Starting phenix.real_space_refine on Wed Aug 5 21:27:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vx1_65405/08_2026/9vx1_65405.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vx1_65405/08_2026/9vx1_65405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vx1_65405/08_2026/9vx1_65405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vx1_65405/08_2026/9vx1_65405.map" model { file = "/net/cci-nas-00/data/ceres_data/9vx1_65405/08_2026/9vx1_65405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vx1_65405/08_2026/9vx1_65405.cif" } resolution = 2.77 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= 0.002 sd= 0.029 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 7304 2.51 5 N 2015 2.21 5 O 2198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s 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: 11572 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3819 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 458} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1846 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "D" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3809 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "E" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1842 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.52, per 1000 atoms: 0.22 Number of scatterers: 11572 At special positions: 0 Unit cell: (90.35, 125.45, 89.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 12 15.00 Mg 2 11.99 O 2198 8.00 N 2015 7.00 C 7304 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: 0.61 Conformation dependent library (CDL) restraints added in 417.2 milliseconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 16 sheets defined 36.0% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.500A pdb=" N LEU A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 64 removed outlier: 3.815A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.607A pdb=" N LYS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 138 removed outlier: 3.615A pdb=" N GLY A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 4.225A pdb=" N ARG A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.189A pdb=" N ILE A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 225 through 243 removed outlier: 3.691A pdb=" N ASN A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.563A pdb=" N ILE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.594A pdb=" N GLY A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 removed outlier: 4.143A pdb=" N GLU A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 462 through 470 removed outlier: 4.248A pdb=" N VAL A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'B' and resid 185 through 195 removed outlier: 3.952A pdb=" N ILE B 190 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.774A pdb=" N SER B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 236 through 241 removed outlier: 3.645A pdb=" N LEU B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 263 removed outlier: 3.954A pdb=" N ARG B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 removed outlier: 4.158A pdb=" N LEU B 358 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 384 Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 23 through 32 removed outlier: 3.518A pdb=" N LEU D 28 " --> pdb=" O PRO D 24 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 64 removed outlier: 3.811A pdb=" N GLU D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.702A pdb=" N LYS D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 138 removed outlier: 3.645A pdb=" N VAL D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 removed outlier: 4.172A pdb=" N ARG D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 201 through 206 removed outlier: 4.212A pdb=" N ILE D 205 " --> pdb=" O TRP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 225 through 243 removed outlier: 3.520A pdb=" N TRP D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 328 removed outlier: 3.615A pdb=" N ILE D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 358 removed outlier: 3.512A pdb=" N ALA D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 353 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 440 removed outlier: 3.515A pdb=" N GLU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 462 through 470 removed outlier: 4.292A pdb=" N VAL D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 485 Processing helix chain 'E' and resid 185 through 195 removed outlier: 3.768A pdb=" N ILE E 190 " --> pdb=" O PRO E 186 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.728A pdb=" N SER E 220 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.512A pdb=" N VAL E 231 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 241 removed outlier: 3.772A pdb=" N LEU E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 263 removed outlier: 3.940A pdb=" N ARG E 250 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN E 257 " --> pdb=" O HIS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 361 removed outlier: 3.618A pdb=" N ALA E 360 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 384 removed outlier: 3.910A pdb=" N LEU E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 4.195A pdb=" N GLU A 4 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 388 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS A 259 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU A 337 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 261 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE A 275 