Starting phenix.real_space_refine on Fri May 16 23:20:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtz_37847/05_2025/8wtz_37847.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtz_37847/05_2025/8wtz_37847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtz_37847/05_2025/8wtz_37847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtz_37847/05_2025/8wtz_37847.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtz_37847/05_2025/8wtz_37847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtz_37847/05_2025/8wtz_37847.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.047 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 92 5.16 5 C 9862 2.51 5 N 2433 2.21 5 O 2541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14930 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3695 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 12, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3650 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3695 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 12, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3654 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 4} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 8.87, per 1000 atoms: 0.59 Number of scatterers: 14930 At special positions: 0 Unit cell: (98.8, 102.96, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 2 15.00 O 2541 8.00 N 2433 7.00 C 9862 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.7 seconds 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 16 sheets defined 71.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'C' and resid 79 through 107 Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 114 through 135 Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.745A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 181 through 186 removed outlier: 3.717A pdb=" N ARG C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.718A pdb=" N ILE C 190 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 208 removed outlier: 3.905A pdb=" N VAL C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 242 removed outlier: 3.806A pdb=" N LEU C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 5.028A pdb=" N GLY C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 287 Processing helix chain 'C' and resid 298 through 329 Processing helix chain 'C' and resid 331 through 349 removed outlier: 3.905A pdb=" N ARG C 349 " --> pdb=" O ARG C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 379 removed outlier: 3.533A pdb=" N THR C 361 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 372 " --> pdb=" O TYR C 368 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 375 " --> pdb=" O SER C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 400 removed outlier: 3.727A pdb=" N LEU C 395 " --> pdb=" O GLN C 391 " (cutoff:3.500A) Proline residue: C 396 - end of helix removed outlier: 3.701A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 417 removed outlier: 3.892A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 478 removed outlier: 3.551A pdb=" N ILE C 476 " --> pdb=" O GLY C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 509 Processing helix chain 'C' and resid 509 through 524 removed outlier: 3.553A pdb=" N ARG C 514 " --> pdb=" O PHE C 510 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 107 removed outlier: 3.646A pdb=" N MET D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 91 " --> pdb=" O MET D 87 " (cutoff:3.500A) Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 135 removed outlier: 4.168A pdb=" N ILE D 116 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 159 removed outlier: 3.649A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 170 through 179 removed outlier: 3.565A pdb=" N GLY D 179 " --> pdb=" O TYR D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.953A pdb=" N ARG D 197 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 242 removed outlier: 3.718A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 5.019A pdb=" N GLY D 249 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 270 through 287 removed outlier: 3.604A pdb=" N THR D 276 " --> pdb=" O TRP D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 330 Processing helix chain 'D' and resid 333 through 349 removed outlier: 3.597A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 370 removed outlier: 3.543A pdb=" N GLN D 359 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 400 removed outlier: 3.967A pdb=" N LYS D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) Proline residue: D 396 - end of helix Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.586A pdb=" N ILE D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 499 through 509 removed outlier: 3.646A pdb=" N ASN D 504 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 524 Processing helix chain 'A' and resid 79 through 107 Proline residue: A 101 - end of helix Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.745A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.718A pdb=" N ARG A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.718A pdb=" N ILE A 190 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.904A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 242 removed outlier: 3.805A pdb=" N LEU A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 5.028A pdb=" N GLY A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 287 Processing helix chain 'A' and resid 