Starting phenix.real_space_refine on Sun Aug 24 07:33:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p49_17402/08_2025/8p49_17402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p49_17402/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p49_17402/08_2025/8p49_17402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p49_17402/08_2025/8p49_17402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p49_17402/08_2025/8p49_17402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p49_17402/08_2025/8p49_17402.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.03, per 1000 atoms: 0.22 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: 1.69 Conformation dependent library (CDL) restraints added in 645.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.58 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: 3.01 Time building geometry restraints manager: 2.25 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: 3.740 Set stop_for_unknowns flag: 0.010 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.210 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG F 190 TYR 0.009 0.001 TYR C 35 PHE 0.008 0.001 PHE E 120 TRP 0.003 0.001 TRP A 226 HIS 0.003 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00217 (18245) covalent geometry : angle 0.44128 (24620) hydrogen bonds : bond 0.16011 ( 856) hydrogen bonds : angle 5.05363 ( 2187) *********************** 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 : 0.786 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: 0.6226 time to fit residues: 155.8090 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 : 0.517 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0170 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 0.0030 overall best weight: 0.4828 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.139045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087753 restraints weight = 29280.072| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.16 r_work: 0.3063 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18245 Z= 0.099 Angle : 0.498 8.972 24620 Z= 0.260 Chirality : 0.042 0.139 2884 Planarity : 0.004 0.036 3083 Dihedral : 4.527 58.117 2372 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.25 % Allowed : 11.18 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.19), residues: 2160 helix: 1.91 (0.19), residues: 782 sheet: 1.00 (0.26), residues: 442 loop : 0.35 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 128 TYR 0.013 0.001 TYR F 110 PHE 0.026 0.001 PHE E 17 TRP 0.004 0.001 TRP A 226 HIS 0.004 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00223 (18245) covalent geometry : angle 0.49788 (24620) hydrogen bonds : bond 0.03558 ( 856) hydrogen bonds : angle 4.37201 ( 2187) *********************** 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 204 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8606 (m-80) cc_final: 0.8273 (m-80) REVERT: A 111 GLN cc_start: 0.7738 (pp30) cc_final: 0.7470 (pp30) REVERT: A 121 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8737 (mp0) REVERT: A 185 THR cc_start: 0.8355 (p) cc_final: 0.8152 (p) REVERT: B 23 MET cc_start: 0.4019 (mmm) cc_final: 0.3124 (mpp) REVERT: B 87 MET cc_start: 0.8384 (mmm) cc_final: 0.8066 (mmp) REVERT: B 169 MET cc_start: 0.8270 (mmm) cc_final: 0.7976 (mmm) REVERT: B 176 ASN cc_start: 0.7860 (m110) cc_final: 0.7449 (p0) REVERT: C 20 MET cc_start: 0.7336 (mpp) cc_final: 0.7128 (mpp) REVERT: C 204 GLU cc_start: 0.8560 (mp0) cc_final: 0.8358 (mp0) REVERT: C 374 LYS cc_start: 0.7112 (mptt) cc_final: 0.6824 (mppt) REVERT: D 290 ILE cc_start: 0.8369 (mt) cc_final: 0.8096 (mp) REVERT: E 56 HIS cc_start: 0.8654 (t-90) cc_final: 0.8395 (t-90) REVERT: E 73 LYS cc_start: 0.7533 (ttpt) cc_final: 0.7265 (ttpt) REVERT: E 149 GLU cc_start: 0.8526 (tp30) cc_final: 0.7930 (pt0) REVERT: E 329 LYS cc_start: 0.8357 (tptp) cc_final: 0.8030 (ttmt) REVERT: F 23 MET cc_start: 0.7977 (pmm) cc_final: 0.7632 (pmm) outliers start: 25 outliers final: 7 residues processed: 196 average time/residue: 0.6086 time to fit residues: 133.2368 Evaluate side-chains 173 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 