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG A 295 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER A 277 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 103 removed outlier: 4.138A pdb=" N GLU A 97 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 46 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N GLY A 99 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 12.062A pdb=" N GLY A 48 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N THR A 101 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL A 145 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS A 43 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 147 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 45 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA A 149 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 47 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.668A pdb=" N THR B 339 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N HIS B 321 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.668A pdb=" N THR B 339 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL B 302 " --> pdb=" O HIS B 321 " (cutoff:3.500A) removed outlier: 13.578A pdb=" N PHE B 323 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 17.387A pdb=" N ALA B 300 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 26.382A pdb=" N THR B 298 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR B 291 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 301 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE B 289 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 303 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.316A pdb=" N GLU D 4 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS D 259 " --> pdb=" O PHE D 335 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU D 337 " --> pdb=" O CYS D 259 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL D 261 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE D 275 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG D 295 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER D 277 " --> pdb=" O GLY D 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB2, first strand: chain 'D' and resid 93 through 103 removed outlier: 4.136A pdb=" N GLU D 97 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL D 46 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLY D 99 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 12.097A pdb=" N GLY D 48 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N THR D 101 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N VAL D 145 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS D 43 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE D 147 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY D 45 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA D 149 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL D 47 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 297 through 298 Processing sheet with id=AB4, first strand: chain 'D' and resid 376 through 377 Processing sheet with id=AB5, first strand: chain 'E' and resid 168 through 170 removed outlier: 3.576A pdb=" N THR E 339 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL E 302 " --> pdb=" O HIS E 321 " (cutoff:3.500A) removed outlier: 13.715A pdb=" N PHE E 323 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 17.482A pdb=" N ALA E 300 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 26.225A pdb=" N THR E 298 " --> pdb=" O PRO E 325 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP E 299 " --> pdb=" O TYR E 291 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR E 291 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN E 301 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N PHE E 289 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 204 through 206 Processing sheet with id=AB7, first strand: chain 'E' and resid 267 through 270 451 hydrogen bonds defined for protein. 1266 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: 1.56 Time building geometry restraints manager: 0.85 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: 2544 1.33 - 1.45: 2742 1.45 - 1.56: 6488 1.56 - 1.68: 22 1.68 - 1.80: 74 Bond restraints: 11870 Sorted by residual: bond pdb=" N PRO E 351 " pdb=" CD PRO E 351 " ideal model delta sigma weight residual 1.473 1.557 -0.084 1.40e-02 5.10e+03 3.58e+01 bond pdb=" N PRO B 351 " pdb=" CD PRO B 351 " ideal model delta sigma weight residual 1.473 1.551 -0.078 1.40e-02 5.10e+03 3.09e+01 bond pdb=" N9 A a 1 " pdb=" C4 A a 1 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.47e+01 bond pdb=" N9 A Z 1 " pdb=" C4 A Z 1 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.45e+01 bond pdb=" CA MET E 330 " pdb=" CB MET E 330 " ideal model delta sigma weight residual 1.526 1.481 0.045 1.49e-02 4.50e+03 9.14e+00 ... (remaining 11865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 15344 1.87 - 3.75: 668 3.75 - 5.62: 86 5.62 - 7.49: 16 7.49 - 9.36: 11 Bond angle restraints: 16125 Sorted by residual: angle pdb=" C1' G a 6 " pdb=" N9 G a 6 " pdb=" C4 G a 6 " ideal model delta sigma weight residual 126.50 132.32 -5.82 1.30e+00 5.92e-01 2.00e+01 angle pdb=" C1' G Z 6 " pdb=" N9 G Z 6 " pdb=" C4 G Z 6 " ideal model delta sigma weight residual 126.50 132.28 -5.78 1.30e+00 5.92e-01 1.97e+01 angle pdb=" N9 G Z 6 " pdb=" C4 G Z 6 " pdb=" N3 G Z 6 " ideal model delta sigma weight residual 126.00 128.58 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N9 G a 6 " pdb=" C4 G a 6 " pdb=" N3 G a 6 " ideal model delta sigma weight residual 126.00 128.54 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" C MET E 330 " pdb=" N ALA E 331 " pdb=" CA ALA E 331 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.80e+01 ... (remaining 16120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6797 17.67 - 35.34: 228 35.34 - 53.01: 55 53.01 - 70.67: 16 70.67 - 88.34: 7 Dihedral angle restraints: 7103 sinusoidal: 2989 harmonic: 4114 Sorted by residual: dihedral pdb=" CD ARG A 248 " pdb=" NE ARG A 248 " pdb=" CZ ARG A 248 " pdb=" NH1 ARG A 248 " ideal model delta sinusoidal sigma weight residual 0.00 88.34 -88.34 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CA ASP E 227 " pdb=" C ASP E 227 " pdb=" N ILE E 228 " pdb=" CA ILE E 228 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA THR A 52 " pdb=" C THR A 52 " pdb=" N ILE A 53 " pdb=" CA ILE A 53 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 7100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1168 0.051 - 0.102: 436 0.102 - 0.153: 115 0.153 - 0.204: 25 0.204 - 0.255: 5 Chirality restraints: 1749 Sorted by residual: chirality pdb=" CB ILE D 457 " pdb=" CA ILE D 457 " pdb=" CG1 ILE D 457 " pdb=" CG2 ILE D 457 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE A 457 " pdb=" CA ILE A 457 " pdb=" CG1 ILE A 457 " pdb=" CG2 ILE A 457 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CG LEU D 291 " pdb=" CB LEU D 291 " pdb=" CD1 LEU D 291 " pdb=" CD2 LEU D 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1746 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG A 248 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 366 " 0.019 2.00e-02 2.50e+03 1.77e-02 7.84e+00 pdb=" CG TRP A 366 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 366 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 366 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 366 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 366 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 366 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 366 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 366 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 366 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 366 " -0.020 2.00e-02 2.50e+03 1.69e-02 7.16e+00 pdb=" CG TRP D 366 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 366 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 366 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 366 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP D 366 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 366 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 366 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 366 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 366 " -0.007 2.00e-02 2.50e+03 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 340 2.70 - 3.25: 10386 3.25 - 3.80: 18234 3.80 - 4.35: 24434 4.35 - 4.90: 40681 Nonbonded interactions: 94075 Sorted by model distance: nonbonded pdb=" OP1 A a 1 " pdb="MG MG D 501 " model vdw 2.150 2.170 nonbonded pdb=" OD1 ASN A 447 " pdb="MG MG A 501 " model vdw 2.201 2.170 nonbonded pdb=" OP1 A Z 1 " pdb="MG MG A 501 " model vdw 2.206 2.170 nonbonded pdb=" OE2 GLU A 284 " pdb=" OH TYR A 323 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU D 284 " pdb=" OH TYR D 323 " model vdw 2.270 3.040 ... (remaining 94070 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 70 or resid 73 through 76 or (resid 77 and (name \ N or name CA or name C or name O or name CB )) or resid 78 through 501)) selection = (chain 'D' and (resid 1 through 165 or (resid 166 and (name N or name CA or name \ C or name O or name CB )) or resid 167 through 501)) } ncs_group { reference = (chain 'B' and (resid 161 through 186 or (resid 187 and (name N or name CA or na \ me C or name O or name CB )) or resid 188 through 294 or (resid 295 through 297 \ and (name N or name CA or name C or name O or name CB )) or resid 298 through 36 \ 6 or (resid 367 and (name N or name CA or name C or name O or name CB )) or resi \ d 368 through 413)) selection = (chain 'E' and (resid 161 through 282 or resid 285 through 413)) } ncs_group { reference = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:5.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.009 0.093 11870 Z= 0.398 Angle : 0.889 9.364 16125 Z= 0.523 Chirality : 0.058 0.255 1749 Planarity : 0.013 0.493 2052 Dihedral : 10.790 88.344 4461 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.18), residues: 1404 helix: -4.39 (0.10), residues: 434 sheet: -1.23 (0.26), residues: 349 loop : -2.13 (0.21), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 483 TYR 0.034 0.003 TYR D 485 PHE 0.033 0.004 PHE E 214 TRP 0.042 0.005 TRP A 366 HIS 0.014 0.003 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.40 (11870) covalent geometry : angle 0.88938 / 0.52 (16125) hydrogen bonds : bond 0.27611 / 18.33 ( 438) hydrogen bonds : angle 10.30757 / 7.29 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6897 (tt0) cc_final: 0.6641 (tt0) REVERT: A 18 HIS cc_start: 0.7260 (m-70) cc_final: 0.7014 (m-70) REVERT: A 123 GLU cc_start: 0.6636 (mt-10) cc_final: 0.5880 (mt-10) REVERT: A 127 ASP cc_start: 0.7283 (m-30) cc_final: 0.6866 (m-30) REVERT: A 132 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 248 ARG cc_start: 0.7299 (ttt90) cc_final: 0.7043 (ttt90) REVERT: A 250 MET cc_start: 0.6723 (mmm) cc_final: 0.6164 (mmm) REVERT: A 351 ILE cc_start: 0.8029 (mp) cc_final: 0.7792 (mm) REVERT: A 355 ASP cc_start: 0.7563 (m-30) cc_final: 0.7363 (m-30) REVERT: A 363 ASP cc_start: 0.7727 (m-30) cc_final: 0.7516 (m-30) REVERT: A 373 THR cc_start: 0.7622 (p) cc_final: 0.6919 (t) REVERT: A 391 ASP cc_start: 0.7152 (t0) cc_final: 0.6934 (t70) REVERT: A 393 HIS cc_start: 0.6649 (m-70) cc_final: 0.6383 (m-70) REVERT: B 271 LYS cc_start: 0.7513 (mtpp) cc_final: 0.7293 (mtpp) REVERT: B 279 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.7854 (mtt90) REVERT: D 123 GLU cc_start: 0.6718 (mt-10) cc_final: 0.5921 (mt-10) REVERT: D 127 ASP cc_start: 0.7147 (m-30) cc_final: 0.6864 (m-30) REVERT: D 153 LYS cc_start: 0.7796 (mttp) cc_final: 0.7577 (mttp) REVERT: D 164 ASP cc_start: 0.6926 (t70) cc_final: 0.6712 (t0) REVERT: D 213 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8214 (mm-40) REVERT: D 250 MET cc_start: 0.6904 (mmm) cc_final: 0.6415 (mmm) REVERT: D 351 ILE cc_start: 0.7828 (mt) cc_final: 0.7527 (mm) REVERT: D 355 ASP cc_start: 0.7579 (m-30) cc_final: 0.7361 (m-30) REVERT: E 190 ILE cc_start: 0.8699 (mt) cc_final: 0.8447 (mt) REVERT: E 194 LEU cc_start: 0.8533 (mt) cc_final: 0.8240 (mp) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.6211 time to fit residues: 235.1811 Evaluate side-chains 293 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN A 198 GLN A 272 GLN A 280 GLN A 450 GLN B 253 HIS B 257 GLN D 198 GLN D 452 ASN E 352 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130149 restraints weight = 14770.856| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.16 r_work: 0.3536 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11870 Z= 0.152 Angle : 0.604 7.565 16125 Z= 0.320 Chirality : 0.043 0.138 1749 Planarity : 0.006 0.060 2052 Dihedral : 8.929 73.556 1738 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.34 % Allowed : 12.10 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.20), residues: 1404 helix: -2.14 (0.19), residues: 453 sheet: -0.93 (0.27), residues: 343 loop : -1.78 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 248 TYR 0.015 0.002 TYR B 343 PHE 0.014 0.002 PHE D 275 TRP 0.024 0.002 TRP D 446 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (11870) covalent geometry : angle 0.60357 / 0.32 (16125) hydrogen bonds : bond 0.05050 / 3.44 ( 438) hydrogen bonds : angle 6.13847 / 4.28 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7822 (tp30) cc_final: 0.7614 (mm-30) REVERT: A 43 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8031 (mtpp) REVERT: A 94 PHE cc_start: 0.8152 (m-80) cc_final: 0.7858 (m-80) REVERT: A 119 TYR cc_start: 0.7983 (t80) cc_final: 0.7552 (t80) REVERT: A 123 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 250 MET cc_start: 0.7343 (mmm) cc_final: 0.6790 (mmm) REVERT: A 272 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7238 (mm-40) REVERT: A 280 GLN cc_start: 0.8117 (mt0) cc_final: 0.7888 (mp10) REVERT: A 345 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7677 (pt0) REVERT: A 373 THR cc_start: 0.8004 (p) cc_final: 0.7229 (t) REVERT: D 62 THR cc_start: 0.7970 (t) cc_final: 0.7750 (p) REVERT: D 67 VAL cc_start: 0.8400 (t) cc_final: 0.8011 (p) REVERT: D 94 PHE cc_start: 0.8122 (m-80) cc_final: 0.7883 (m-80) REVERT: D 123 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6692 (mt-10) REVERT: D 127 ASP cc_start: 0.7691 (m-30) cc_final: 0.7384 (m-30) REVERT: D 213 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8494 (mm-40) REVERT: D 250 MET cc_start: 0.7425 (mmm) cc_final: 0.6873 (mmm) REVERT: D 355 ASP cc_start: 0.8002 (m-30) cc_final: 0.7773 (m-30) REVERT: D 403 SER cc_start: 0.8810 (m) cc_final: 0.8496 (p) REVERT: D 463 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7453 (ttp-170) REVERT: E 163 ASP cc_start: 0.7714 (m-30) cc_final: 0.7454 (m-30) outliers start: 28 outliers final: 11 residues processed: 292 average time/residue: 0.6074 time to fit residues: 189.7625 Evaluate side-chains 292 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 279 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain E residue 179 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 112 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 16 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN A 326 HIS A 433 GLN D 21 HIS D 198 GLN D 326 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126805 restraints weight = 14914.791| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.20 r_work: 0.3504 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11870 Z= 0.185 Angle : 0.567 7.663 16125 Z= 0.298 Chirality : 0.044 0.214 1749 Planarity : 0.005 0.060 2052 Dihedral : 8.658 73.372 1738 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.42 % Allowed : 13.44 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.85 (0.21), residues: 1404 helix: -1.04 (0.22), residues: 454 sheet: -0.81 (0.27), residues: 343 loop : -1.49 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 6 TYR 0.015 0.002 TYR D 482 PHE 0.015 0.002 PHE E 278 TRP 0.017 0.002 TRP D 446 HIS 0.005 0.001 HIS E 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (11870) covalent geometry : angle 0.56746 / 0.30 (16125) hydrogen bonds : bond 0.04418 / 3.00 ( 438) hydrogen bonds : angle 5.64478 / 3.94 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TYR cc_start: 0.7983 (t80) cc_final: 0.7744 (t80) REVERT: A 127 ASP cc_start: 0.7847 (m-30) cc_final: 0.7500 (m-30) REVERT: A 250 MET cc_start: 0.7268 (mmm) cc_final: 0.6672 (mmm) REVERT: A 345 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7599 (mt-10) REVERT: A 373 THR cc_start: 0.8180 (p) cc_final: 0.7465 (t) REVERT: A 378 ARG cc_start: 0.8245 (mtp85) cc_final: 0.8013 (mtp180) REVERT: A 393 HIS cc_start: 0.7481 (m-70) cc_final: 0.7277 (m-70) REVERT: B 257 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: B 359 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7265 (mm) REVERT: D 30 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7259 (mt-10) REVERT: D 67 VAL cc_start: 0.8387 (t) cc_final: 0.8003 (p) REVERT: D 123 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6688 (mt-10) REVERT: D 127 ASP cc_start: 0.7570 (m-30) cc_final: 0.7320 (m-30) REVERT: D 213 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8492 (mm-40) REVERT: D 250 MET cc_start: 0.7406 (mmm) cc_final: 0.6886 (mmm) REVERT: D 257 SER cc_start: 0.7877 (t) cc_final: 0.7615 (t) REVERT: D 284 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: D 403 SER cc_start: 0.8808 (m) cc_final: 0.8535 (p) REVERT: D 463 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7434 (ttp-170) REVERT: D 483 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7616 (mtm-85) REVERT: E 163 ASP cc_start: 0.7730 (m-30) cc_final: 0.7495 (m-30) REVERT: E 257 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7616 (mp10) outliers start: 29 outliers final: 12 residues processed: 291 average time/residue: 0.6472 time to fit residues: 201.5314 Evaluate side-chains 302 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 284 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Chi-restraints excluded: chain E residue 257 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 HIS A 272 GLN A 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.146121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126005 restraints weight = 14839.496| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.18 r_work: 0.3488 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 11870 Z= 0.232 Angle : 0.581 7.640 16125 Z= 0.305 Chirality : 0.046 0.173 1749 Planarity : 0.005 0.052 2052 Dihedral : 8.557 73.286 1738 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.17 % Allowed : 13.69 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.52 (0.21), residues: 1404 helix: -0.63 (0.23), residues: 454 sheet: -0.65 (0.28), residues: 336 loop : -1.39 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 483 TYR 0.015 0.002 TYR B 343 PHE 0.020 0.002 PHE E 278 TRP 0.029 0.002 TRP A 446 HIS 0.008 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.23 (11870) covalent geometry : angle 0.58061 / 0.31 (16125) hydrogen bonds : bond 0.04237 / 2.88 ( 438) hydrogen bonds : angle 5.49978 / 3.84 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8254 (t) cc_final: 0.7996 (p) REVERT: A 119 TYR cc_start: 0.8018 (t80) cc_final: 0.7759 (t80) REVERT: A 127 ASP cc_start: 0.7831 (m-30) cc_final: 0.7463 (m-30) REVERT: A 250 MET cc_start: 0.7280 (mmm) cc_final: 0.6700 (mmm) REVERT: A 345 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 373 THR cc_start: 0.8231 (p) cc_final: 0.7574 (t) REVERT: A 378 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7817 (mtp85) REVERT: A 404 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: B 168 MET cc_start: 0.8212 (ptp) cc_final: 0.7951 (mtm) REVERT: B 227 ASP cc_start: 0.7063 (t70) cc_final: 0.6837 (t70) REVERT: B 257 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: B 359 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7282 (mm) REVERT: D 30 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7261 (mt-10) REVERT: D 93 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7513 (ttp80) REVERT: D 123 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6698 (mt-10) REVERT: D 127 ASP cc_start: 0.7553 (m-30) cc_final: 0.7311 (m-30) REVERT: D 213 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8503 (mm-40) REVERT: D 250 MET cc_start: 0.7429 (mmm) cc_final: 0.6919 (mmm) REVERT: D 257 SER cc_start: 0.7953 (t) cc_final: 0.7710 (t) REVERT: D 284 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: D 403 SER cc_start: 0.8827 (m) cc_final: 0.8501 (p) REVERT: D 463 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7401 (ttp-170) REVERT: D 483 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7834 (mtm-85) REVERT: E 163 ASP cc_start: 0.7714 (m-30) cc_final: 0.7489 (m-30) outliers start: 38 outliers final: 22 residues processed: 306 average time/residue: 0.6734 time to fit residues: 220.7052 Evaluate side-chains 315 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 138 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 HIS A 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.148343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128590 restraints weight = 14779.181| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.16 r_work: 0.3512 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11870 Z= 0.131 Angle : 0.527 8.112 16125 Z= 0.276 Chirality : 0.042 0.184 1749 Planarity : 0.004 0.043 2052 Dihedral : 8.389 73.569 1738 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.59 % Allowed : 14.86 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.22), residues: 1404 helix: -0.10 (0.24), residues: 454 sheet: -0.67 (0.28), residues: 331 loop : -1.26 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 6 TYR 0.012 0.001 TYR B 343 PHE 0.014 0.001 PHE E 211 TRP 0.028 0.002 TRP D 446 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (11870) covalent geometry : angle 0.52660 / 0.28 (16125) hydrogen bonds : bond 0.03631 / 2.47 ( 438) hydrogen bonds : angle 5.30135 / 3.68 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 TYR cc_start: 0.7930 (t80) cc_final: 0.7709 (t80) REVERT: A 