Starting phenix.real_space_refine on Tue Nov 19 01:22:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/11_2024/8p49_17402.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/11_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_17402/11_2024/8p49_17402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/11_2024/8p49_17402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/11_2024/8p49_17402.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p49_17402/11_2024/8p49_17402.cif" } 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. Time to flip 19 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 11.49, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.3 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: 3.00 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: 7.04 Time building geometry restraints manager: 5.34 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: 0.00 - 1.44: 24299 1.44 - 2.88: 254 2.88 - 4.31: 56 4.31 - 5.75: 10 5.75 - 7.19: 1 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 3.040 nonbonded pdb=" OE1 GLU D 136 " pdb=" OG1 THR D 185 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG A 65 " pdb=" OH TYR A 110 " model vdw 2.267 3.120 nonbonded pdb=" O PRO D 264 " pdb=" OH TYR D 308 " model vdw 2.305 3.040 nonbonded pdb=" O LYS F 73 " pdb=" OG1 THR F 103 " model vdw 2.324 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 6.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 43.510 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.840 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 2.132 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: 1.4368 time to fit residues: 359.6700 Evaluate side-chains 169 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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: 5.9990 chunk 163 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.8244 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18245 Z= 0.233 Angle : 0.529 8.824 24620 Z= 0.275 Chirality : 0.043 0.141 2884 Planarity : 0.004 0.037 3083 Dihedral : 4.684 60.133 2372 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.45 % Allowed : 11.08 % Favored : 87.48 % 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: 1.41 (0.19), residues: 2160 helix: 1.79 (0.19), residues: 787 sheet: 0.94 (0.26), residues: 442 loop : 0.29 (0.22), residues: 931 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 0.025 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 200 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8705 (m-80) cc_final: 0.8372 (m-80) REVERT: A 111 GLN cc_start: 0.7994 (pp30) cc_final: 0.7737 (pp30) REVERT: A 121 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8722 (mp0) REVERT: B 23 MET cc_start: 0.4015 (mmm) cc_final: 0.3169 (mpp) REVERT: B 87 MET cc_start: 0.8431 (mmm) cc_final: 0.8109 (mmp) REVERT: B 169 MET cc_start: 0.8557 (mmm) cc_final: 0.8260 (mmm) REVERT: B 176 ASN cc_start: 0.8162 (m110) cc_final: 0.7779 (p0) REVERT: C 20 MET cc_start: 0.7697 (mpp) cc_final: 0.7458 (mpp) REVERT: C 111 GLN cc_start: 0.6504 (pm20) cc_final: 0.6291 (pm20) REVERT: C 204 GLU cc_start: 0.8414 (mp0) cc_final: 0.8201 (mp0) REVERT: C 374 LYS cc_start: 0.7316 (mptt) cc_final: 0.7053 (mppt) REVERT: E 56 HIS cc_start: 0.8663 (t-90) cc_final: 0.8398 (t-90) REVERT: E 73 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7429 (ttpt) REVERT: E 149 GLU cc_start: 0.8419 (tp30) cc_final: 0.8081 (pt0) REVERT: E 329 LYS cc_start: 0.8589 (tptp) cc_final: 0.8257 (ttmt) REVERT: F 23 MET cc_start: 0.8285 (pmm) cc_final: 0.7892 (pmm) REVERT: F 111 GLN cc_start: 0.8795 (pp30) cc_final: 0.8575 (pp30) outliers start: 29 outliers final: 9 residues processed: 192 average time/residue: 1.3576 time to fit residues: 292.3539 Evaluate side-chains 169 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain E residue 72 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: 20.0000 chunk 60 optimal weight: 0.5980 chunk 163 optimal weight: 0.0980 chunk 133 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8268 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18245 