E residue 72 ASP Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 387 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 167 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 0.0980 chunk 200 optimal weight: 1.9990 chunk 106 optimal weight: 0.0040 chunk 183 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.137664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086129 restraints weight = 29656.853| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.17 r_work: 0.2984 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18245 Z= 0.125 Angle : 0.494 6.854 24620 Z= 0.259 Chirality : 0.043 0.155 2884 Planarity : 0.004 0.039 3083 Dihedral : 4.198 48.471 2360 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.55 % Allowed : 12.43 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.19), residues: 2160 helix: 2.01 (0.19), residues: 771 sheet: 1.02 (0.26), residues: 441 loop : 0.30 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 128 TYR 0.010 0.001 TYR E 35 PHE 0.026 0.001 PHE E 17 TRP 0.005 0.001 TRP A 226 HIS 0.004 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00310 (18245) covalent geometry : angle 0.49413 (24620) hydrogen bonds : bond 0.03759 ( 856) hydrogen bonds : angle 4.39199 ( 2187) *********************** 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 198 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8579 (m-80) cc_final: 0.8249 (m-80) REVERT: A 111 GLN cc_start: 0.7734 (pp30) cc_final: 0.7457 (pp30) REVERT: A 121 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8752 (mp0) REVERT: B 23 MET cc_start: 0.4049 (mmm) cc_final: 0.3158 (mpp) REVERT: B 65 ARG cc_start: 0.7186 (ptm160) cc_final: 0.6545 (ttt90) REVERT: B 87 MET cc_start: 0.8377 (mmm) cc_final: 0.8069 (mmp) REVERT: B 169 MET cc_start: 0.8321 (mmm) cc_final: 0.7999 (mmm) REVERT: B 176 ASN cc_start: 0.7875 (m110) cc_final: 0.7461 (p0) REVERT: C 20 MET cc_start: 0.7349 (mpp) cc_final: 0.7022 (mpp) REVERT: C 171 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8674 (mt-10) REVERT: C 204 GLU cc_start: 0.8591 (mp0) cc_final: 0.8387 (mp0) REVERT: C 374 LYS cc_start: 0.7249 (mptt) cc_final: 0.6985 (mppt) REVERT: D 33 LYS cc_start: 0.5878 (OUTLIER) cc_final: 0.5676 (tptp) REVERT: D 209 TYR cc_start: 0.8498 (t80) cc_final: 0.8297 (t80) REVERT: D 290 ILE cc_start: 0.8360 (mt) cc_final: 0.8060 (mp) REVERT: E 56 HIS cc_start: 0.8660 (t-90) cc_final: 0.8396 (t-90) REVERT: E 111 GLN cc_start: 0.7587 (pp30) cc_final: 0.7338 (pp30) REVERT: E 149 GLU cc_start: 0.8518 (tp30) cc_final: 0.7964 (pt0) REVERT: E 329 LYS cc_start: 0.8380 (tptp) cc_final: 0.8052 (ttmt) REVERT: F 23 MET cc_start: 0.7961 (pmm) cc_final: 0.7610 (pmm) REVERT: F 172 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8242 (tt) outliers start: 31 outliers final: 10 residues processed: 190 average time/residue: 0.6168 time to fit residues: 130.9102 Evaluate side-chains 169 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 281 VAL Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 172 LEU 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 49 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.135683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.084339 restraints weight = 29606.093| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.39 r_work: 0.2952 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18245 Z= 0.179 Angle : 0.533 8.916 24620 Z= 0.277 Chirality : 0.044 0.260 2884 Planarity : 0.004 0.042 3083 Dihedral : 4.353 48.541 2360 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.95 % Allowed : 12.43 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 2160 helix: 1.86 (0.19), residues: 777 sheet: 0.97 (0.26), residues: 440 loop : 0.22 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 345 TYR 0.012 0.001 TYR D 246 PHE 0.026 0.001 PHE E 17 TRP 0.005 0.001 TRP A 226 HIS 0.004 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00459 (18245) covalent geometry : angle 0.53303 (24620) hydrogen bonds : bond 0.04254 ( 856) hydrogen bonds : angle 4.47758 ( 2187) *********************** 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 212 