Starting phenix.real_space_refine on Mon May 19 06:01:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p49_17402/05_2025/8p49_17402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p49_17402/05_2025/8p49_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/cci-nas-00/data/ceres_data/8p49_17402/05_2025/8p49_17402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p49_17402/05_2025/8p49_17402.map" model { file = "/net/cci-nas-00/data/ceres_data/8p49_17402/05_2025/8p49_17402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p49_17402/05_2025/8p49_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.16, per 1000 atoms: 0.57 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: 4.10 Conformation dependent library (CDL) restraints added in 2.2 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4172 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 38 sheets defined 44.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.570A pdb=" N ASN A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 91 Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.629A pdb=" N GLU A 132 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP A 133 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 removed outlier: 3.783A pdb=" N VAL A 145 " --> pdb=" O PHE A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.774A pdb=" N LYS A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.577A pdb=" N LYS A 352 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 371 Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 81 through 91 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.511A pdb=" N VAL B 134 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 145 removed outlier: 3.973A pdb=" N VAL B 145 " --> pdb=" O PHE B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.559A pdb=" N MET B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 3.749A pdb=" N LEU B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 341 through 346 removed outlier: 3.511A pdb=" N ILE B 346 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 353 through 371 Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'C' and resid 38 through 53 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 142 through 145 removed outlier: 3.824A pdb=" N VAL C 145 " --> pdb=" O PHE C 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 148 through 156 removed outlier: 3.799A pdb=" N LYS C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 265 through 279 Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.502A pdb=" N LYS C 352 " --> pdb=" O PRO C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 371 Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'D' and resid 38 through 54 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.615A pdb=" N GLU D 132 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP D 133 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 156 removed outlier: 3.739A pdb=" N LYS D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.620A pdb=" N ASP D 235 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.692A pdb=" N ARG D 307 " --> pdb=" O HIS D 304 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 309 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'D' and resid 353 through 371 Processing helix chain 'D' and resid 375 through 389 Processing helix chain 'E' and resid 38 through 53 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 81 through 92 Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 131 through 135 removed outlier: 3.591A pdb=" N VAL E 134 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 145 Processing helix chain 'E' and resid 148 through 156 removed outlier: 3.640A pdb=" N LYS E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 265 through 279 Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 348 through 352 Processing helix chain 'E' and resid 353 through 371 Processing helix chain 'E' and resid 375 through 388 Processing helix chain 'F' and resid 38 through 53 Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 142 through 145 removed outlier: 3.617A pdb=" N VAL F 145 " --> pdb=" O PHE F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 145' Processing helix chain 'F' and resid 148 through 156 Processing helix chain 'F' and resid 157 through 161 removed outlier: 3.515A pdb=" N MET F 161 " --> pdb=" O LEU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 181 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.537A pdb=" N ASP F 235 " --> pdb=" O SER F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 265 through 279 Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.866A pdb=" N ARG F 307 " --> pdb=" O HIS F 304 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR F 308 " --> pdb=" O PRO F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 336 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 348 through 352 Processing helix chain 'F' and resid 353 through 371 Processing helix chain 'F' and resid 375 through 389 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 