Starting phenix.real_space_refine on Fri Aug 7 00:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12bk_76281/08_2026/12bk_76281.cif Found real_map, /net/cci-nas-00/data/ceres_data/12bk_76281/08_2026/12bk_76281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12bk_76281/08_2026/12bk_76281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12bk_76281/08_2026/12bk_76281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12bk_76281/08_2026/12bk_76281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12bk_76281/08_2026/12bk_76281.map" } resolution = 3.87 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= 0.019 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 82 5.16 5 C 11162 2.51 5 N 3008 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17528 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2848 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 359} Chain breaks: 1 Chain: "F" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2955 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 371} Chain: "A" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2860 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2955 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 371} Chain: "C" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2955 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 371} Chain: "D" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2955 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 371} Time building chain proxies: 4.45, per 1000 atoms: 0.25 Number of scatterers: 17528 At special positions: 0 Unit cell: (112.028, 114.574, 173.135, 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 82 16.00 O 3276 8.00 N 3008 7.00 C 11162 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: 1.33 Conformation dependent library (CDL) restraints added in 768.7 milliseconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 26 sheets defined 42.0% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'E' and resid 13 through 24 Processing helix chain 'E' and resid 27 through 37 removed outlier: 3.829A pdb=" N GLY E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 86 through 109 removed outlier: 3.526A pdb=" N LYS E 90 " --> pdb=" O PRO E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 139 removed outlier: 3.840A pdb=" N ILE E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 262 through 273 Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'E' and resid 364 through 376 removed outlier: 3.588A pdb=" N CYS E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 394 removed outlier: 3.537A pdb=" N VAL E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 24 removed outlier: 3.543A pdb=" N CYS F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 36 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 86 through 109 Processing helix chain 'F' and resid 111 through 115 removed outlier: 3.926A pdb=" N VAL F 115 " --> pdb=" O ALA F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 removed outlier: 3.898A pdb=" N ILE F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU F 139 " --> pdb=" O GLY F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 removed outlier: 3.506A pdb=" N LEU F 174 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 201 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 274 removed outlier: 3.709A pdb=" N GLY F 274 " --> pdb=" O THR F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 302 through 313 Processing helix chain 'F' and resid 364 through 376 removed outlier: 3.821A pdb=" N CYS F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 396 removed outlier: 3.660A pdb=" N VAL F 382 " --> pdb=" O PRO F 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.573A pdb=" N CYS A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.739A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.857A pdb=" N CYS A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 removed outlier: 4.162A pdb=" N ALA A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 27 through 36 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 86 through 109 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 122 through 139 removed outlier: 3.960A pdb=" N ILE B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.792A pdb=" N GLY B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 302 through 313 Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.656A pdb=" N CYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 395 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 36 through 39 removed outlier: 3.592A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 39' Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 86 through 109 Processing helix chain 'C' and resid 122 through 139 removed outlier: 3.933A pdb=" N ILE C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 262 through 274 removed outlier: 3.747A pdb=" N GLY C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 302 through 314 Processing helix chain 'C' and resid 364 through 376 removed outlier: 3.509A pdb=" N CYS C 368 " --> pdb=" O GLU C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 