127 ASP cc_start: 0.7811 (m-30) cc_final: 0.7446 (m-30) REVERT: A 250 MET cc_start: 0.7252 (mmm) cc_final: 0.6697 (mmm) REVERT: A 345 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 373 THR cc_start: 0.8213 (p) cc_final: 0.7550 (t) REVERT: A 378 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7966 (mtp180) REVERT: A 470 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8147 (ptmm) REVERT: A 483 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7893 (mtt90) REVERT: B 257 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: B 359 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7289 (mm) REVERT: D 30 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7248 (mt-10) REVERT: D 93 ARG cc_start: 0.7699 (ttp80) cc_final: 0.7487 (ttp80) REVERT: D 123 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6590 (mt-10) REVERT: D 127 ASP cc_start: 0.7491 (m-30) cc_final: 0.7247 (m-30) REVERT: D 213 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8471 (mm-40) REVERT: D 250 MET cc_start: 0.7361 (mmm) cc_final: 0.6856 (mmm) REVERT: D 257 SER cc_start: 0.7938 (t) cc_final: 0.7658 (t) REVERT: D 284 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: D 403 SER cc_start: 0.8795 (m) cc_final: 0.8487 (p) REVERT: D 483 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7808 (mtm-85) REVERT: E 163 ASP cc_start: 0.7697 (m-30) cc_final: 0.7478 (m-30) outliers start: 31 outliers final: 17 residues processed: 294 average time/residue: 0.6400 time to fit residues: 201.3069 Evaluate side-chains 297 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126766 restraints weight = 14839.857| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.17 r_work: 0.3509 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11870 Z= 0.165 Angle : 0.546 10.021 16125 Z= 0.282 Chirality : 0.043 0.163 1749 Planarity : 0.004 0.042 2052 Dihedral : 8.303 73.425 1738 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.84 % Allowed : 14.77 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.22), residues: 1404 helix: 0.11 (0.24), residues: 455 sheet: -0.57 (0.28), residues: 336 loop : -1.18 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 93 TYR 0.013 0.001 TYR B 343 PHE 0.014 0.002 PHE E 278 TRP 0.027 0.002 TRP D 446 HIS 0.005 0.001 HIS A 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.16 (11870) covalent geometry : angle 0.54584 / 0.28 (16125) hydrogen bonds : bond 0.03673 / 2.49 ( 438) hydrogen bonds : angle 5.24374 / 3.65 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8451 (tppp) cc_final: 0.8117 (mmmm) REVERT: A 119 TYR cc_start: 0.7977 (t80) cc_final: 0.7731 (t80) REVERT: A 127 ASP cc_start: 0.7812 (m-30) cc_final: 0.7443 (m-30) REVERT: A 250 MET cc_start: 0.7244 (mmm) cc_final: 0.6705 (mmm) REVERT: A 345 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 373 THR cc_start: 0.8234 (p) cc_final: 0.7566 (t) REVERT: A 378 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7941 (mtp180) REVERT: A 391 ASP cc_start: 0.7813 (t0) cc_final: 0.7593 (t0) REVERT: A 470 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8157 (ptmm) REVERT: A 483 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8055 (mtt90) REVERT: B 257 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: B 359 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7288 (mm) REVERT: D 30 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7240 (mt-10) REVERT: D 93 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7490 (ttp80) REVERT: D 123 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6600 (mt-10) REVERT: D 127 ASP cc_start: 0.7482 (m-30) cc_final: 0.7249 (m-30) REVERT: D 213 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8468 (mm-40) REVERT: D 257 SER cc_start: 0.7973 (t) cc_final: 0.7678 (t) REVERT: D 284 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: D 403 SER cc_start: 0.8801 (m) cc_final: 0.8487 (p) REVERT: D 463 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7618 (ttp-170) REVERT: D 483 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7824 (mtm-85) outliers start: 34 outliers final: 18 residues processed: 291 average time/residue: 0.6876 time to fit residues: 213.8403 Evaluate side-chains 299 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 0.0980 chunk 9 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127770 restraints weight = 14859.645| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.17 r_work: 0.3518 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11870 Z= 0.125 Angle : 0.512 8.821 16125 Z= 0.265 Chirality : 0.042 0.148 1749 Planarity : 0.004 0.038 2052 Dihedral : 8.152 73.562 1738 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.50 % Allowed : 15.53 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1404 helix: 0.44 (0.25), residues: 453 sheet: -0.51 (0.28), residues: 331 loop : -1.03 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 93 TYR 0.012 0.001 TYR B 343 PHE 0.014 0.001 PHE E 211 TRP 0.027 0.002 TRP D 446 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11870) covalent geometry : angle 0.51229 / 0.26 (16125) hydrogen bonds : bond 0.03386 / 2.30 ( 438) hydrogen bonds : angle 5.12229 / 3.56 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8112 (mmmm) REVERT: A 119 TYR cc_start: 0.7921 (t80) cc_final: 0.7689 (t80) REVERT: A 127 ASP cc_start: 0.7794 (m-30) cc_final: 0.7436 (m-30) REVERT: A 132 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 250 MET cc_start: 0.7232 (mmm) cc_final: 0.6680 (mmm) REVERT: A 345 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 