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7752 (pp30) cc_final: 0.7497 (pp30) REVERT: A 121 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8763 (mp0) REVERT: A 195 GLU cc_start: 0.6976 (mp0) cc_final: 0.6675 (pm20) REVERT: B 23 MET cc_start: 0.3878 (mmm) cc_final: 0.3089 (mpp) REVERT: B 31 PHE cc_start: 0.5606 (OUTLIER) cc_final: 0.5269 (t80) REVERT: B 87 MET cc_start: 0.8398 (mmm) cc_final: 0.8052 (mmp) REVERT: B 169 MET cc_start: 0.8331 (mmm) cc_final: 0.8012 (mmm) REVERT: B 176 ASN cc_start: 0.7929 (m110) cc_final: 0.7492 (p0) REVERT: B 195 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7514 (mp0) REVERT: C 20 MET cc_start: 0.7312 (mpp) cc_final: 0.6968 (mpp) REVERT: C 171 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8810 (mt-10) REVERT: C 204 GLU cc_start: 0.8607 (mp0) cc_final: 0.8395 (mp0) REVERT: D 173 GLU cc_start: 0.7636 (mp0) cc_final: 0.7422 (pm20) REVERT: D 185 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6620 (t) REVERT: E 56 HIS cc_start: 0.8677 (t-90) cc_final: 0.8403 (t-90) REVERT: E 111 GLN cc_start: 0.7752 (pp30) cc_final: 0.7488 (pp30) REVERT: E 149 GLU cc_start: 0.8581 (tp30) cc_final: 0.8060 (pt0) REVERT: E 329 LYS cc_start: 0.8388 (tptp) cc_final: 0.8053 (ttmt) REVERT: E 387 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7777 (mt) REVERT: F 23 MET cc_start: 0.7922 (pmm) cc_final: 0.7558 (pmm) REVERT: F 109 LEU cc_start: 0.8364 (tp) cc_final: 0.8141 (tm) REVERT: F 132 GLU cc_start: 0.8122 (mp0) cc_final: 0.7875 (mp0) REVERT: F 382 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8480 (tt0) outliers start: 39 outliers final: 20 residues processed: 198 average time/residue: 0.6096 time to fit residues: 135.4091 Evaluate side-chains 179 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 31 PHE 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 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 185 THR Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 380 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 126 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 C 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.135183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084594 restraints weight = 29239.012| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.23 r_work: 0.3021 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18245 Z= 0.131 Angle : 0.508 7.463 24620 Z= 0.266 Chirality : 0.043 0.158 2884 Planarity : 0.004 0.041 3083 Dihedral : 4.183 40.265 2360 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.05 % Allowed : 13.32 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.19), residues: 2160 helix: 1.90 (0.19), residues: 777 sheet: 0.94 (0.26), residues: 441 loop : 0.24 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 345 TYR 0.010 0.001 TYR F 110 PHE 0.027 0.001 PHE E 17 TRP 0.005 0.001 TRP A 226 HIS 0.006 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00327 (18245) covalent geometry : angle 0.50772 (24620) hydrogen bonds : bond 0.03721 ( 856) hydrogen bonds : angle 4.39765 ( 2187) *********************** 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 214 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8603 (m-80) cc_final: 0.8301 (m-80) REVERT: A 111 GLN cc_start: 0.7842 (pp30) cc_final: 0.7562 (pp30) REVERT: A 121 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8788 (mp0) REVERT: B 23 MET cc_start: 0.3884 (mmm) cc_final: 0.3058 (mpp) REVERT: B 65 ARG cc_start: 0.7169 (ptm160) cc_final: 0.6533 (ttt90) REVERT: B 87 MET cc_start: 0.8415 (mmm) cc_final: 0.8064 (mmp) REVERT: B 169 MET cc_start: 0.8364 (mmm) cc_final: 0.8042 (mmm) REVERT: B 176 ASN cc_start: 0.7938 (m110) cc_final: 0.7504 (p0) REVERT: B 195 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7520 (mp0) REVERT: C 20 MET cc_start: 0.7506 (mpp) cc_final: 0.7044 (mpp) REVERT: C 171 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8786 (mt-10) REVERT: C 204 GLU cc_start: 0.8580 (mp0) cc_final: 0.8349 (mp0) REVERT: D 185 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.6719 (t) REVERT: D 242 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7257 (tm-30) REVERT: E 56 HIS cc_start: 0.8651 (t-90) cc_final: 0.8379 (t-90) REVERT: E 111 GLN cc_start: 0.7930 (pp30) cc_final: 0.7638 (pp30) REVERT: E 149 GLU cc_start: 0.8535 (tp30) cc_final: 0.8046 (pt0) REVERT: F 23 MET cc_start: 0.7905 (pmm) cc_final: 0.7512 (pmm) REVERT: F 132 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: F 382 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8453 (tt0) outliers start: 41 outliers final: 14 residues processed: 200 average time/residue: 0.6646 time to fit residues: 148.2534 Evaluate side-chains 175 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 B residue 267 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 186 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 171 optimal weight: 0.4980 chunk 174 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 201 optimal weight: 0.4980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN C 56 HIS D 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.135099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.083842 restraints weight = 29346.920| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.35 r_work: 0.2940 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18245 Z= 0.178 Angle : 0.552 10.393 24620 Z= 0.285 Chirality : 0.045 0.280 2884 Planarity : 0.004 0.043 3083 Dihedral : 4.223 40.308 2358 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.10 % Allowed : 13.57 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.19), residues: 2160 helix: 1.85 (0.19), residues: 770 sheet: 0.96 (0.26), residues: 436 loop : 0.17 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 289 TYR 0.023 0.001 TYR D 209 PHE 0.028 0.001 PHE E 17 TRP 0.006 0.001 TRP A 226 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00454 (18245) covalent geometry : angle 0.55201 (24620) hydrogen bonds : bond 0.04214 ( 856) hydrogen bonds : angle 4.49567 ( 2187) *********************** 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 211 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8528 (m-80) cc_final: 0.8264 (m-80) REVERT: A 111 GLN cc_start: 0.7758 (pp30) cc_final: 0.7489 (pp30) REVERT: A 121 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8779 (mp0) REVERT: B 23 MET cc_start: 0.3870 (mmm) cc_final: 0.3050 (mpp) REVERT: B 87 MET cc_start: 0.8398 (mmm) cc_final: 0.8058 (mmp) REVERT: B 169 MET cc_start: 0.8335 (mmm) cc_final: 0.8000 (mmm) REVERT: B 176 ASN cc_start: 0.7884 (m110) cc_final: 0.7504 (p0) REVERT: B 195 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7521 (mp0) REVERT: B 243 GLU cc_start: 0.8687 (tt0) cc_final: 0.8460 (tm-30) REVERT: C 20 MET cc_start: 0.7296 (mpp) cc_final: 0.6880 (mpp) REVERT: C 87 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7085 (mpp) REVERT: C 171 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8764 (mt-10) REVERT: C 204 GLU cc_start: 0.8604 (mp0) cc_final: 0.8373 (mp0) REVERT: E 40 LYS cc_start: 0.8993 (pptt) cc_final: 0.8726 (tmmm) REVERT: E 56 HIS cc_start: 0.8665 (t-90) cc_final: 0.8400 (t-90) REVERT: E 111 GLN cc_start: 0.7924 (pp30) cc_final: 0.7625 (pp30) REVERT: E 149 GLU cc_start: 0.8555 (tp30) cc_final: 0.8051 (pt0) REVERT: F 23 MET cc_start: 0.7834 (pmm) cc_final: 0.7449 (pmm) REVERT: F 109 LEU cc_start: 0.8377 (tp) cc_final: 0.8151 (tm) REVERT: F 118 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8829 (pm20) REVERT: F 132 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: F 382 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8428 (tt0) outliers start: 42 outliers final: 21 residues processed: 199 average time/residue: 0.6082 time to fit residues: 135.7818 Evaluate side-chains 184 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 267 ASP 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 E residue 91 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 0.0030 chunk 156 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.136281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085242 restraints weight = 29472.132| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.32 r_work: 0.2964 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18245 Z= 0.121 Angle : 0.524 7.108 24620 