395 removed outlier: 3.566A pdb=" N VAL C 382 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 24 Processing helix chain 'D' and resid 27 through 37 removed outlier: 4.112A pdb=" N GLY D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 82 removed outlier: 3.513A pdb=" N ASN D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 109 Processing helix chain 'D' and resid 122 through 139 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 190 through 201 Processing helix chain 'D' and resid 240 through 245 removed outlier: 3.982A pdb=" N GLY D 244 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.659A pdb=" N GLY D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 364 through 376 removed outlier: 3.943A pdb=" N CYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 396 removed outlier: 3.714A pdb=" N VAL D 382 " --> pdb=" O PRO D 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 203 through 204 removed outlier: 3.717A pdb=" N SER E 203 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS E 2 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE E 145 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA E 4 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 231 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU E 230 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE E 217 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU E 232 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL E 215 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU E 234 " --> pdb=" O THR E 213 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 236 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU F 149 " --> pdb=" O TYR F 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 43 through 52 Processing sheet with id=AA3, first strand: chain 'E' and resid 248 through 255 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 248 through 255 current: chain 'E' and resid 290 through 298 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 290 through 298 current: chain 'F' and resid 290 through 298 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 290 through 298 current: chain 'D' and resid 290 through 299 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 331 through 338 Processing sheet with id=AA5, first strand: chain 'F' and resid 203 through 204 removed outlier: 4.455A pdb=" N SER F 203 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER F 146 " --> pdb=" O SER F 203 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS F 143 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 231 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU F 230 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE F 217 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU F 232 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL F 215 " --> pdb=" O LEU F 232 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU F 234 " --> pdb=" O THR F 213 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU F 236 " --> pdb=" O ASN F 211 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU D 149 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 43 through 51 removed outlier: 3.950A pdb=" N GLU F 44 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN F 63 " --> pdb=" O GLU F 44 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG F 46 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 154 through 158 removed outlier: 4.079A pdb=" N GLY F 154 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 331 through 338 removed outlier: 3.512A pdb=" N GLY F 348 " --> pdb=" O ASN F 360 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 360 " --> pdb=" O GLY F 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 203 through 204 removed outlier: 4.301A pdb=" N SER A 203 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 146 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 231 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 232 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 214 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 52 Processing sheet with id=AB2, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AB3, first strand: chain 'A' and resid 210 through 211 removed outlier: 6.344A pdb=" N LEU B 149 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 248 through 255 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 248 through 255 current: chain 'A' and resid 290 through 298 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 290 through 298 current: chain 'B' and resid 290 through 298 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 290 through 298 current: chain 'C' and resid 290 through 299 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 330 through 337 removed outlier: 4.345A pdb=" N GLN A 330 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 349 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 336 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 346 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 362 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 203 through 204 removed outlier: 4.053A pdb=" N SER B 203 