298 through 329 Processing helix chain 'A' and resid 331 through 349 removed outlier: 3.904A pdb=" N ARG A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 379 removed outlier: 3.532A pdb=" N THR A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.726A pdb=" N LEU A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) Proline residue: A 396 - end of helix removed outlier: 3.700A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.892A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.552A pdb=" N ILE A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 509 through 524 removed outlier: 3.553A pdb=" N ARG A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 107 removed outlier: 3.646A pdb=" N MET B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) Proline residue: B 101 - end of helix Processing helix chain 'B' and resid 111 through 135 removed outlier: 4.168A pdb=" N ILE B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.648A pdb=" N ARG B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.565A pdb=" N GLY B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 193 through 207 removed outlier: 3.953A pdb=" N ARG B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 242 removed outlier: 3.719A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 5.018A pdb=" N GLY B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 270 through 287 removed outlier: 3.604A pdb=" N THR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 330 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.598A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 370 removed outlier: 3.543A pdb=" N GLN B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.966A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.586A pdb=" N ILE B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 499 through 509 removed outlier: 3.645A pdb=" N ASN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 Processing sheet with id=AA1, first strand: chain 'C' and resid 137 through 139 removed outlier: 3.802A pdb=" N TYR C 137 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 146 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 139 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG C 144 " --> pdb=" O ASP C 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA3, first strand: chain 'C' and resid 420 through 424 removed outlier: 6.261A pdb=" N ARG C 493 " --> pdb=" O CYS C 444 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 441 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 463 through 465 removed outlier: 3.752A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.643A pdb=" N ASP D 139 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 144 " --> pdb=" O ASP D 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 257 through 258 Processing sheet with id=AA7, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.564A pdb=" N PHE D 424 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 463 through 465 removed outlier: 3.732A pdb=" N ALA D 463 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 137 through 139 removed outlier: 3.802A pdb=" N TYR A 137 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 146 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A 139 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 144 " --> pdb=" O ASP A 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 258 Processing sheet with id=AB2, first strand: chain 'A' and resid 420 through 424 removed outlier: 6.262A pdb=" N ARG A 493 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 441 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.751A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.643A pdb=" N ASP B 139 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 144 " --> pdb=" O ASP B 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AB6, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.563A pdb=" N PHE B 424 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 463 through 465 removed outlier: 3.731A pdb=" N ALA B 463 " --> pdb=" O GLU B 450 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2532 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: 4.80 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2233 1.31 - 1.44: 4380 1.44 - 1.56: 8498 1.56 - 1.69: 8 1.69 - 1.82: 156 Bond restraints: 15275 Sorted by residual: bond pdb=" C TYR B 372 " pdb=" O TYR B 372 " ideal model delta sigma weight residual 1.235 1.412 -0.176 1.26e-02 6.30e+03 1.96e+02 bond pdb=" C TYR D 372 " pdb=" O TYR D 372 " ideal model delta sigma weight residual 1.235 1.411 -0.176 1.26e-02 6.30e+03 1.95e+02 bond pdb=" C VAL B 377 " pdb=" O VAL B 377 " ideal model delta sigma weight residual 1.237 1.337 -0.100 1.14e-02 7.69e+03 7.75e+01 bond pdb=" C VAL D 377 " pdb=" O VAL D 377 " ideal model delta sigma weight residual 1.237 1.336 -0.099 1.14e-02 7.69e+03 7.61e+01 bond pdb=" N ILE B 381 " pdb=" CA ILE B 381 " ideal model delta sigma weight residual 1.461 1.561 -0.100 1.23e-02 6.61e+03 6.61e+01 ... (remaining 15270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 20413 3.86 - 7.72: 134 7.72 - 11.58: 18 11.58 - 15.45: 2 15.45 - 19.31: 8 Bond angle restraints: 20575 Sorted by residual: angle pdb=" N ASP D 380 " pdb=" CA ASP D 380 " pdb=" C ASP D 380 " ideal model delta sigma weight residual 110.06 129.37 -19.31 1.43e+00 4.89e-01 1.82e+02 angle pdb=" O SER D 371 " pdb=" C SER D 371 " pdb=" N TYR D 372 " ideal model delta sigma weight