5.718A pdb=" N VAL A 62 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE A 115 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASP A 30 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.574A pdb=" N LEU A 101 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.509A pdb=" N ILE A 224 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR A 262 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP A 226 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 259 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP A 301 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 261 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 165 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU A 319 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE A 167 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 191 through 194 removed outlier: 3.710A pdb=" N GLU A 242 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 247 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS A 240 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 280 through 285 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.902A pdb=" N PHE B 31 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 115 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL B 62 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.566A pdb=" N ILE B 224 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR B 262 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP B 226 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 259 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP B 301 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 261 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE B 165 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 319 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE B 167 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 189 Processing sheet with id=AB4, first strand: chain 'B' and resid 191 through 194 removed outlier: 6.629A pdb=" N ILE B 247 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS B 240 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 280 through 285 Processing sheet with id=AB6, first strand: chain 'C' and resid 18 through 23 removed outlier: 6.720A pdb=" N VAL C 18 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 34 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET C 20 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C 32 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY C 22 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASP C 30 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C 64 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE C 115 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL C 62 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 139 through 140 Processing sheet with id=AB8, first strand: chain 'C' and resid 223 through 227 removed outlier: 6.455A pdb=" N ILE C 224 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR C 262 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TRP C 226 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU C 259 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP C 301 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU C 261 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 186 through 189 Processing sheet with id=AC1, first strand: chain 'C' and resid 191 through 194 removed outlier: 6.264A pdb=" N ILE C 198 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 242 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 247 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS C 240 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 280 through 285 Processing sheet with id=AC3, first strand: chain 'D' and resid 18 through 20 removed outlier: 6.631A pdb=" N GLN D 111 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG D 65 " --> pdb=" O GLN D 111 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR D 113 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 139 through 140 Processing sheet with id=AC5, first strand: chain 'D' and resid 223 through 227 removed outlier: 6.494A pdb=" N ILE D 224 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR D 262 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP D 226 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU D 259 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP D 301 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU D 261 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 165 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU D 319 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE D 167 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 186 through 189 Processing sheet with id=AC7, first strand: chain 'D' and resid 191 through 194 removed outlier: 7.430A pdb=" N ILE D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 241 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 280 through 285 Processing sheet with id=AC9, first strand: chain 