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 146 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS B 2 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ILE B 145 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA B 4 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 232 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU B 236 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU B 212 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 149 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR C 180 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 51 Processing sheet with id=AB8, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.505A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 330 through 338 removed outlier: 3.663A pdb=" N GLN B 330 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 346 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 348 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 360 " --> pdb=" O GLY B 348 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 203 through 204 removed outlier: 3.773A pdb=" N SER C 203 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 146 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C 143 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 231 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 230 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE C 217 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 232 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 215 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU C 234 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 43 through 51 removed outlier: 3.637A pdb=" N ALA C 57 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 155 through 158 Processing sheet with id=AC4, first strand: chain 'C' and resid 330 through 338 removed outlier: 3.522A pdb=" N TYR C 350 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 203 through 204 removed outlier: 4.171A pdb=" N SER D 203 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 146 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS D 2 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE D 145 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA D 4 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 231 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG D 214 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU D 236 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU D 212 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 43 through 51 Processing sheet with id=AC7, first strand: chain 'D' and resid 155 through 158 removed outlier: 3.561A pdb=" N GLY D 161 " --> pdb=" O CYS D 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 330 through 338 removed outlier: 3.525A pdb=" N VAL D 336 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 343 " --> pdb=" O VAL D 336 " (cutoff:3.500A) 822 hydrogen bonds defined for protein. 2409 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: 2.96 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5032 1.33 - 1.45: 2614 1.45 - 1.57: 10107 1.57 - 1.69: 0 1.69 - 1.81: 124 Bond restraints: 17877 Sorted by residual: bond pdb=" N ARG E 320 " pdb=" CA ARG E 320 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.23e-02 6.61e+03 6.55e+00 bond pdb=" N LEU E 319 " pdb=" CA LEU E 319 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.29e-02 6.01e+03 6.55e+00 bond pdb=" N LEU E 317 " pdb=" CA LEU E 317 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.38e-02 5.25e+03 5.65e+00 bond pdb=" N GLY E 318 " pdb=" CA GLY E 318 " ideal model delta sigma weight residual 1.449 1.474 -0.025 1.45e-02 4.76e+03 2.95e+00 bond pdb=" CB ASP B 157 " pdb=" CG ASP B 157 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.24e+00 ... (remaining 17872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 24021 2.27 - 4.55: 237 4.55 - 6.82: 28 6.82 - 9.09: 6 9.09 - 11.37: 5 Bond angle restraints: 24297 Sorted by residual: angle pdb=" C PRO D 148 " pdb=" N LEU D 149 " pdb=" CA LEU D 149 " ideal model delta sigma weight residual 120.94 130.49 -9.55 1.90e+00 2.77e-01 2.53e+01 angle pdb=" C THR A 199 " pdb=" N LEU A 200 " pdb=" CA LEU A 200 " ideal model delta sigma weight residual 121.80 114.44 7.36 2.16e+00 2.14e-01 1.16e+01 angle pdb=" CA GLU E 91 " pdb=" CB GLU E 91 " pdb=" CG GLU E 91 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CA LEU A 79 " pdb=" CB LEU A 79 " pdb=" CG LEU A 79 " ideal model delta sigma weight residual 116.30 127.67 -11.37 3.50e+00 8.16e-02 1.05e+01 angle pdb=" N GLY B 154 " pdb=" CA GLY B 154 " pdb=" C GLY B 154 " ideal model delta sigma weight residual 111.21 114.54 -3.33 1.04e+00 9.25e-01 1.03e+01 ... (remaining 24292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 9593 17.81 - 35.61: 905 35.61 - 53.42: 225 53.42 - 71.23: 22 71.23 - 89.03: 24 Dihedral angle restraints: 10769 sinusoidal: 4115 harmonic: 6654 Sorted by residual: dihedral pdb=" CD ARG E 320 " pdb=" NE ARG E 320 " pdb=" CZ ARG E 320 " pdb=" NH1 ARG E 320 " ideal model delta sinusoidal sigma weight residual 0.00 -72.58 72.58 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB GLU A 300 " pdb=" CG GLU A 300 " pdb=" CD GLU A 300 " pdb=" OE1 GLU A 300 " ideal model delta sinusoidal sigma weight residual 0.00 89.03 -89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG A 46 " pdb=" CD ARG A 46 " pdb=" NE ARG A 46 " pdb=" CZ ARG A 46 " ideal model delta sinusoidal sigma weight residual 90.00 133.02 -43.02 2 1.50e+01 4.44e-03 9.93e+00 ... (remaining 10766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2243 0.046 - 0.093: 418 0.093 - 0.139: 175 0.139 - 0.185: 2 0.185 - 0.231: 2 Chirality restraints: 2840 Sorted by residual: chirality pdb=" CB THR B 198 " pdb=" CA THR B 198 " pdb=" OG1 THR B 198 " pdb=" CG2 THR B 198 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU E 77 " pdb=" CB LEU E 77 " pdb=" CD1 LEU E 77 " pdb=" CD2 LEU E 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE F 127 " pdb=" CA ILE F 127 " pdb=" CG1 ILE F 127 " pdb=" CG2 ILE F 127 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 2837 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 320 " 1.046 9.50e-02 1.11e+02 4.69e-01 1.33e+02 pdb=" NE ARG E 320 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG E 320 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 320 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 320 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 163 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO B 164 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 157 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ASP B 157 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP B 157 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS B 158 " -0.011 2.00e-02 2.50e+03 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 191 2.65 - 3.21: 15568 3.21 - 3.78: 25209 3.78 - 4.34: 31646 4.34 - 4.90: 54452 Nonbonded interactions: 127066 Sorted by model distance: nonbonded pdb=" OG1 THR B 182 " pdb=" OD1 ASP B 184 " model vdw 2.091 3.040 nonbonded pdb=" OD2 ASP A 111 " pdb=" OG SER A 113 " model vdw 2.186 3.040 nonbonded pdb=" OG SER B 27 " pdb=" OD1 ASP B 29 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR E 383 " pdb=" OE1 GLU C 261 " model vdw 2.230 3.040 nonbonded pdb=" O ALA F 167 " pdb=" OG1 THR F 170 " model vdw 2.235 3.040 ... (remaining 127061 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 1 through 167 or resid 170 through 396)) selection = (chain 'B' and (resid 1 through 153 or resid 166 through 167 or resid 170 throug \ h 396)) selection = (chain 'C' and (resid 1 through 153 or resid 166 through 167 or resid 170 throug \ h 396)) selection = (chain 'D' and (resid 1 through 153 or resid 166 through 167 or resid 170 throug \ h 396)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 153 or resid 166 through 167 or resid 170 throug \ h 396)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.210 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.003 0.043 17877 Z= 0.129 Angle : 0.591 11.368 24297 Z= 0.304 Chirality : 0.042 0.231 2840 Planarity : 0.009 0.469 3163 Dihedral : 14.932 89.033 6505 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.38 % Allowed : 16.10 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.28 (0.17), residues: 2334 helix: 2.11 (0.18), residues: 886 sheet: 0.67 (0.19), residues: 692 loop : -0.45 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 331 TYR 0.023 0.001 TYR A 180 PHE 0.019 0.001 PHE E 9 TRP 0.011 0.001 TRP B 155 HIS 0.007 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (17877) covalent geometry : angle 0.59058 / 0.30 (24297) hydrogen bonds : bond 0.19433 / 13.51 ( 822) hydrogen bonds : angle 6.61011 / 4.56 ( 2409) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 319 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8717 (pp) REVERT: F 268 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 231 ARG cc_start: 0.7851 (ttt180) cc_final: 0.7440 (ttp80) outliers start: 7 outliers final: 1 residues processed: 181 average time/residue: 0.1084 time to fit residues: 32.1246 Evaluate side-chains 167 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain F residue 126 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 226 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104981 restraints weight = 28640.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102408 restraints weight = 30131.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103808 restraints weight = 29087.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106155 restraints weight = 18735.