Z= 0.273 Chirality : 0.044 0.213 2884 Planarity : 0.004 0.040 3083 Dihedral : 4.130 40.967 2358 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.90 % Allowed : 14.17 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 2160 helix: 1.88 (0.19), residues: 776 sheet: 0.97 (0.26), residues: 435 loop : 0.21 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 345 TYR 0.012 0.001 TYR F 209 PHE 0.028 0.001 PHE E 17 TRP 0.005 0.001 TRP A 226 HIS 0.003 0.000 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00298 (18245) covalent geometry : angle 0.52375 (24620) hydrogen bonds : bond 0.03577 ( 856) hydrogen bonds : angle 4.40572 ( 2187) *********************** 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: 38 poor density : 167 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8481 (m-80) cc_final: 0.8186 (m-80) REVERT: A 111 GLN cc_start: 0.7770 (pp30) cc_final: 0.7493 (pp30) REVERT: A 121 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8820 (mp0) REVERT: A 375 ASP cc_start: 0.6598 (p0) cc_final: 0.6301 (p0) REVERT: B 23 MET cc_start: 0.3837 (mmm) cc_final: 0.3017 (mpp) REVERT: B 65 ARG cc_start: 0.7173 (ptm160) cc_final: 0.6485 (ttt90) REVERT: B 87 MET cc_start: 0.8410 (mmm) cc_final: 0.8053 (mmp) REVERT: B 169 MET cc_start: 0.8329 (mmm) cc_final: 0.7995 (mmm) REVERT: B 176 ASN cc_start: 0.7896 (m110) cc_final: 0.7453 (p0) REVERT: B 195 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7524 (mp0) REVERT: C 20 MET cc_start: 0.7352 (mpp) cc_final: 0.6917 (mpp) REVERT: C 87 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7146 (mpp) REVERT: C 171 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8786 (mt-10) REVERT: C 204 GLU cc_start: 0.8575 (mp0) cc_final: 0.8339 (mp0) REVERT: E 56 HIS cc_start: 0.8638 (t-90) cc_final: 0.8372 (t-90) REVERT: E 111 GLN cc_start: 0.7941 (pp30) cc_final: 0.7646 (pp30) REVERT: E 149 GLU cc_start: 0.8498 (tp30) cc_final: 0.7977 (pt0) REVERT: F 23 MET cc_start: 0.7892 (pmm) cc_final: 0.7512 (pmm) REVERT: F 118 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8815 (pm20) REVERT: F 132 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: F 161 MET cc_start: 0.8138 (mmm) cc_final: 0.7836 (mmm) REVERT: F 382 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8395 (tt0) outliers start: 38 outliers final: 20 residues processed: 195 average time/residue: 0.6037 time to fit residues: 131.9085 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 : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 380 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 167 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083850 restraints weight = 29520.649| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.35 r_work: 0.2944 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1688 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= 0.177 Angle : 0.582 13.319 24620 Z= 0.296 Chirality : 0.045 0.244 2884 Planarity : 0.004 0.042 3083 Dihedral : 4.259 41.052 2358 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.70 % Allowed : 14.87 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.19), residues: 2160 helix: 1.76 (0.19), residues: 779 sheet: 0.90 (0.25), residues: 436 loop : 0.18 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 345 TYR 0.020 0.001 TYR D 209 PHE 0.028 0.001 PHE E 17 TRP 0.005 0.001 TRP A 226 HIS 0.004 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00452 (18245) covalent geometry : angle 0.58212 (24620) hydrogen bonds : bond 0.04218 ( 856) hydrogen bonds : angle 4.54018 ( 2187) *********************** 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 204 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8486 (m-80) cc_final: 0.8223 (m-80) REVERT: A 111 GLN cc_start: 0.7732 (pp30) cc_final: 0.7492 (pp30) REVERT: A 121 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: B 23 MET cc_start: 0.3709 (mmm) cc_final: 0.2876 (mpp) REVERT: B 87 MET cc_start: 0.8401 (mmm) cc_final: 0.8049 (mmp) REVERT: B 169 MET cc_start: 0.8340 (mmm) cc_final: 0.8004 (mmm) REVERT: B 176 ASN cc_start: 0.7884 (m110) cc_final: 0.7505 (p0) REVERT: B 195 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7526 (mp0) REVERT: C 20 MET cc_start: 0.7187 (mpp) cc_final: 0.6709 (mpp) REVERT: C 87 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7114 (mpp) REVERT: C 171 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8787 (mt-10) REVERT: C 204 GLU cc_start: 0.8593 (mp0) cc_final: 0.8361 (mp0) REVERT: E 40 LYS cc_start: 0.8994 (pptt) cc_final: 0.8666 (tmmm) REVERT: E 56 HIS cc_start: 0.8646 (t-90) cc_final: 0.8388 (t-90) REVERT: E 111 GLN cc_start: 0.7979 (pp30) cc_final: 0.7683 (pp30) REVERT: E 149 GLU cc_start: 0.8537 (tp30) cc_final: 0.8053 (pt0) REVERT: F 23 MET cc_start: 0.7987 (pmm) cc_final: 0.7728 (pmm) REVERT: F 118 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8826 (pm20) REVERT: F 132 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: F 161 MET cc_start: 0.8158 (mmm) cc_final: 0.7849 (mmm) REVERT: F 382 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8411 (tt0) outliers start: 34 outliers final: 22 residues processed: 196 average time/residue: 0.5880 time to fit residues: 129.2169 Evaluate side-chains 181 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 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 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 344 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.137028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086006 restraints weight = 29246.726| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.31 r_work: 0.2975 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18245 Z= 0.110 Angle : 0.565 14.938 24620 Z= 0.288 Chirality : 0.044 0.269 2884 Planarity : 0.004 0.058 3083 Dihedral : 4.142 41.908 2358 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.50 % Allowed : 15.52 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.19), residues: 2160 helix: 1.86 (0.19), residues: 779 sheet: 0.96 (0.26), residues: 427 loop : 0.25 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 289 TYR 0.016 0.001 TYR C 110 PHE 0.028 0.001 PHE E 17 TRP 0.005 0.001 TRP A 226 HIS 0.005 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00261 (18245) covalent geometry : angle 0.56485 (24620) hydrogen bonds : bond 0.03389 ( 856) hydrogen bonds : angle 4.48444 ( 2187) *********************** 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 194 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.495 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: 0.8441 (m-80) cc_final: 0.8202 (m-80) REVERT: A 111 GLN cc_start: 0.7765 (pp30) cc_final: 0.7520 (pp30) REVERT: A 121 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8807 (mp0) REVERT: B 23 MET cc_start: 0.3650 (mmm) cc_final: 0.2748 (mpp) REVERT: B 87 MET cc_start: 0.8422 (mmm) cc_final: 0.8060 (mmp) REVERT: B 169 MET cc_start: 0.8327 (mmm) cc_final: 0.7928 (mmm) REVERT: B 176 ASN cc_start: 0.7888 (m110) cc_final: 0.7445 (p0) REVERT: B 195 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7499 (mp0) REVERT: B 345 ARG cc_start: 0.8478 (pmt170) cc_final: 0.8245 (pmt170) REVERT: C 20 MET cc_start: 0.7254 (mpp) cc_final: 0.6812 (mpp) REVERT: C 87 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7127 (mpp) REVERT: C 171 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8778 (mt-10) REVERT: C 204 GLU cc_start: 0.8576 (mp0) cc_final: 0.8339 (mp0) REVERT: E 40 LYS cc_start: 0.8987 (pptt) cc_final: 0.8649 (tmmm) REVERT: E 56 HIS cc_start: 0.8637 (t-90) cc_final: 0.8382 (t-90) REVERT: E 111 GLN cc_start: 0.7968 (pp30) cc_final: 0.7658 (pp30) REVERT: E 149 GLU cc_start: 0.8436 (tp30) cc_final: 0.7915 (pt0) REVERT: F 23 MET cc_start: 0.7930 (pmm) cc_final: 0.7669 (pmm) REVERT: F 53 ASN cc_start: 0.8279 (m-40) cc_final: 0.8021 (m-40) REVERT: F 118 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8792 (pm20) REVERT: F 132 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: F 382 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8362 (tt0) outliers start: 30 outliers final: 19 residues processed: 185 average time/residue: 0.6146 time to fit residues: 127.5052 Evaluate side-chains 179 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 186 optimal weight: 4.9990 chunk 117 optimal weight: 0.0370 