'E' and resid 60 through 69 removed outlier: 5.546A pdb=" N VAL E 62 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE E 115 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP E 30 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD2, first strand: chain 'E' and resid 136 through 140 removed outlier: 5.122A pdb=" N LYS E 137 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR E 185 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 223 through 227 removed outlier: 6.245A pdb=" N LEU E 259 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP E 301 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU E 261 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 191 through 194 removed outlier: 6.344A pdb=" N ILE E 198 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 280 through 285 Processing sheet with id=AD6, first strand: chain 'F' and resid 60 through 69 removed outlier: 5.335A pdb=" N VAL F 62 " --> pdb=" O ILE F 115 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE F 115 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASP F 30 " --> pdb=" O SER F 116 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.565A pdb=" N LEU F 101 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 136 through 140 removed outlier: 5.340A pdb=" N LYS F 137 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR F 185 " --> pdb=" O LYS F 137 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 223 through 227 removed outlier: 6.553A pdb=" N ILE F 224 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR F 262 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TRP F 226 " --> pdb=" O THR F 262 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU F 259 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP F 301 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU F 261 " --> pdb=" O ASP F 301 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE F 165 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU F 319 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE F 167 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 191 through 194 removed outlier: 6.604A pdb=" N ILE F 198 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 280 through 285 856 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 4.83 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: 2.940 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 39.320 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.330 ------------------------------------------------------------------------------- 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= 0.098 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 Details of bonding type rmsd hydrogen bonds : bond 0.16011 ( 856) hydrogen bonds : angle 5.05363 ( 2187) covalent geometry : bond 0.00217 (18245) covalent geometry : angle 0.44128 (24620) *********************** 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 : 2.160 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: 1.3320 time to fit residues: 334.6221 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 : 1.929 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.136948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.085395 restraints weight = 29471.309| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.16 r_work: 0.3022 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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= 0.146 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 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 856) hydrogen bonds : angle 4.48832 ( 2187) covalent geometry : bond 0.00364 (18245) covalent geometry : angle 0.52868 (24620) *********************** 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 : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8627 (m-80) cc_final: 0.8293 (m-80) REVERT: A 111 GLN cc_start: 0.7754 (pp30) cc_final: 0.7494 (pp30) REVERT: A 121 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8741 (mp0) REVERT: B 23 MET cc_start: 0.4022 (mmm) cc_final: 0.3200 (mpp) REVERT: B 87 MET cc_start: 0.8392 (mmm) cc_final: 0.8085 (mmp) REVERT: B 169 MET cc_start: 0.8300 (mmm) cc_final: 0.7983 (mmm) REVERT: B 176 ASN cc_start: 0.7913 (m110) cc_final: 0.7492 (p0) REVERT: C 20 MET cc_start: 0.7343 (mpp) cc_final: 0.7132 (mpp) REVERT: C 204 GLU cc_start: 0.8563 (mp0) cc_final: 0.8363 (mp0) REVERT: C 374 LYS cc_start: 0.7265 (mptt) cc_final: 0.6984 (mppt) REVERT: E 56 HIS cc_start: 0.8653 (t-90) cc_final: 0.8396 (t-90) REVERT: E 73 LYS cc_start: 0.7543 (ttpt) cc_final: 0.7314 (ttpt) REVERT: E 149 GLU cc_start: 0.8587 (tp30) cc_final: 0.7968 (pt0) REVERT: E 329 LYS cc_start: 0.8373 (tptp) cc_final: 0.8047 (ttmt) REVERT: F 23 MET cc_start: 0.7987 (pmm) cc_final: 0.7640 (pmm) REVERT: F 111 GLN cc_start: 0.8517 (pp30) cc_final: 0.8258 (pp30) outliers start: 29 outliers final: 9 residues processed: 192 average time/residue: 1.2372 time to fit residues: 267.0643 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 : 1.916 