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106337 restraints weight = 15656.155| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17877 Z= 0.143 Angle : 0.560 10.767 24297 Z= 0.277 Chirality : 0.043 0.220 2840 Planarity : 0.005 0.058 3163 Dihedral : 3.721 52.104 2500 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.07 % Allowed : 15.39 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.31 (0.17), residues: 2334 helix: 2.20 (0.17), residues: 901 sheet: 0.63 (0.19), residues: 687 loop : -0.52 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.014 0.001 TYR C 177 PHE 0.015 0.001 PHE B 117 TRP 0.008 0.001 TRP B 155 HIS 0.005 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (17877) covalent geometry : angle 0.56002 / 0.28 (24297) hydrogen bonds : bond 0.03846 / 2.66 ( 822) hydrogen bonds : angle 4.70857 / 3.28 ( 2409) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 21 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9010 (mm) REVERT: F 210 MET cc_start: 0.8822 (ptp) cc_final: 0.8577 (ptt) REVERT: B 258 MET cc_start: 0.8759 (ttt) cc_final: 0.8268 (ttm) outliers start: 38 outliers final: 21 residues processed: 202 average time/residue: 0.1014 time to fit residues: 34.5699 Evaluate side-chains 182 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 170 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 160 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 81 ASN F 356 GLN A 72 HIS A 226 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104097 restraints weight = 29190.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102398 restraints weight = 31531.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103493 restraints weight = 30654.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106384 restraints weight = 19128.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106326 restraints weight = 15361.568| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17877 Z= 0.136 Angle : 0.544 11.241 24297 Z= 0.265 Chirality : 0.042 0.201 2840 Planarity : 0.005 0.052 3163 Dihedral : 3.633 49.374 2498 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.10 % Allowed : 16.15 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.26 (0.17), residues: 2334 helix: 2.16 (0.17), residues: 902 sheet: 0.63 (0.20), residues: 670 loop : -0.56 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.010 0.001 TYR C 383 PHE 0.017 0.001 PHE B 117 TRP 0.007 0.001 TRP B 155 HIS 0.003 0.001 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (17877) covalent geometry : angle 0.54367 / 0.27 (24297) hydrogen bonds : bond 0.03540 / 2.44 ( 822) hydrogen bonds : angle 4.35611 / 3.06 ( 2409) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 171 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 210 MET cc_start: 0.8823 (ptp) cc_final: 0.8510 (ptt) REVERT: F 333 MET cc_start: 0.7299 (tpp) cc_final: 0.7035 (tpp) REVERT: B 349 LEU cc_start: 0.8884 (pp) cc_final: 0.8469 (tp) REVERT: C 172 TYR cc_start: 0.8752 (m-80) cc_final: 0.8407 (m-80) outliers start: 57 outliers final: 31 residues processed: 210 average time/residue: 0.1041 time to fit residues: 36.7401 Evaluate side-chains 188 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 35 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 0.0070 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 226 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104489 restraints weight = 28884.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102527 restraints weight = 30553.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104113 restraints weight = 31374.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104726 restraints weight = 19253.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106235 restraints weight = 17336.077| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17877 Z= 0.113 Angle : 0.532 11.282 24297 Z= 0.256 Chirality : 0.042 0.183 2840 Planarity : 0.005 0.047 3163 Dihedral : 3.538 48.493 2496 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.83 % Allowed : 16.86 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.32 (0.17), residues: 2334 helix: 2.25 (0.17), residues: 902 sheet: 0.65 (0.20), residues: 658 loop : -0.54 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.018 0.001 TYR A 180 PHE 0.018 0.001 PHE B 117 TRP 0.008 0.001 TRP B 155 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (17877) covalent geometry : angle 0.53216 / 0.26 (24297) hydrogen bonds : bond 0.03151 / 2.17 ( 822) hydrogen bonds : angle 4.16056 / 2.92 ( 2409) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 258 MET cc_start: 0.8788 (ttt) cc_final: 0.8580 (ttt) REVERT: F 210 MET cc_start: 0.8819 (ptp) cc_final: 0.8542 (ptt) REVERT: F 333 MET cc_start: 0.7266 (tpp) cc_final: 0.6881 (tpp) REVERT: A 180 TYR cc_start: 0.7103 (p90) cc_final: 0.6809 (p90) REVERT: B 258 MET cc_start: 0.8681 (ttt) cc_final: 0.8287 (ttt) REVERT: B 349 LEU cc_start: 0.8883 (pp) cc_final: 0.8469 (tp) REVERT: C 172 TYR cc_start: 0.8757 (m-80) cc_final: 0.8401 (m-80) REVERT: C 258 MET cc_start: 0.8611 (ttt) cc_final: 0.8120 (ttt) REVERT: C 285 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8571 (mmm) outliers start: 52 outliers final: 32 residues processed: 203 average time/residue: 0.1028 time to fit residues: 35.2449 Evaluate side-chains 191 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 24 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 129 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 123 optimal weight: 0.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 81 ASN A 72 HIS A 226 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.143686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103182 restraints weight = 28880.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101751 restraints weight = 28069.