chunk 118 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 178 optimal weight: 0.0870 chunk 41 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- 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 C 124 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.137312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.086480 restraints weight = 29223.530| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.30 r_work: 0.3028 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18245 Z= 0.119 Angle : 0.580 12.648 24620 Z= 0.293 Chirality : 0.045 0.357 2884 Planarity : 0.004 0.047 3083 Dihedral : 4.099 42.272 2358 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.30 % Allowed : 15.67 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.19), residues: 2160 helix: 1.89 (0.19), residues: 779 sheet: 0.96 (0.26), residues: 427 loop : 0.29 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 289 TYR 0.019 0.001 TYR D 209 PHE 0.028 0.001 PHE E 17 TRP 0.005 0.001 TRP A 226 HIS 0.006 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00292 (18245) covalent geometry : angle 0.58023 (24620) hydrogen bonds : bond 0.03450 ( 856) hydrogen bonds : angle 4.49958 ( 2187) ********************** 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 180 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8428 (m-80) cc_final: 0.8199 (m-80) REVERT: A 111 GLN cc_start: 0.7809 (pp30) cc_final: 0.7545 (pp30) REVERT: A 121 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8804 (mp0) REVERT: A 132 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 23 MET cc_start: 0.3502 (mmm) cc_final: 0.2595 (mpp) REVERT: B 87 MET cc_start: 0.8435 (mmm) cc_final: 0.8061 (mmp) REVERT: B 169 MET cc_start: 0.8334 (mmm) cc_final: 0.7932 (mmm) REVERT: B 176 ASN cc_start: 0.7862 (m110) cc_final: 0.7420 (p0) REVERT: B 195 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7491 (mp0) REVERT: B 345 ARG cc_start: 0.8485 (pmt170) cc_final: 0.8242 (pmt170) REVERT: C 20 MET cc_start: 0.7421 (mpp) cc_final: 0.6926 (mpp) REVERT: C 87 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7153 (mpp) REVERT: C 171 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8772 (mt-10) REVERT: C 204 GLU cc_start: 0.8591 (mp0) cc_final: 0.8348 (mp0) REVERT: E 40 LYS cc_start: 0.8955 (pptt) cc_final: 0.8688 (tmmm) REVERT: E 56 HIS cc_start: 0.8653 (t-90) cc_final: 0.8388 (t-90) REVERT: E 111 GLN cc_start: 0.8020 (pp30) cc_final: 0.7733 (pp30) REVERT: E 149 GLU cc_start: 0.8416 (tp30) cc_final: 0.7915 (pt0) REVERT: F 23 MET cc_start: 0.7984 (pmm) cc_final: 0.7728 (pmm) REVERT: F 118 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8734 (pm20) REVERT: F 132 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: F 382 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8339 (tt0) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.6761 time to fit residues: 129.5688 Evaluate side-chains 174 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 74 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 199 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.136143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.085291 restraints weight = 29528.071| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.35 r_work: 0.3007 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18245 Z= 0.151 Angle : 0.582 12.619 24620 Z= 0.297 Chirality : 0.045 0.378 2884 Planarity : 0.004 0.044 3083 Dihedral : 4.179 42.362 2358 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.55 % Allowed : 15.47 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 2160 helix: 1.86 (0.19), residues: 772 sheet: 0.93 (0.26), residues: 427 loop : 0.27 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 289 TYR 0.016 0.001 TYR C 110 PHE 0.028 0.001 PHE E 17 TRP 0.005 0.001 TRP A 226 HIS 0.006 0.001 HIS F 56 Details of bonding type rmsd covalent geometry : bond 0.00382 (18245) covalent geometry : angle 0.58236 (24620) hydrogen bonds : bond 0.03889 ( 856) hydrogen bonds : angle 4.58775 ( 2187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5973.26 seconds wall clock time: 102 minutes 32.54 seconds (6152.54 seconds total)