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.0040 chunk 179 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.085091 restraints weight = 29355.128| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.14 r_work: 0.3016 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1221 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= 0.147 Angle : 0.513 6.836 24620 Z= 0.269 Chirality : 0.043 0.153 2884 Planarity : 0.004 0.040 3083 Dihedral : 4.385 59.180 2360 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.60 % Allowed : 12.57 % Favored : 85.83 % 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: 1.41 (0.19), residues: 2160 helix: 1.87 (0.19), residues: 777 sheet: 0.94 (0.26), residues: 442 loop : 0.23 (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 0.025 0.001 PHE E 17 TYR 0.011 0.001 TYR C 35 ARG 0.003 0.000 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 856) hydrogen bonds : angle 4.48000 ( 2187) covalent geometry : bond 0.00370 (18245) covalent geometry : angle 0.51315 (24620) *********************** 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 200 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8615 (m-80) cc_final: 0.8283 (m-80) REVERT: A 111 GLN cc_start: 0.7753 (pp30) cc_final: 0.7491 (pp30) REVERT: A 121 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8755 (mp0) REVERT: B 23 MET cc_start: 0.3978 (mmm) cc_final: 0.3126 (mpp) REVERT: B 65 ARG cc_start: 0.7216 (ptm160) cc_final: 0.6606 (ttt90) REVERT: B 87 MET cc_start: 0.8412 (mmm) cc_final: 0.8074 (mmp) REVERT: B 169 MET cc_start: 0.8316 (mmm) cc_final: 0.7974 (mmm) REVERT: B 176 ASN cc_start: 0.7920 (m110) cc_final: 0.7490 (p0) REVERT: B 195 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7468 (mp0) REVERT: C 20 MET cc_start: 0.7418 (mpp) cc_final: 0.7097 (mpp) REVERT: C 111 GLN cc_start: 0.6134 (pm20) cc_final: 0.5748 (pm20) REVERT: C 204 GLU cc_start: 0.8563 (mp0) cc_final: 0.8332 (mp0) REVERT: C 374 LYS cc_start: 0.7267 (mptt) cc_final: 0.7064 (mppt) REVERT: D 33 LYS cc_start: 0.5964 (OUTLIER) cc_final: 0.5742 (tptp) REVERT: E 56 HIS cc_start: 0.8665 (t-90) cc_final: 0.8407 (t-90) REVERT: E 111 GLN cc_start: 0.7642 (pp30) cc_final: 0.7381 (pp30) REVERT: E 149 GLU cc_start: 0.8614 (tp30) cc_final: 0.8008 (pt0) REVERT: E 329 LYS cc_start: 0.8374 (tptp) cc_final: 0.8048 (ttmt) REVERT: F 23 MET cc_start: 0.7939 (pmm) cc_final: 0.7575 (pmm) REVERT: F 109 LEU cc_start: 0.8361 (tp) cc_final: 0.8148 (tm) REVERT: F 111 GLN cc_start: 0.8535 (pp30) cc_final: 0.8312 (pp30) outliers start: 32 outliers final: 11 residues processed: 191 average time/residue: 1.2911 time to fit residues: 277.2685 Evaluate side-chains 168 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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 33 LYS 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 343 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 F 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.134482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083383 restraints weight = 29530.254| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.35 r_work: 0.2924 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 18245 Z= 0.223 Angle : 0.569 6.773 24620 Z= 0.296 Chirality : 0.045 0.170 2884 Planarity : 0.004 0.045 3083 Dihedral : 4.446 39.608 2360 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 12.38 % Favored : 85.48 % 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: 1.17 (0.19), residues: 2160 helix: 1.62 (0.19), residues: 786 sheet: 0.86 (0.25), residues: 439 loop : 0.11 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.006 0.001 HIS F 56 PHE 0.026 0.002 PHE E 17 TYR 0.013 0.001 TYR D 246 ARG 0.003 0.000 ARG D 282 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 856) hydrogen bonds : angle 4.60958 ( 2187) covalent geometry : bond 0.00574 (18245) covalent geometry : angle 0.56907 (24620) *********************** 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 216 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6980 (mtm) REVERT: A 111 GLN cc_start: 0.7759 (pp30) cc_final: 0.7498 (pp30) REVERT: A 121 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8765 (mp0) REVERT: B 23 MET cc_start: 0.3913 (mmm) cc_final: 0.3105 (mpp) REVERT: B 31 PHE cc_start: 0.5626 (OUTLIER) cc_final: 0.5250 (t80) REVERT: B 87 MET cc_start: 0.8405 (mmm) cc_final: 0.8067 (mmp) REVERT: B 169 MET cc_start: 0.8358 (mmm) cc_final: 0.8029 (mmm) REVERT: B 195 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7532 (mp0) REVERT: C 20 MET cc_start: 0.7295 (mpp) cc_final: 0.6975 (mpp) REVERT: C 87 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7061 (mpp) REVERT: C 204 GLU cc_start: 0.8585 (mp0) cc_final: 0.8371 (mp0) REVERT: E 56 HIS cc_start: 0.8643 (t-90) cc_final: 0.8388 (t-90) REVERT: E 111 GLN cc_start: 0.7788 (pp30) cc_final: 0.7528 (pp30) REVERT: E 149 GLU cc_start: 0.8632 (tp30) cc_final: 0.8070 (pt0) REVERT: F 23 MET cc_start: 0.7921 (pmm) cc_final: 0.7540 (pmm) REVERT: F 111 GLN cc_start: 0.8518 (pp30) cc_final: 0.8291 (pp30) REVERT: F 132 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7808 (mp0) outliers start: 43 outliers final: 18 residues processed: 201 average time/residue: 1.2187 time to fit residues: 276.0095 Evaluate side-chains 176 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 A residue 370 THR Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 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 108 LYS Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 B 176 ASN C 56 HIS C 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.135695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084331 restraints weight = 29590.225| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.15 r_work: 0.3004 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18245 Z= 0.145 Angle : 0.531 10.497 24620 Z= 0.274 Chirality : 0.044 0.328 2884 Planarity : 0.004 0.042 3083 Dihedral : 4.261 40.302 2358 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.25 % Allowed : 13.07 % Favored : 84.68 % 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: 1.25 (0.19), residues: 2160 helix: 1.78 (0.19), residues: 780 sheet: 0.82 (0.25), residues: 438 loop : 0.13 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.004 0.001 HIS F 56 PHE 0.027 0.001 PHE E 17 TYR 0.012 0.001 TYR F 209 ARG 0.003 0.000 ARG B 289 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 856) hydrogen bonds : angle 4.46496 ( 2187) covalent geometry : bond 0.00366 (18245) covalent geometry : angle 0.53102 (24620) *********************** 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 216 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8574 (m-80) cc_final: 0.8267 (m-80) REVERT: A 111 GLN cc_start: 0.7755 (pp30) cc_final: 0.7488 (pp30) REVERT: A 121 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8793 (mp0) REVERT: B 23 MET cc_start: 0.3873 (mmm) cc_final: 0.3025 (mpp) REVERT: B 65 ARG cc_start: 0.7197 (ptm160) cc_final: 0.6592 (ttt90) REVERT: B 87 MET cc_start: 0.8399 (mmm) cc_final: 0.8044 (mmp) REVERT: B 169 MET cc_start: 0.8327 (mmm) cc_final: 0.7982 (mmm) REVERT: B 176 ASN cc_start: 0.8022 (m110) cc_final: 0.7551 (p0) REVERT: B 195 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7514 (mp0) REVERT: B 289 ARG cc_start: 0.8266 (ttt-90) cc_final: 0.8034 (ttt-90) REVERT: C 20 MET cc_start: 0.7474 (mpp) cc_final: 0.7183 (mpp) REVERT: C 204 GLU cc_start: 0.8547 (mp0) cc_final: 0.8312 (mp0) REVERT: D 242 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7315 (tm-30) REVERT: E 56 HIS cc_start: 0.8652 (t-90) cc_final: 0.8395 (t-90) REVERT: E 111 GLN cc_start: 0.7909 (pp30) cc_final: 0.7620 (pp30) REVERT: E 149 GLU cc_start: 0.8551 (tp30) cc_final: 0.8033 (pt0) REVERT: F 23 MET cc_start: 0.7863 (pmm) cc_final: 0.7471 (pmm) REVERT: F 109 LEU cc_start: 0.8391 (tp) cc_final: 0.8173 (tm) REVERT: F 118 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8863 (pm20) REVERT: F 132 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7807 (mp0) outliers start: 45 outliers final: 23 residues processed: 201 average time/residue: 1.2124 time to fit residues: 274.5260 Evaluate side-chains 184 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 B residue 267 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain D residue 77 THR 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 108 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 387 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 135 optimal weight: 0.0770 chunk 214 optimal weight: 0.7980 chunk 136 optimal weight: 0.0870 chunk 133 optimal weight: 0.0060 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 overall best weight: 0.3732 ------------------------------------------------------------------------------- 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 D 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.137635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086965 restraints weight = 29448.558| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.37 r_work: 0.2989 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18245 Z= 0.093 Angle : 0.494 6.815 24620 Z= 0.258 Chirality : 0.043 0.156 2884 Planarity : 0.004 0.038 3083 Dihedral : 4.055 41.085 2358 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.75 % Allowed : 14.17 % Favored : 84.08 % 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: 1.98 (0.19), residues: 775 sheet: 0.93 (0.26), residues: 437 loop : 0.24 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 226 HIS 0.002 0.000 HIS F 56 PHE 0.027 0.001 PHE E 17 TYR 0.012 0.001 TYR D 246 ARG 0.003 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 856) hydrogen bonds : angle 4.28634 ( 2187) covalent geometry : bond 0.00212 (18245) covalent geometry : angle 0.49373 (24620) *********************** 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 213 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7315 (tpp) cc_final: 0.6872 (ttm) REVERT: A 111 GLN cc_start: 0.7728 (pp30) cc_final: 0.7460 (pp30) REVERT: A 121 