Z= 0.285 Angle : 0.532 6.903 24620 Z= 0.278 Chirality : 0.044 0.151 2884 Planarity : 0.004 0.042 3083 Dihedral : 4.435 54.243 2360 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.85 % Allowed : 12.13 % Favored : 86.03 % 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: 1.35 (0.19), residues: 2160 helix: 1.82 (0.19), residues: 777 sheet: 0.90 (0.26), residues: 442 loop : 0.20 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.003 0.001 HIS F 56 PHE 0.026 0.001 PHE E 17 TYR 0.011 0.001 TYR C 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 209 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8694 (m-80) cc_final: 0.8345 (m-80) REVERT: A 111 GLN cc_start: 0.8000 (pp30) cc_final: 0.7737 (pp30) REVERT: A 121 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8734 (mp0) REVERT: B 23 MET cc_start: 0.3884 (mmm) cc_final: 0.3020 (mpp) REVERT: B 65 ARG cc_start: 0.7244 (ptm160) cc_final: 0.6612 (ttt90) REVERT: B 87 MET cc_start: 0.8450 (mmm) cc_final: 0.8101 (mmp) REVERT: B 169 MET cc_start: 0.8578 (mmm) cc_final: 0.8294 (mmm) REVERT: B 176 ASN cc_start: 0.8191 (m110) cc_final: 0.7787 (p0) REVERT: B 195 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7532 (mp0) REVERT: C 20 MET cc_start: 0.7726 (mpp) cc_final: 0.7395 (mpp) REVERT: C 111 GLN cc_start: 0.6683 (pm20) cc_final: 0.5931 (pm20) REVERT: C 204 GLU cc_start: 0.8427 (mp0) cc_final: 0.8189 (mp0) REVERT: E 53 ASN cc_start: 0.8976 (m-40) cc_final: 0.8711 (m-40) REVERT: E 56 HIS cc_start: 0.8678 (t-90) cc_final: 0.8418 (t-90) REVERT: E 111 GLN cc_start: 0.8046 (pp30) cc_final: 0.7823 (pp30) REVERT: E 149 GLU cc_start: 0.8479 (tp30) cc_final: 0.8145 (pt0) REVERT: E 329 LYS cc_start: 0.8609 (tptp) cc_final: 0.8275 (ttmt) REVERT: F 23 MET cc_start: 0.8235 (pmm) cc_final: 0.7812 (pmm) outliers start: 37 outliers final: 13 residues processed: 197 average time/residue: 1.2989 time to fit residues: 288.8616 Evaluate side-chains 172 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 55 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 387 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 186 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8250 moved from start: 0.1370 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= 0.196 Angle : 0.499 6.838 24620 Z= 0.261 Chirality : 0.043 0.159 2884 Planarity : 0.004 0.040 3083 Dihedral : 4.225 40.036 2360 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.00 % Allowed : 12.57 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 2160 helix: 1.90 (0.19), residues: 776 sheet: 0.93 (0.26), residues: 438 loop : 0.20 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.008 0.001 HIS F 56 PHE 0.027 0.001 PHE E 17 TYR 0.013 0.001 TYR D 246 ARG 0.003 0.000 ARG B 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 213 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 2.201 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: 0.7732 (pp30) REVERT: A 121 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8747 (mp0) REVERT: A 195 GLU cc_start: 0.6930 (mp0) cc_final: 0.6655 (pm20) REVERT: B 23 MET cc_start: 0.3878 (mmm) cc_final: 0.3021 (mpp) REVERT: B 87 MET cc_start: 0.8450 (mmm) cc_final: 0.8102 (mmp) REVERT: B 110 TYR cc_start: 0.7356 (t80) cc_final: 0.7133 (t80) REVERT: B 169 MET cc_start: 0.8578 (mmm) cc_final: 0.8273 (mmm) REVERT: B 176 ASN cc_start: 0.8178 (m110) cc_final: 0.7778 (p0) REVERT: B 195 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7589 (mp0) REVERT: C 20 MET cc_start: 0.7715 (mpp) cc_final: 0.7361 (mpp) REVERT: C 111 GLN cc_start: 0.6618 (pm20) cc_final: 0.6251 (pm20) REVERT: C 204 GLU cc_start: 0.8413 (mp0) cc_final: 0.8190 (mp0) REVERT: E 56 HIS cc_start: 0.8665 (t-90) cc_final: 0.8403 (t-90) REVERT: E 111 GLN cc_start: 0.8131 (pp30) cc_final: 0.7865 (pp30) REVERT: E 149 GLU cc_start: 0.8369 (tp30) cc_final: 0.8128 (pt0) REVERT: F 23 MET cc_start: 0.8170 (pmm) cc_final: 0.7742 (pmm) REVERT: F 109 LEU cc_start: 0.8692 (tp) cc_final: 0.8442 (tm) outliers start: 40 outliers final: 18 residues processed: 200 average time/residue: 1.4112 time to fit residues: 