373 THR cc_start: 0.8224 (p) cc_final: 0.7557 (t) REVERT: A 378 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7984 (mtp180) REVERT: A 391 ASP cc_start: 0.7800 (t0) cc_final: 0.7578 (t70) REVERT: A 470 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8144 (ptmm) REVERT: A 483 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8073 (mtt90) REVERT: B 257 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: B 359 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7296 (mm) REVERT: D 30 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7238 (mt-10) REVERT: D 123 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6502 (mt-10) REVERT: D 127 ASP cc_start: 0.7454 (m-30) cc_final: 0.7224 (m-30) REVERT: D 132 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7533 (mt-10) REVERT: D 213 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8383 (mm-40) REVERT: D 257 SER cc_start: 0.7966 (t) cc_final: 0.7644 (t) REVERT: D 284 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: D 403 SER cc_start: 0.8772 (m) cc_final: 0.8495 (p) REVERT: D 428 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7933 (mt-10) REVERT: D 463 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7553 (ttp-170) REVERT: D 483 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7810 (mtm-85) REVERT: E 377 MET cc_start: 0.8330 (ttp) cc_final: 0.8096 (ttp) outliers start: 30 outliers final: 14 residues processed: 281 average time/residue: 0.6883 time to fit residues: 206.4388 Evaluate side-chains 288 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128147 restraints weight = 14808.678| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.15 r_work: 0.3501 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11870 Z= 0.184 Angle : 0.550 9.137 16125 Z= 0.283 Chirality : 0.044 0.159 1749 Planarity : 0.004 0.052 2052 Dihedral : 8.182 73.388 1738 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.50 % Allowed : 16.69 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1404 helix: 0.48 (0.25), residues: 452 sheet: -0.35 (0.28), residues: 341 loop : -1.02 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 6 TYR 0.013 0.001 TYR B 343 PHE 0.018 0.002 PHE E 278 TRP 0.034 0.002 TRP A 446 HIS 0.006 0.001 HIS A 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.18 (11870) covalent geometry : angle 0.54968 / 0.28 (16125) hydrogen bonds : bond 0.03691 / 2.51 ( 438) hydrogen bonds : angle 5.18285 / 3.61 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8450 (tppp) cc_final: 0.8122 (mmmm) REVERT: A 119 TYR cc_start: 0.7989 (t80) cc_final: 0.7761 (t80) REVERT: A 127 ASP cc_start: 0.7778 (m-30) cc_final: 0.7407 (m-30) REVERT: A 132 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 250 MET cc_start: 0.7193 (mmm) cc_final: 0.6642 (mmm) REVERT: A 345 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 373 THR cc_start: 0.8241 (p) cc_final: 0.7574 (t) REVERT: A 378 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7978 (mtp180) REVERT: A 391 ASP cc_start: 0.7800 (t0) cc_final: 0.7556 (t70) REVERT: A 470 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8165 (ptmm) REVERT: A 483 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8105 (mtt90) REVERT: B 257 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7608 (mp10) REVERT: B 330 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.6960 (mpt) REVERT: B 359 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7335 (mm) REVERT: D 30 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7250 (mt-10) REVERT: D 123 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6530 (mt-10) REVERT: D 127 ASP cc_start: 0.7483 (m-30) cc_final: 0.7208 (m-30) REVERT: D 213 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8369 (mm-40) REVERT: D 257 SER cc_start: 0.7985 (t) cc_final: 0.7668 (t) REVERT: D 284 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: D 403 SER cc_start: 0.8812 (m) cc_final: 0.8515 (p) REVERT: D 428 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7939 (mt-10) REVERT: D 463 ARG cc_start: 0.7872 (tpp-160) cc_final: 0.7630 (ttp-170) REVERT: D 483 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7814 (mtm-85) outliers start: 30 outliers final: 15 residues processed: 286 average time/residue: 0.7099 time to fit residues: 217.1442 Evaluate side-chains 294 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 272 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 224 GLN D 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.149429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129537 restraints weight = 14598.514| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.13 r_work: 0.3524 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11870 Z= 0.128 Angle : 0.530 9.229 16125 Z= 0.273 Chirality : 0.042 0.151 1749 Planarity : 0.004 0.066 2052 Dihedral : 8.116 73.522 1738 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.34 % Allowed : 16.61 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1404 helix: 0.71 (0.25), residues: 452 sheet: -0.37 (0.28), residues: 331 loop : -0.97 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 6 TYR 0.011 0.001 TYR B 343 PHE 0.014 0.002 PHE E 211 TRP 0.038 0.002 TRP A 446 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11870) covalent geometry : angle 0.52956 / 0.27 (16125) hydrogen bonds : bond 0.03364 / 2.29 ( 438) hydrogen bonds : angle 5.10320 / 3.55 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8112 (mmmm) REVERT: A 119 TYR cc_start: 0.7910 (t80) cc_final: 0.7704 (t80) REVERT: A 127 ASP cc_start: 