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8807 (mp0) REVERT: B 23 MET cc_start: 0.3835 (mmm) cc_final: 0.2925 (mpp) REVERT: B 87 MET cc_start: 0.8386 (mmm) cc_final: 0.8028 (mmp) REVERT: B 169 MET cc_start: 0.8311 (mmm) cc_final: 0.7929 (mmm) REVERT: B 176 ASN cc_start: 0.7978 (m110) cc_final: 0.7459 (p0) REVERT: B 195 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7516 (mp0) REVERT: C 20 MET cc_start: 0.7377 (mpp) cc_final: 0.7101 (mpp) REVERT: C 204 GLU cc_start: 0.8563 (mp0) cc_final: 0.8330 (mp0) REVERT: D 242 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7342 (tm-30) REVERT: E 40 LYS cc_start: 0.8964 (pptt) cc_final: 0.8708 (tmmm) REVERT: E 56 HIS cc_start: 0.8637 (t-90) cc_final: 0.8379 (t-90) REVERT: E 111 GLN cc_start: 0.7940 (pp30) cc_final: 0.7633 (pp30) REVERT: E 149 GLU cc_start: 0.8407 (tp30) cc_final: 0.7924 (pt0) REVERT: F 23 MET cc_start: 0.7896 (pmm) cc_final: 0.7533 (pmm) REVERT: F 118 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8785 (pm20) REVERT: F 132 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: F 351 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: F 382 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8437 (tt0) outliers start: 35 outliers final: 13 residues processed: 202 average time/residue: 1.2681 time to fit residues: 287.1033 Evaluate side-chains 178 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TYR 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 B residue 288 LYS 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 F residue 118 GLU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 132 GLU 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 36 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 165 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 135 GLN D 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.133415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.083040 restraints weight = 29271.592| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.25 r_work: 0.3002 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18245 Z= 0.185 Angle : 0.588 12.200 24620 Z= 0.298 Chirality : 0.045 0.258 2884 Planarity : 0.004 0.043 3083 Dihedral : 4.243 40.811 2358 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.85 % Allowed : 14.77 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 2160 helix: 1.80 (0.19), residues: 778 sheet: 0.92 (0.26), residues: 426 loop : 0.17 (0.21), residues: 956 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 0.011 0.001 TYR F 209 ARG 0.008 0.000 ARG F 345 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 856) hydrogen bonds : angle 4.51792 ( 2187) covalent geometry : bond 0.00474 (18245) covalent geometry : angle 0.58771 (24620) *********************** 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 205 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 2.255 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: 0.8596 (m-80) cc_final: 0.8292 (m-80) REVERT: A 111 GLN cc_start: 0.7773 (pp30) cc_final: 0.7540 (pp30) REVERT: A 121 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8778 (mp0) REVERT: B 23 MET cc_start: 0.3719 (mmm) cc_final: 0.2872 (mpp) REVERT: B 87 MET cc_start: 0.8415 (mmm) cc_final: 0.8036 (mmp) REVERT: B 169 MET cc_start: 0.8366 (mmm) cc_final: 0.8023 (mmm) REVERT: B 176 ASN cc_start: 0.7990 (m110) cc_final: 0.7492 (p0) REVERT: B 195 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7545 (mp0) REVERT: C 20 MET cc_start: 0.7387 (mpp) cc_final: 0.7014 (mpp) REVERT: C 87 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7135 (mpp) REVERT: C 204 GLU cc_start: 0.8583 (mp0) cc_final: 0.8349 (mp0) REVERT: E 56 HIS cc_start: 0.8632 (t-90) cc_final: 0.8381 (t-90) REVERT: E 111 GLN cc_start: 0.8034 (pp30) cc_final: 0.7720 (pp30) REVERT: E 149 GLU cc_start: 0.8548 (tp30) cc_final: 0.8082 (pt0) REVERT: F 23 MET cc_start: 0.7909 (pmm) cc_final: 0.7489 (pmm) REVERT: F 118 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8809 (pm20) REVERT: F 132 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: F 161 MET cc_start: 0.8204 (mmm) cc_final: 0.7889 (mmm) REVERT: F 351 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: F 382 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8474 (tt0) outliers start: 37 outliers final: 19 residues processed: 195 average time/residue: 1.2660 time to fit residues: 277.4541 Evaluate side-chains 182 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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 B residue 288 LYS 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 F residue 108 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 114 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 171 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.136618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085994 restraints weight = 29481.170| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.28 r_work: 0.3021 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1713 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= 