 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8307 (p) REVERT: B 23 MET cc_start: 0.4016 (mmm) cc_final: 0.3142 (mpp) REVERT: B 87 MET cc_start: 0.8422 (mmm) cc_final: 0.8043 (mmp) REVERT: B 169 MET cc_start: 0.8576 (mmm) cc_final: 0.8245 (mmm) REVERT: B 176 ASN cc_start: 0.8172 (m110) cc_final: 0.7765 (p0) REVERT: B 195 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7556 (mp0) REVERT: C 111 GLN cc_start: 0.6755 (pm20) cc_final: 0.6315 (pm20) REVERT: C 124 GLN cc_start: 0.8755 (mt0) cc_final: 0.8492 (mt0) REVERT: D 185 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.6993 (t) REVERT: E 56 HIS cc_start: 0.8656 (t-90) cc_final: 0.8396 (t-90) REVERT: E 111 GLN cc_start: 0.8326 (pp30) cc_final: 0.8033 (pp30) REVERT: F 23 MET cc_start: 0.8242 (pmm) cc_final: 0.7835 (pmm) REVERT: F 109 LEU cc_start: 0.8675 (tp) cc_final: 0.8431 (tm) REVERT: F 118 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: F 161 MET cc_start: 0.8390 (mmm) cc_final: 0.8073 (mmm) outliers start: 32 outliers final: 20 residues processed: 183 average time/residue: 1.2599 time to fit residues: 260.1346 Evaluate side-chains 178 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 194 optimal weight: 0.0010 chunk 116 optimal weight: 0.0020 chunk 84 optimal weight: 3.9990 chunk 152 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 127 optimal weight: 0.2980 overall best weight: 0.2212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN C 56 HIS ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18245 Z= 0.129 Angle : 0.530 12.829 24620 Z= 0.269 Chirality : 0.043 0.294 2884 Planarity : 0.004 0.038 3083 Dihedral : 3.908 39.190 2358 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.10 % Allowed : 16.37 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.19), residues: 2160 helix: 2.01 (0.19), residues: 780 sheet: 1.03 (0.26), residues: 431 loop : 0.27 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 226 HIS 0.003 0.000 HIS F 56 PHE 0.027 0.001 PHE E 17 TYR 0.010 0.001 TYR F 209 ARG 0.003 0.000 ARG F 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8022 (pp30) cc_final: 0.7807 (pp30) REVERT: A 121 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8791 (mp0) REVERT: A 132 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 185 THR cc_start: 0.8425 (p) cc_final: 0.8208 (p) REVERT: B 23 MET cc_start: 0.3965 (mmm) cc_final: 0.3111 (mpp) REVERT: B 87 MET cc_start: 0.8410 (mmm) cc_final: 0.8028 (mmp) REVERT: B 169 MET cc_start: 0.8582 (mmm) cc_final: 0.8200 (mmm) REVERT: B 176 ASN cc_start: 0.8099 (m110) cc_final: 0.7722 (p0) REVERT: B 195 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7522 (mp0) REVERT: B 375 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6878 (p0) REVERT: C 111 GLN cc_start: 0.6801 (pm20) cc_final: 0.6431 (pm20) REVERT: C 124 GLN cc_start: 0.8748 (mt0) cc_final: 0.8481 (mt0) REVERT: D 185 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.6978 (t) REVERT: D 290 ILE cc_start: 0.8713 (mt) cc_final: 0.8396 (mp) REVERT: E 40 LYS cc_start: 0.8996 (pptt) cc_final: 0.8696 (tmmm) REVERT: E 56 HIS cc_start: 0.8620 (t-90) cc_final: 0.8365 (t-90) REVERT: E 111 GLN cc_start: 0.8341 (pp30) cc_final: 0.8039 (pp30) REVERT: E 171 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8744 (mt-10) REVERT: E 329 LYS cc_start: 0.8588 (tptp) cc_final: 0.8262 (ttmt) REVERT: F 23 MET cc_start: 0.8289 (pmm) cc_final: 0.8018 (pmm) REVERT: F 109 LEU cc_start: 0.8662 (tp) cc_final: 0.8417 (tm) REVERT: F 118 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8713 (pm20) REVERT: F 382 GLU cc_start: 0.8721 (tp30) cc_final: 0.8310 (tt0) outliers start: 22 outliers final: 14 residues processed: 188 average time/residue: 1.2411 time to fit residues: 262.7895 Evaluate side-chains 177 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 142 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN C 56 HIS ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18245 Z= 0.214 Angle : 0.552 13.871 24620 Z= 0.281 Chirality : 0.044 0.183 2884 Planarity : 0.004 0.056 3083 Dihedral : 3.991 38.886 2358 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.15 % Allowed : 16.62 % Favored : 82.24 % 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: 1.54 (0.19), residues: 2160 helix: 2.03 (0.20), residues: 775 sheet: 0.97 (0.26), residues: 445 loop : 0.29 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.003 0.001 HIS F 56 PHE 0.028 0.001 PHE E 31 TYR 0.010 0.001 TYR D 246 ARG 0.012 0.000 ARG B 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8047 (pp30) cc_final: 0.7815 (pp30) REVERT: A 121 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8800 (mp0) REVERT: A 132 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 185 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8258 (p) REVERT: B 23 MET cc_start: 0.3954 (mmm) cc_final: 0.3088 (mpp) REVERT: B 87 MET cc_start: 0.8419 (mmm) cc_final: 0.8047 (mmp) REVERT: B 169 MET cc_start: 0.8603 (mmm) cc_final: 0.8263 (mmm) REVERT: B 176 ASN cc_start: 0.8110 (m110) cc_final: 0.7723 (p0) REVERT: B 195 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7523 (mp0) REVERT: B 375 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6920 (p0) REVERT: C 111 GLN cc_start: 0.6949 (pm20) cc_final: 0.6477 (pm20) REVERT: D 185 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7027 (t) REVERT: D 290 ILE cc_start: 0.8718 (mt) cc_final: 0.8390 (mp) REVERT: E 40 LYS cc_start: 0.8932 (pptt) cc_final: 0.8637 (tmmm) REVERT: E 56 HIS cc_start: 0.8653 (t-90) cc_final: 0.8391 (t-90) REVERT: E 111 GLN cc_start: 0.8362 (pp30) cc_final: 0.8078 (pp30) REVERT: F 23 MET cc_start: 0.8271 (pmm) cc_final: 0.7986 (pmm) REVERT: F 109 LEU cc_start: 0.8663 (tp) cc_final: 0.8426 (tm) REVERT: F 118 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8680 (pm20) outliers start: 23 outliers final: 15 residues processed: 175 average time/residue: 1.2624 time to fit residues: 248.9805 Evaluate side-chains 176 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 150 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.138483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088092 restraints weight = 29296.361| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.32 r_work: 0.3007 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18245 Z= 0.144 Angle : 0.536 13.008 24620 Z= 0.271 Chirality : 0.043 0.321 2884 Planarity : 0.004 0.039 3083 Dihedral : 3.896 39.457 2358 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.10 % Allowed : 16.77 % Favored : 82.14 % 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 (0.19), residues: 2160 helix: 2.02 (0.20), residues: 781 sheet: 0.97 (0.26), residues: 444 loop : 0.35 (0.22), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.003 0.000 HIS F 56 PHE 0.027 0.001 PHE E 17 TYR 0.010 0.001 TYR F 209 ARG 0.010 0.000 ARG B 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5434.83 seconds wall clock time: 97 minutes 50.32 seconds (5870.32 seconds total)