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103008 restraints weight = 30196.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103763 restraints weight = 18865.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104701 restraints weight = 16927.039| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17877 Z= 0.127 Angle : 0.542 12.907 24297 Z= 0.262 Chirality : 0.042 0.192 2840 Planarity : 0.005 0.044 3163 Dihedral : 3.552 47.674 2496 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.94 % Allowed : 17.94 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.33 (0.17), residues: 2334 helix: 2.29 (0.17), residues: 901 sheet: 0.60 (0.20), residues: 659 loop : -0.54 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 102 TYR 0.015 0.001 TYR A 180 PHE 0.011 0.001 PHE D 97 TRP 0.006 0.001 TRP B 155 HIS 0.002 0.000 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (17877) covalent geometry : angle 0.54212 / 0.26 (24297) hydrogen bonds : bond 0.03261 / 2.25 ( 822) hydrogen bonds : angle 4.13473 / 2.90 ( 2409) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 210 MET cc_start: 0.8840 (ptp) cc_final: 0.8529 (ptt) REVERT: F 333 MET cc_start: 0.7350 (tpp) cc_final: 0.6909 (tpp) REVERT: F 364 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: B 258 MET cc_start: 0.8728 (ttt) cc_final: 0.8304 (ttm) REVERT: C 27 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7977 (p) REVERT: C 142 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: C 172 TYR cc_start: 0.8797 (m-80) cc_final: 0.8429 (m-80) REVERT: C 258 MET cc_start: 0.8703 (ttt) cc_final: 0.8351 (ttt) REVERT: C 285 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8592 (mmm) REVERT: D 77 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8472 (mm) outliers start: 54 outliers final: 33 residues processed: 202 average time/residue: 0.0900 time to fit residues: 30.9060 Evaluate side-chains 196 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 118 HIS F 175 GLN A 28 GLN A 72 HIS A 226 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS C 82 ASN C 108 HIS D 175 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098695 restraints weight = 29343.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097315 restraints weight = 31299.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097972 restraints weight = 36072.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099153 restraints weight = 20698.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100838 restraints weight = 17417.266| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 17877 Z= 0.293 Angle : 0.706 11.513 24297 Z= 0.354 Chirality : 0.047 0.233 2840 Planarity : 0.005 0.048 3163 Dihedral : 4.394 49.472 2496 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.64 % Allowed : 18.54 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 0.63 (0.17), residues: 2334 helix: 1.88 (0.17), residues: 898 sheet: 0.02 (0.20), residues: 676 loop : -0.92 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 231 TYR 0.015 0.002 TYR A 383 PHE 0.027 0.002 PHE B 9 TRP 0.006 0.001 TRP B 155 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.29 (17877) covalent geometry : angle 0.70591 / 0.35 (24297) hydrogen bonds : bond 0.05068 / 3.49 ( 822) hydrogen bonds : angle 4.69233 / 3.27 ( 2409) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 207 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8248 (t80) REVERT: F 210 MET cc_start: 0.8926 (ptp) cc_final: 0.8724 (ptt) REVERT: F 323 ARG cc_start: 0.7559 (mtt90) cc_final: 0.6909 (ttm110) REVERT: F 333 MET cc_start: 0.7328 (tpp) cc_final: 0.6867 (tpp) REVERT: F 364 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: B 258 MET cc_start: 0.8800 (ttt) cc_final: 0.8497 (ttt) REVERT: B 349 LEU cc_start: 0.8925 (pp) cc_final: 0.8435 (tt) REVERT: C 30 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7636 (tm-30) REVERT: C 142 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: C 285 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8788 (mmm) REVERT: D 77 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8507 (mm) REVERT: D 383 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8355 (t80) outliers start: 67 outliers final: 47 residues processed: 213 average time/residue: 0.0901 time to fit residues: 31.8991 Evaluate side-chains 200 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 26 optimal weight: 0.0980 chunk 62 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 81 ASN F 284 GLN A 72 HIS ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113198 restraints weight = 28561.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111648 restraints weight = 34485.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112870 restraints weight = 34423.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113867 restraints weight = 20499.