0.110 Angle : 0.544 12.252 24620 Z= 0.278 Chirality : 0.043 0.212 2884 Planarity : 0.004 0.039 3083 Dihedral : 4.120 41.539 2358 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.55 % Allowed : 15.62 % Favored : 82.83 % 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: 1.43 (0.19), residues: 2160 helix: 1.92 (0.19), residues: 775 sheet: 0.96 (0.26), residues: 427 loop : 0.23 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.004 0.000 HIS F 56 PHE 0.028 0.001 PHE E 17 TYR 0.011 0.001 TYR D 246 ARG 0.005 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 856) hydrogen bonds : angle 4.39915 ( 2187) covalent geometry : bond 0.00265 (18245) covalent geometry : angle 0.54416 (24620) *********************** 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 197 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 2.108 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: 0.8547 (m-80) cc_final: 0.8233 (m-80) REVERT: A 111 GLN cc_start: 0.7802 (pp30) cc_final: 0.7540 (pp30) REVERT: A 121 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8793 (mp0) REVERT: B 23 MET cc_start: 0.3510 (mmm) cc_final: 0.2591 (mpp) REVERT: B 65 ARG cc_start: 0.7210 (ptm160) cc_final: 0.6582 (ttt90) REVERT: B 87 MET cc_start: 0.8444 (mmm) cc_final: 0.8061 (mmp) REVERT: B 169 MET cc_start: 0.8332 (mmm) cc_final: 0.7975 (mmm) REVERT: B 176 ASN cc_start: 0.8007 (m110) cc_final: 0.7494 (p0) REVERT: B 195 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7527 (mp0) REVERT: C 20 MET cc_start: 0.7408 (mpp) cc_final: 0.7099 (mpp) REVERT: C 204 GLU cc_start: 0.8580 (mp0) cc_final: 0.8340 (mp0) REVERT: E 40 LYS cc_start: 0.9023 (pptt) cc_final: 0.8685 (tmmm) REVERT: E 56 HIS cc_start: 0.8659 (t-90) cc_final: 0.8384 (t-90) REVERT: E 111 GLN cc_start: 0.8039 (pp30) cc_final: 0.7726 (pp30) REVERT: E 149 GLU cc_start: 0.8453 (tp30) cc_final: 0.7953 (pt0) REVERT: F 23 MET cc_start: 0.8006 (pmm) cc_final: 0.7730 (pmm) REVERT: F 118 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8788 (pm20) REVERT: F 132 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: F 351 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: F 382 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8463 (tt0) outliers start: 31 outliers final: 18 residues processed: 192 average time/residue: 1.2439 time to fit residues: 268.7235 Evaluate side-chains 185 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 TYR 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 B residue 288 LYS 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 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 124 GLN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL 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 205 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 0.0370 chunk 60 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.135351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084949 restraints weight = 29307.427| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.28 r_work: 0.3029 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1750 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= 0.128 Angle : 0.588 15.370 24620 Z= 0.295 Chirality : 0.044 0.287 2884 Planarity : 0.004 0.047 3083 Dihedral : 4.150 41.767 2358 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.40 % Allowed : 16.17 % 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: 1.39 (0.19), residues: 2160 helix: 1.85 (0.19), residues: 779 sheet: 0.91 (0.26), residues: 435 loop : 0.25 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 226 HIS 0.005 0.001 HIS F 56 PHE 0.028 0.001 PHE E 17 TYR 0.023 0.001 TYR D 209 ARG 0.012 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 856) hydrogen bonds : angle 4.48288 ( 2187) covalent geometry : bond 0.00320 (18245) covalent geometry : angle 0.58806 (24620) *********************** 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 199 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 2.088 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 60 PHE cc_start: 0.8491 (m-80) cc_final: 0.8180 (m-80) REVERT: A 111 GLN cc_start: 0.7836 (pp30) cc_final: 0.7572 (pp30) REVERT: A 121 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8797 (mp0) REVERT: A 132 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 23 MET cc_start: 0.3523 (mmm) cc_final: 0.2599 (mpp) REVERT: B 65 ARG cc_start: 0.7222 (ptm160) cc_final: 0.6497 (ttt90) REVERT: B 87 MET cc_start: 0.8450 (mmm) cc_final: 0.8059 (mmp) REVERT: B 169 MET cc_start: 0.8363 (mmm) cc_final: 0.8007 (mmm) REVERT: B 176 ASN cc_start: 0.7960 (m110) cc_final: 0.7529 (p0) REVERT: B 195 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7530 (mp0) REVERT: C 20 MET cc_start: 0.7413 (mpp) cc_final: 0.7026 (mpp) REVERT: C 204 GLU cc_start: 0.8584 (mp0) cc_final: 0.8350 (mp0) REVERT: E 40 LYS cc_start: 0.9002 (pptt) cc_final: 0.8663 (tmmm) REVERT: E 56 HIS cc_start: 0.8624 (t-90) cc_final: 0.8367 (t-90) REVERT: E 111 GLN cc_start: 0.8093 (pp30) cc_final: 0.7775 (pp30) REVERT: E 149 