316.2178 Evaluate side-chains 175 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 370 THR Chi-restraints excluded: chain B residue 288 LYS 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 124 GLN Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain E residue 55 ILE 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 F residue 343 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 0.0370 chunk 178 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 187 optimal weight: 0.0000 chunk 52 optimal weight: 5.9990 overall best weight: 0.5464 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18245 Z= 0.140 Angle : 0.501 11.079 24620 Z= 0.258 Chirality : 0.043 0.306 2884 Planarity : 0.004 0.037 3083 Dihedral : 4.010 40.583 2358 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.60 % Allowed : 13.57 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2160 helix: 2.01 (0.19), residues: 775 sheet: 0.92 (0.26), residues: 439 loop : 0.26 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 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 0.003 0.000 ARG B 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 205 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8067 (pp30) cc_final: 0.7838 (pp30) REVERT: A 121 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8744 (mp0) REVERT: B 23 MET cc_start: 0.3886 (mmm) cc_final: 0.2942 (mpp) REVERT: B 87 MET cc_start: 0.8460 (mmm) cc_final: 0.8085 (mmp) REVERT: B 169 MET cc_start: 0.8578 (mmm) cc_final: 0.8237 (mmm) REVERT: B 176 ASN cc_start: 0.8100 (m110) cc_final: 0.7732 (p0) REVERT: B 195 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7563 (mp0) REVERT: C 20 MET cc_start: 0.7739 (mpp) cc_final: 0.7466 (mpp) REVERT: C 87 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7252 (mpp) REVERT: C 111 GLN cc_start: 0.6716 (pm20) cc_final: 0.6246 (pm20) REVERT: C 204 GLU cc_start: 0.8404 (mp0) cc_final: 0.8175 (mp0) REVERT: E 56 HIS cc_start: 0.8654 (t-90) cc_final: 0.8383 (t-90) REVERT: E 111 GLN cc_start: 0.8209 (pp30) cc_final: 0.7922 (pp30) REVERT: E 149 GLU cc_start: 0.8260 (tp30) cc_final: 0.8043 (pt0) REVERT: F 23 MET cc_start: 0.8222 (pmm) cc_final: 0.7812 (pmm) REVERT: F 118 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8792 (pm20) outliers start: 32 outliers final: 13 residues processed: 194 average time/residue: 1.4173 time to fit residues: 307.2545 Evaluate side-chains 168 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 267 ASP Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 124 GLN 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 344 VAL Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 343 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18245 Z= 0.410 Angle : 0.598 8.766 24620 Z= 0.307 Chirality : 0.046 0.231 2884 Planarity : 0.004 0.044 3083 Dihedral : 4.319 40.205 2358 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.25 % Allowed : 13.72 % Favored : 84.03 % 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: 1.23 (0.19), residues: 2160 helix: 1.69 (0.19), residues: 780 sheet: 0.87 (0.25), residues: 435 loop : 0.14 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 226 HIS 0.004 0.001 HIS F 56 PHE 0.027 0.002 PHE E 17 TYR 0.012 0.002 TYR D 246 ARG 0.005 0.000 ARG F 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 215 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8668 (m-80) cc_final: 0.8358 (m-80) REVERT: A 111 GLN cc_start: 0.7993 (pp30) cc_final: 0.7760 (pp30) REVERT: A 121 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8723 (mp0) REVERT: B 23 MET cc_start: 0.3906 (mmm) cc_final: 0.3025 (mpp) REVERT: B 87 MET cc_start: 0.8451 (mmm) cc_final: 0.8077 (mmp) REVERT: B 169 MET cc_start: 0.8590 (mmm) cc_final: 0.8262 (mmm) REVERT: B 195 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7614 (mp0) REVERT: C 20 MET cc_start: 0.7791 (mpp) cc_final: 0.7204 (mpp) REVERT: C 87 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7221 (mpp) REVERT: C 111 GLN cc_start: 0.6659 (pm20) cc_final: 0.6150 (pm20) REVERT: C 204 GLU cc_start: 0.8405 (mp0) cc_final: 0.8168 (mp0) REVERT: E 40 LYS cc_start: 0.8976 (pptt) cc_final: 0.8695 (tmmm) REVERT: E 56 HIS cc_start: 0.8657 (t-90) cc_final: 0.8400 (t-90) REVERT: E 111 GLN cc_start: 0.8289 (pp30) cc_final: 0.7997 (pp30) REVERT: E 149 GLU cc_start: 0.8448 (tp30) cc_final: 0.8194 (pt0) REVERT: F 23 MET cc_start: 0.8163 (pmm) cc_final: 0.7721 (pmm) REVERT: F 109 LEU cc_start: 0.8673 (tp) cc_final: 0.8461 (tm) REVERT: F 118 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8748 (pm20) REVERT: F 161 MET cc_start: 0.8415 (mmm) cc_final: 0.8138 (mmm) REVERT: F 351 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8027 (m-80) outliers start: 45 outliers final: 21 residues processed: 202 average time/residue: 1.3716 time to fit residues: 311.8134 Evaluate side-chains 179 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 A residue 370 THR Chi-restraints excluded: chain B residue 267 ASP 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 214 PHE Chi-restraints excluded: chain E residue 55 ILE 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 344 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 351 TYR 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: 0.5980 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 176 ASN 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: 0.8246 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18245 Z= 0.163 Angle : 0.537 10.796 24620 Z= 0.275 Chirality : 0.043 0.237 2884 Planarity : 0.004 0.039 3083 Dihedral : 4.149 41.065 2358 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.45 % Allowed : 15.22 % 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: 1.40 (0.19), residues: 2160 helix: 1.89 (0.19), residues: 775 sheet: 0.94 (0.26), residues: 426 loop : 0.21 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.003 0.000 HIS F 56 PHE 0.028 0.001 PHE F 17 TYR 0.012 0.001 TYR F 209 ARG 0.005 0.000 ARG B 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 199 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8611 (m-80) cc_final: 0.8286 (m-80) REVERT: A 111 GLN cc_start: 0.7988 (pp30) cc_final: 0.7744 (pp30) REVERT: A 121 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: B 23 MET cc_start: 0.3795 (mmm) cc_final: 0.2910 (mpp) REVERT: B 87 MET cc_start: 0.8444 (mmm) cc_final: 0.8064 (mmp) REVERT: B 169 MET cc_start: 0.8567 (mmm) cc_final: 0.8253 (mmm) REVERT: B 176 ASN cc_start: 0.8317 (m110) cc_final: 0.7841 (p0) REVERT: B 195 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7568 (mp0) REVERT: C 20 MET cc_start: 0.7716 (mpp) cc_final: 0.7326 (mpp) REVERT: C 87 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7248 (mpp) REVERT: C 111 GLN cc_start: 0.6709 (pm20) cc_final: 0.6205 (pm20) REVERT: C 204 GLU cc_start: 0.8390 (mp0) cc_final: 0.8151 (mp0) REVERT: E 40 LYS cc_start: 0.8975 (pptt) cc_final: 0.8708 (tmmm) REVERT: E 56 HIS cc_start: 0.8620 (t-90) cc_final: 0.8340 (t-90) REVERT: E 111 GLN cc_start: 0.8288 (pp30) cc_final: 0.7998 (pp30) REVERT: E 149 GLU cc_start: 0.8315 (tp30) cc_final: 0.8088 (pt0) REVERT: F 23 MET cc_start: 0.8160 (pmm) cc_final: 0.7705 (pmm) REVERT: F 109 LEU cc_start: 0.8651 (tp) cc_final: 0.8433 (tm) REVERT: F 118 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8691 (pm20) REVERT: F 161 MET cc_start: 0.8354 (mmm) cc_final: 0.8043 (mmm) outliers start: 29 outliers final: 12 residues processed: 191 average time/residue: 1.3903 time to fit residues: 297.7581 Evaluate side-chains 174 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 267 ASP Chi-restraints excluded: chain C residue 87 MET 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 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 344 VAL Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18245 Z= 0.212 Angle : 0.542 9.642 24620 Z= 0.279 Chirality : 0.043 0.165 2884 Planarity : 0.004 0.041 3083 Dihedral : 4.146 41.339 2358 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.50 % Allowed : 15.57 % Favored : 82.93 % 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: 1.39 (0.19), residues: 2160 helix: 1.85 (0.19), residues: 779 sheet: 0.93 (0.26), residues: 427 loop : 