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114574 restraints weight = 17892.381| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17877 Z= 0.109 Angle : 0.553 13.274 24297 Z= 0.266 Chirality : 0.042 0.218 2840 Planarity : 0.005 0.045 3163 Dihedral : 3.823 48.970 2496 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.77 % Allowed : 20.23 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.00 (0.17), residues: 2334 helix: 2.22 (0.17), residues: 896 sheet: 0.25 (0.20), residues: 660 loop : -0.78 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.021 0.001 TYR A 180 PHE 0.010 0.001 PHE D 6 TRP 0.016 0.001 TRP A 43 HIS 0.011 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17877) covalent geometry : angle 0.55258 / 0.27 (24297) hydrogen bonds : bond 0.03153 / 2.18 ( 822) hydrogen bonds : angle 4.15741 / 2.91 ( 2409) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: E 324 ASP cc_start: 0.8086 (m-30) cc_final: 0.7808 (m-30) REVERT: F 117 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.6917 (t80) REVERT: F 333 MET cc_start: 0.7351 (tpp) cc_final: 0.6872 (tpp) REVERT: F 364 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: A 180 TYR cc_start: 0.7039 (p90) cc_final: 0.6773 (p90) REVERT: B 258 MET cc_start: 0.8679 (ttt) cc_final: 0.8274 (ttm) REVERT: B 349 LEU cc_start: 0.8809 (pp) cc_final: 0.8348 (tt) REVERT: C 285 MET cc_start: 0.8794 (tpp) cc_final: 0.8586 (mmm) REVERT: C 333 MET cc_start: 0.7987 (mmm) cc_final: 0.7641 (mmm) REVERT: D 77 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8394 (mm) REVERT: D 383 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8288 (t80) outliers start: 51 outliers final: 36 residues processed: 199 average time/residue: 0.0824 time to fit residues: 28.1716 Evaluate side-chains 189 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 284 GLN Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 28 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 118 HIS F 284 GLN A 72 HIS A 116 HIS B 70 HIS B 116 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 330 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113531 restraints weight = 28483.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110788 restraints weight = 31981.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112499 restraints weight = 32224.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113218 restraints weight = 19398.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115633 restraints weight = 17000.781| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17877 Z= 0.102 Angle : 0.543 10.985 24297 Z= 0.262 Chirality : 0.042 0.227 2840 Planarity : 0.005 0.045 3163 Dihedral : 3.640 46.759 2496 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.61 % Allowed : 20.45 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.07 (0.17), residues: 2334 helix: 2.21 (0.17), residues: 899 sheet: 0.35 (0.20), residues: 659 loop : -0.72 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.019 0.001 TYR A 180 PHE 0.012 0.001 PHE D 6 TRP 0.014 0.001 TRP A 43 HIS 0.012 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (17877) covalent geometry : angle 0.54291 / 0.26 (24297) hydrogen bonds : bond 0.03063 / 2.09 ( 822) hydrogen bonds : angle 4.06325 / 2.84 ( 2409) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 16 MET cc_start: 0.7845 (ptp) cc_final: 0.7513 (ptm) REVERT: E 324 ASP cc_start: 0.8089 (m-30) cc_final: 0.7731 (m-30) REVERT: F 117 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6839 (t80) REVERT: F 333 MET cc_start: 0.7329 (tpp) cc_final: 0.6904 (tpp) REVERT: F 364 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: A 180 TYR cc_start: 0.7141 (p90) cc_final: 0.6903 (p90) REVERT: B 349 LEU cc_start: 0.8789 (pp) cc_final: 0.8312 (tt) REVERT: C 142 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: C 285 MET cc_start: 0.8761 (tpp) cc_final: 0.8549 (mmm) REVERT: C 333 MET cc_start: 0.7943 (mmm) cc_final: 0.7587 (mmm) REVERT: D 77 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8424 (mm) REVERT: D 383 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8256 (t80) outliers start: 48 outliers final: 34 residues processed: 197 average time/residue: 0.0932 time to fit residues: 31.2227 Evaluate side-chains 191 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 284 GLN Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 148 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 229 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 118 HIS F 284 GLN A 72 HIS A 116 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.151409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111787 restraints weight = 28605.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108341 restraints weight = 28458.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109868 restraints weight = 31604.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110751 restraints weight = 19274.