0.7779 (m-30) cc_final: 0.7408 (m-30) REVERT: A 132 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 250 MET cc_start: 0.7198 (mmm) cc_final: 0.6668 (mmm) REVERT: A 345 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7575 (mt-10) REVERT: A 373 THR cc_start: 0.8229 (p) cc_final: 0.7535 (t) REVERT: A 378 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7940 (mtp180) REVERT: A 391 ASP cc_start: 0.7788 (t0) cc_final: 0.7582 (t70) REVERT: A 470 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8158 (ptmm) REVERT: A 483 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8096 (mtt90) REVERT: B 257 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: B 359 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7302 (mm) REVERT: D 30 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7268 (mt-10) REVERT: D 123 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6465 (mt-10) REVERT: D 127 ASP cc_start: 0.7481 (m-30) cc_final: 0.7253 (m-30) REVERT: D 132 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7495 (mt-10) REVERT: D 213 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8376 (mm-40) REVERT: D 284 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: D 403 SER cc_start: 0.8778 (m) cc_final: 0.8503 (p) REVERT: D 428 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7997 (mt-10) REVERT: D 483 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7815 (mtm-85) outliers start: 28 outliers final: 18 residues processed: 280 average time/residue: 0.6925 time to fit residues: 207.2919 Evaluate side-chains 294 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 115 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN D 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124631 restraints weight = 14741.886| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.12 r_work: 0.3483 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11870 Z= 0.258 Angle : 0.615 8.854 16125 Z= 0.317 Chirality : 0.047 0.207 1749 Planarity : 0.005 0.054 2052 Dihedral : 8.271 73.273 1738 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.42 % Allowed : 16.78 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1404 helix: 0.41 (0.24), residues: 452 sheet: -0.27 (0.28), residues: 340 loop : -0.99 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 93 TYR 0.017 0.002 TYR D 90 PHE 0.022 0.002 PHE E 278 TRP 0.033 0.003 TRP A 446 HIS 0.009 0.002 HIS D 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.26 (11870) covalent geometry : angle 0.61528 / 0.32 (16125) hydrogen bonds : bond 0.04066 / 2.78 ( 438) hydrogen bonds : angle 5.30066 / 3.70 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8116 (mmmm) REVERT: A 119 TYR cc_start: 0.8007 (t80) cc_final: 0.7800 (t80) REVERT: A 127 ASP cc_start: 0.7789 (m-30) cc_final: 0.7435 (m-30) REVERT: A 132 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 250 MET cc_start: 0.7188 (mmm) cc_final: 0.6636 (mmm) REVERT: A 345 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 373 THR cc_start: 0.8271 (p) cc_final: 0.7633 (t) REVERT: A 378 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7943 (mtp180) REVERT: A 391 ASP cc_start: 0.7830 (t0) cc_final: 0.7600 (t70) REVERT: A 470 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8169 (ptmm) REVERT: A 483 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8167 (mtt90) REVERT: B 257 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: B 359 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7272 (mm) REVERT: D 30 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7250 (mt-10) REVERT: D 53 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8440 (mp) REVERT: D 123 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6498 (mt-10) REVERT: D 127 ASP cc_start: 0.7527 (m-30) cc_final: 0.7249 (m-30) REVERT: D 130 ILE cc_start: 0.8393 (mm) cc_final: 0.8191 (mp) REVERT: D 132 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 213 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8390 (mm-40) REVERT: D 284 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: D 403 SER cc_start: 0.8813 (m) cc_final: 0.8486 (p) REVERT: D 428 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 483 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7814 (mtm-85) outliers start: 29 outliers final: 19 residues processed: 286 average time/residue: 0.6934 time to fit residues: 211.9757 Evaluate side-chains 297 residues out of total 1211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 483 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128208 restraints weight = 14740.983| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.15 r_work: 0.3518 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11870 Z= 0.117 Angle : 0.539 9.507 16125 Z= 0.278 Chirality : 0.042 0.152 1749 Planarity : 0.004 0.058 2052 Dihedral : 8.131 73.571 1738 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.34 % Allowed : 17.28 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.36 (0.23), residues: 1404 helix: 0.81 (0.25), residues: 452 sheet: -0.29 (0.28), residues: 331 loop : -0.93 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 93 TYR 0.011 0.001 TYR B 343 PHE 0.014 0.001 PHE E 211 TRP 0.036 0.002 TRP A 446 HIS 0.004 0.001 HIS D 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11870) covalent geometry : angle 0.53906 / 0.28 (16125) hydrogen bonds : bond 0.03320 / 2.27 ( 438) hydrogen bonds : angle 5.13612 / 3.56 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5110.67 seconds wall clock time: 87 minutes 27.92 seconds (5247.92 seconds total)