0.24 (0.21), residues: 954 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 0.028 0.001 PHE E 17 TYR 0.013 0.001 TYR B 110 ARG 0.006 0.000 ARG B 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 198 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8621 (m-80) cc_final: 0.8350 (m-80) REVERT: A 111 GLN cc_start: 0.8000 (pp30) cc_final: 0.7750 (pp30) REVERT: A 121 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8743 (mp0) REVERT: B 23 MET cc_start: 0.3589 (mmm) cc_final: 0.2708 (mpp) REVERT: B 87 MET cc_start: 0.8454 (mmm) cc_final: 0.8071 (mmp) REVERT: B 169 MET cc_start: 0.8585 (mmm) cc_final: 0.8258 (mmm) REVERT: B 176 ASN cc_start: 0.8202 (m110) cc_final: 0.7772 (p0) REVERT: B 195 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7583 (mp0) REVERT: C 20 MET cc_start: 0.7692 (mpp) cc_final: 0.7262 (mpp) REVERT: C 87 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7240 (mpp) REVERT: C 111 GLN cc_start: 0.6771 (pm20) cc_final: 0.6360 (pm20) REVERT: C 204 GLU cc_start: 0.8397 (mp0) cc_final: 0.8161 (mp0) REVERT: E 56 HIS cc_start: 0.8663 (t-90) cc_final: 0.8392 (t-90) REVERT: E 111 GLN cc_start: 0.8312 (pp30) cc_final: 0.8021 (pp30) REVERT: E 149 GLU cc_start: 0.8310 (tp30) cc_final: 0.8086 (pt0) REVERT: F 23 MET cc_start: 0.8257 (pmm) cc_final: 0.7979 (pmm) REVERT: F 53 ASN cc_start: 0.8521 (m-40) cc_final: 0.8251 (m-40) REVERT: F 118 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8716 (pm20) REVERT: F 351 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: F 365 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8105 (tm-30) outliers start: 30 outliers final: 18 residues processed: 192 average time/residue: 1.3421 time to fit residues: 289.8068 Evaluate side-chains 180 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 306 GLU 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 87 MET 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 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 344 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 351 TYR 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: 0.5980 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.0670 chunk 183 optimal weight: 0.9980 chunk 193 optimal weight: 0.0270 chunk 127 optimal weight: 10.0000 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 C 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 18245 Z= 0.155 Angle : 0.559 14.667 24620 Z= 0.285 Chirality : 0.044 0.331 2884 Planarity : 0.004 0.040 3083 Dihedral : 4.061 41.973 2358 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.10 % Allowed : 16.22 % Favored : 82.68 % 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: 1.94 (0.19), residues: 775 sheet: 0.97 (0.26), residues: 427 loop : 0.30 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.005 0.001 HIS F 56 PHE 0.028 0.001 PHE E 17 TYR 0.024 0.001 TYR D 209 ARG 0.011 0.000 ARG B 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 191 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8538 (m-80) cc_final: 0.8270 (m-80) REVERT: A 111 GLN cc_start: 0.8042 (pp30) cc_final: 0.7778 (pp30) REVERT: A 121 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8751 (mp0) REVERT: B 23 MET cc_start: 0.3505 (mmm) cc_final: 0.2558 (mpp) REVERT: B 87 MET cc_start: 0.8469 (mmm) cc_final: 0.8084 (mmp) REVERT: B 169 MET cc_start: 0.8569 (mmm) cc_final: 0.8187 (mmm) REVERT: B 176 ASN cc_start: 0.8261 (m110) cc_final: 0.7776 (p0) REVERT: B 195 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7583 (mp0) REVERT: B 345 ARG cc_start: 0.8402 (pmt170) cc_final: 0.8175 (pmt170) REVERT: C 20 MET cc_start: 0.7687 (mpp) cc_final: 0.7346 (mpp) REVERT: C 87 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7255 (mpp) REVERT: C 111 GLN cc_start: 0.6848 (pm20) cc_final: 0.6434 (pm20) REVERT: C 204 GLU cc_start: 0.8408 (mp0) cc_final: 0.8165 (mp0) REVERT: E 40 LYS cc_start: 0.8967 (pptt) cc_final: 0.8628 (tmmm) REVERT: E 56 HIS cc_start: 0.8655 (t-90) cc_final: 0.8381 (t-90) REVERT: E 111 GLN cc_start: 0.8328 (pp30) cc_final: 0.8031 (pp30) REVERT: E 149 GLU cc_start: 0.8222 (tp30) cc_final: 0.8013 (pt0) REVERT: F 23 MET cc_start: 0.8260 (pmm) cc_final: 0.8000 (pmm) REVERT: F 53 ASN cc_start: 0.8489 (m-40) cc_final: 0.8226 (m-40) REVERT: F 118 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8691 (pm20) REVERT: F 365 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8138 (tm-30) outliers start: 22 outliers final: 14 residues processed: 186 average time/residue: 1.3712 time to fit residues: 286.4590 Evaluate side-chains 179 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 306 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU 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 344 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 C 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18245 Z= 0.186 Angle : 0.568 11.581 24620 Z= 0.293 Chirality : 0.045 0.351 2884 Planarity : 0.004 0.040 3083 Dihedral : 4.101 42.192 2358 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.00 % Allowed : 16.52 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 2160 helix: 1.92 (0.19), residues: 775 sheet: 0.93 (0.26), residues: 435 loop : 0.31 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.005 0.001 HIS F 56 PHE 0.028 0.001 PHE E 17 TYR 0.018 0.001 TYR A 35 ARG 0.008 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 184 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8509 (m-80) cc_final: 0.8262 (m-80) REVERT: A 111 GLN cc_start: 0.8024 (pp30) cc_final: 0.7820 (pp30) REVERT: A 121 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8783 (mp0) REVERT: B 23 MET cc_start: 0.3549 (mmm) cc_final: 0.2569 (mpp) REVERT: B 87 MET cc_start: 0.8473 (mmm) cc_final: 0.8087 (mmp) REVERT: B 169 MET cc_start: 0.8555 (mmm) cc_final: 0.8166 (mmm) REVERT: B 176 ASN cc_start: 0.8235 (m110) cc_final: 0.7757 (p0) REVERT: B 195 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7601 (mp0) REVERT: B 345 ARG cc_start: 0.8406 (pmt170) cc_final: 0.8169 (pmt170) REVERT: C 20 MET cc_start: 0.7761 (mpp) cc_final: 0.7457 (mpp) REVERT: C 87 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7225 (mpp) REVERT: C 111 GLN cc_start: 0.6857 (pm20) cc_final: 0.6441 (pm20) REVERT: C 204 GLU cc_start: 0.8416 (mp0) cc_final: 0.8178 (mp0) REVERT: E 40 LYS cc_start: 0.8933 (pptt) cc_final: 0.8600 (tmmm) REVERT: E 56 HIS cc_start: 0.8654 (t-90) cc_final: 0.8378 (t-90) REVERT: E 111 GLN cc_start: 0.8332 (pp30) cc_final: 0.8057 (pp30) REVERT: E 149 GLU cc_start: 0.8264 (tp30) cc_final: 0.8052 (pt0) REVERT: F 23 MET cc_start: 0.8289 (pmm) cc_final: 0.8037 (pmm) REVERT: F 53 ASN cc_start: 0.8439 (m-40) cc_final: 0.8168 (m-40) REVERT: F 118 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: F 365 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8128 (tm-30) outliers start: 20 outliers final: 15 residues processed: 179 average time/residue: 1.4034 time to fit residues: 281.4904 Evaluate side-chains 178 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 306 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU 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 344 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 171 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 C 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.136698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085901 restraints weight = 29311.210| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.36 r_work: 0.2981 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18245 Z= 0.190 Angle : 0.573 12.308 24620 Z= 0.294 Chirality : 0.045 0.347 2884 Planarity : 0.004 0.040 3083 Dihedral : 4.099 42.462 2358 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.30 % Allowed : 16.27 % Favored : 82.44 % 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: 1.48 (0.19), residues: 2160 helix: 1.93 (0.19), residues: 774 sheet: 0.93 (0.26), residues: 435 loop : 0.31 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.006 0.001 HIS F 56 PHE 0.029 0.001 PHE E 17 TYR 0.020 0.001 TYR D 209 ARG 0.008 0.000 ARG B 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5841.22 seconds wall clock time: 106 minutes 58.31 seconds (6418.31 seconds total)