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112639 restraints weight = 16793.942| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17877 Z= 0.127 Angle : 0.561 14.483 24297 Z= 0.270 Chirality : 0.043 0.319 2840 Planarity : 0.005 0.045 3163 Dihedral : 3.629 45.706 2496 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.39 % Allowed : 20.77 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.08 (0.17), residues: 2334 helix: 2.19 (0.17), residues: 901 sheet: 0.32 (0.20), residues: 665 loop : -0.65 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.018 0.001 TYR A 180 PHE 0.012 0.001 PHE D 6 TRP 0.014 0.001 TRP A 43 HIS 0.011 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (17877) covalent geometry : angle 0.56111 / 0.27 (24297) hydrogen bonds : bond 0.03203 / 2.20 ( 822) hydrogen bonds : angle 4.07456 / 2.85 ( 2409) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: E 16 MET cc_start: 0.7917 (ptp) cc_final: 0.7599 (ptm) REVERT: E 81 ASN cc_start: 0.8505 (m-40) cc_final: 0.8156 (t0) REVERT: F 117 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6860 (t80) REVERT: F 333 MET cc_start: 0.7408 (tpp) cc_final: 0.6928 (tpp) REVERT: F 364 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: B 349 LEU cc_start: 0.8816 (pp) cc_final: 0.8351 (tt) REVERT: C 142 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: C 333 MET cc_start: 0.7973 (mmm) cc_final: 0.7623 (mmm) REVERT: D 77 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8452 (mm) REVERT: D 383 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8274 (t80) outliers start: 44 outliers final: 37 residues processed: 186 average time/residue: 0.1028 time to fit residues: 33.0191 Evaluate side-chains 192 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 284 GLN Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 284 GLN A 72 HIS A 116 HIS C 82 ASN C 108 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111978 restraints weight = 28485.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110984 restraints weight = 33542.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111870 restraints weight = 34166.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112947 restraints weight = 20184.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114149 restraints weight = 17204.631| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17877 Z= 0.142 Angle : 0.572 13.842 24297 Z= 0.275 Chirality : 0.043 0.300 2840 Planarity : 0.005 0.046 3163 Dihedral : 3.669 45.470 2496 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.39 % Allowed : 20.77 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 1.06 (0.17), residues: 2334 helix: 2.20 (0.17), residues: 900 sheet: 0.29 (0.20), residues: 665 loop : -0.69 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.010 0.001 TYR D 350 PHE 0.012 0.001 PHE D 6 TRP 0.013 0.001 TRP A 43 HIS 0.011 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (17877) covalent geometry : angle 0.57154 / 0.28 (24297) hydrogen bonds : bond 0.03327 / 2.29 ( 822) hydrogen bonds : angle 4.09226 / 2.86 ( 2409) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 16 MET cc_start: 0.7871 (ptp) cc_final: 0.7582 (ptm) REVERT: E 81 ASN cc_start: 0.8519 (m-40) cc_final: 0.8170 (t0) REVERT: F 117 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6668 (t80) REVERT: F 333 MET cc_start: 0.7366 (tpp) cc_final: 0.6903 (tpp) REVERT: F 364 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: B 349 LEU cc_start: 0.8825 (pp) cc_final: 0.8372 (tt) REVERT: C 142 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: C 333 MET cc_start: 0.8053 (mmm) cc_final: 0.7721 (mmm) REVERT: D 383 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8264 (t80) outliers start: 44 outliers final: 37 residues processed: 187 average time/residue: 0.0988 time to fit residues: 31.4928 Evaluate side-chains 192 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 284 GLN Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 364 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 55 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 207 optimal weight: 0.0060 chunk 202 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 284 GLN A 72 HIS C 82 ASN C 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108857 restraints weight = 28331.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105685 restraints weight = 33273.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107674 restraints weight = 29980.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110152 restraints weight = 18607.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.110476 restraints weight = 15556.632| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17877 Z= 0.166 Angle : 0.591 12.960 24297 Z= 0.286 Chirality : 0.043 0.284 2840 Planarity : 0.005 0.046 3163 Dihedral : 3.760 45.552 2496 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.39 % Allowed : 20.88 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 are not related in a simple way. whole: 0.95 (0.17), residues: 2334 helix: 2.15 (0.17), residues: 900 sheet: 0.20 (0.20), residues: 673 loop : -0.77 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.022 0.001 TYR A 180 PHE 0.014 0.002 PHE B 9 TRP 0.012 0.001 TRP A 43 HIS 0.011 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (17877) covalent geometry : angle 0.59105 / 0.29 (24297) hydrogen bonds : bond 0.03566 / 2.46 ( 822) hydrogen bonds : angle 4.15767 / 2.91 ( 2409) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.17 seconds wall clock time: 39 minutes 17.91 seconds (2357.91 seconds total)