GLU cc_start: 0.8472 (tp30) cc_final: 0.7978 (pt0) REVERT: F 23 MET cc_start: 0.8009 (pmm) cc_final: 0.7734 (pmm) REVERT: F 53 ASN cc_start: 0.8335 (m-40) cc_final: 0.8090 (m-40) REVERT: F 118 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8791 (pm20) REVERT: F 132 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: F 351 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: F 382 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8469 (tt0) outliers start: 28 outliers final: 18 residues processed: 193 average time/residue: 1.2613 time to fit residues: 273.3340 Evaluate side-chains 185 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 B residue 288 LYS 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 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 124 GLN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.6980 chunk 142 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.131341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080745 restraints weight = 29454.828| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.25 r_work: 0.2970 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 18245 Z= 0.305 Angle : 0.702 11.483 24620 Z= 0.357 Chirality : 0.049 0.344 2884 Planarity : 0.005 0.045 3083 Dihedral : 4.544 41.430 2358 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.55 % Allowed : 16.22 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2160 helix: 1.47 (0.19), residues: 771 sheet: 0.73 (0.25), residues: 443 loop : 0.02 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 226 HIS 0.006 0.001 HIS F 56 PHE 0.028 0.002 PHE E 17 TYR 0.013 0.002 TYR E 35 ARG 0.010 0.001 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.05391 ( 856) hydrogen bonds : angle 4.88430 ( 2187) covalent geometry : bond 0.00786 (18245) covalent geometry : angle 0.70206 (24620) ********************** 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 199 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 2.075 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 60 PHE cc_start: 0.8509 (m-80) cc_final: 0.8227 (m-80) REVERT: A 111 GLN cc_start: 0.7792 (pp30) cc_final: 0.7574 (pp30) REVERT: A 121 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8787 (mp0) REVERT: B 23 MET cc_start: 0.3565 (mmm) cc_final: 0.2714 (mpp) REVERT: B 87 MET cc_start: 0.8456 (mmm) cc_final: 0.8064 (mmp) REVERT: B 169 MET cc_start: 0.8345 (mmm) cc_final: 0.7979 (mmm) REVERT: B 176 ASN cc_start: 0.7870 (m110) cc_final: 0.7500 (p0) REVERT: B 195 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7571 (mp0) REVERT: B 345 ARG cc_start: 0.8388 (pmt170) cc_final: 0.8181 (pmt170) REVERT: C 20 MET cc_start: 0.7532 (mpp) cc_final: 0.7154 (mpp) REVERT: C 204 GLU cc_start: 0.8599 (mp0) cc_final: 0.8366 (mp0) REVERT: D 173 GLU cc_start: 0.7728 (mp0) cc_final: 0.7481 (pm20) REVERT: E 40 LYS cc_start: 0.8978 (pptt) cc_final: 0.8710 (tmmm) REVERT: E 56 HIS cc_start: 0.8655 (t-90) cc_final: 0.8379 (t-90) REVERT: E 111 GLN cc_start: 0.8091 (pp30) cc_final: 0.7795 (pp30) REVERT: E 149 GLU cc_start: 0.8618 (tp30) cc_final: 0.8108 (pt0) REVERT: E 196 ASP cc_start: 0.8157 (t0) cc_final: 0.7939 (t0) REVERT: F 23 MET cc_start: 0.7979 (pmm) cc_final: 0.7681 (pmm) REVERT: F 118 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8819 (pm20) REVERT: F 132 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: F 351 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: F 382 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8489 (tt0) outliers start: 31 outliers final: 19 residues processed: 192 average time/residue: 1.2615 time to fit residues: 271.8434 Evaluate side-chains 181 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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 53 ASN Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 214 PHE 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 F residue 118 GLU Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 190 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.134771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084215 restraints weight = 29230.888| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.31 r_work: 0.3025 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18245 Z= 0.117 Angle : 0.598 12.737 24620 Z= 0.306 Chirality : 0.045 0.357 2884 Planarity : 0.004 0.056 3083 Dihedral : 4.269 43.289 2358 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.05 % Allowed : 17.07 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 2160 helix: 1.79 (0.19), residues: 771 sheet: 0.84 (0.26), residues: 431 loop : 0.16 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.006 0.001 HIS F 56 PHE 0.028 0.001 PHE E 17 TYR 0.023 0.001 TYR D 209 ARG 0.013 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 856) hydrogen bonds : angle 4.60629 ( 2187) covalent geometry : bond 0.00281 (18245) covalent geometry : angle 0.59842 (24620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11885.39 seconds wall clock time: 205 minutes 17.52 seconds (12317.52 seconds total)