residual 122.59 104.70 17.89 1.33e+00 5.65e-01 1.81e+02 angle pdb=" N ASP B 380 " pdb=" CA ASP B 380 " pdb=" C ASP B 380 " ideal model delta sigma weight residual 110.06 129.27 -19.21 1.43e+00 4.89e-01 1.80e+02 angle pdb=" O SER B 371 " pdb=" C SER B 371 " pdb=" N TYR B 372 " ideal model delta sigma weight residual 122.59 104.85 17.74 1.33e+00 5.65e-01 1.78e+02 angle pdb=" N TYR B 372 " pdb=" CA TYR B 372 " pdb=" C TYR B 372 " ideal model delta sigma weight residual 110.80 129.69 -18.89 2.13e+00 2.20e-01 7.86e+01 ... (remaining 20570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7631 17.98 - 35.97: 1014 35.97 - 53.95: 365 53.95 - 71.94: 55 71.94 - 89.92: 11 Dihedral angle restraints: 9076 sinusoidal: 3822 harmonic: 5254 Sorted by residual: dihedral pdb=" N ASP B 380 " pdb=" C ASP B 380 " pdb=" CA ASP B 380 " pdb=" CB ASP B 380 " ideal model delta harmonic sigma weight residual 122.80 137.50 -14.70 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" N ASP D 380 " pdb=" C ASP D 380 " pdb=" CA ASP D 380 " pdb=" CB ASP D 380 " ideal model delta harmonic sigma weight residual 122.80 137.47 -14.67 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" C ASP B 380 " pdb=" N ASP B 380 " pdb=" CA ASP B 380 " pdb=" CB ASP B 380 " ideal model delta harmonic sigma weight residual -122.60 -136.14 13.54 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 9073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2221 0.145 - 0.290: 33 0.290 - 0.434: 8 0.434 - 0.579: 2 0.579 - 0.724: 2 Chirality restraints: 2266 Sorted by residual: chirality pdb=" CA ASP D 380 " pdb=" N ASP D 380 " pdb=" C ASP D 380 " pdb=" CB ASP D 380 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ASP B 380 " pdb=" N ASP B 380 " pdb=" C ASP B 380 " pdb=" CB ASP B 380 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C2 PC1 C 901 " pdb=" C1 PC1 C 901 " pdb=" C3 PC1 C 901 " pdb=" O21 PC1 C 901 " both_signs ideal model delta sigma weight residual False -2.49 -1.91 -0.58 2.00e-01 2.50e+01 8.35e+00 ... (remaining 2263 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 371 " -0.072 2.00e-02 2.50e+03 1.27e-01 1.60e+02 pdb=" C SER D 371 " 0.219 2.00e-02 2.50e+03 pdb=" O SER D 371 " -0.079 2.00e-02 2.50e+03 pdb=" N TYR D 372 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 371 " 0.072 2.00e-02 2.50e+03 1.26e-01 1.60e+02 pdb=" C SER B 371 " -0.219 2.00e-02 2.50e+03 pdb=" O SER B 371 " 0.079 2.00e-02 2.50e+03 pdb=" N TYR B 372 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 372 " -0.030 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C TYR B 372 " 0.095 2.00e-02 2.50e+03 pdb=" O TYR B 372 " -0.035 2.00e-02 2.50e+03 pdb=" N THR B 373 " -0.030 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 22 2.30 - 2.95: 6584 2.95 - 3.60: 22192 3.60 - 4.25: 34761 4.25 - 4.90: 58082 Nonbonded interactions: 121641 Sorted by model distance: nonbonded pdb=" CE2 TYR C 346 " pdb=" CB ALA B 376 " model vdw 1.650 3.760 nonbonded pdb=" CB ALA D 376 " pdb=" CE2 TYR A 346 " model vdw 1.660 3.760 nonbonded pdb=" CD2 LEU C 364 " pdb=" OD2 ASP B 380 " model vdw 1.830 3.460 nonbonded pdb=" OD2 ASP D 380 " pdb=" CD2 LEU A 364 " model vdw 1.861 3.460 nonbonded pdb=" CD2 TYR C 346 " pdb=" CB ALA B 376 " model vdw 1.980 3.760 ... (remaining 121636 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 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'B' and (resid 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'C' and (resid 76 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 524 or (resid 901 and (name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or re \ sid 902 or (resid 903 and (name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38)))) selection = (chain 'D' and (resid 76 through 524 or (resid 901 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38)) or resid 902 or (resi \ d 903 and (name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38)))) } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.280 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.006 0.215 15276 Z= 0.439 Angle : 0.849 19.307 20575 Z= 0.523 Chirality : 0.058 0.724 2266 Planarity : 0.006 0.127 2523 Dihedral : 18.201 89.923 5704 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.57 % Allowed : 1.48 % Favored : 97.96 % Rotamer: Outliers : 2.15 % Allowed : 19.99 % Favored : 77.86 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1762 helix: 0.07 (0.15), residues: 1080 sheet: 0.69 (0.43), residues: 128 loop : 0.34 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 171 HIS 0.009 0.001 HIS A 445 PHE 0.015 0.001 PHE A 115 TYR 0.013 0.001 TYR A 368 ARG 0.006 0.000 ARG B 496 Details of bonding type rmsd hydrogen bonds : bond 0.25502 ( 902) hydrogen bonds : angle 8.22613 ( 2532) covalent geometry : bond 0.00570 (15275) covalent geometry : angle 0.84923 (20575) Misc. bond : bond 0.21459 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 80 ARG cc_start: 0.7162 (ppt170) cc_final: 0.6235 (ptt180) REVERT: C 87 MET cc_start: 0.7855 (mmt) cc_final: 0.7649 (mmt) REVERT: C 183 GLU cc_start: 0.7494 (mp0) cc_final: 0.7054 (pm20) REVERT: C 216 THR cc_start: 0.8431 (t) cc_final: 0.8231 (m) REVERT: C 222 ILE cc_start: 0.8240 (tp) cc_final: 0.7976 (tp) REVERT: C 344 MET cc_start: 0.7239 (mtt) cc_final: 0.6942 (mtt) REVERT: D 87 MET cc_start: 0.8215 (tpp) cc_final: 0.7952 (tpp) REVERT: D 469 HIS cc_start: 0.7636 (m90) cc_final: 0.7374 (m90) REVERT: D 503 MET cc_start: 0.6126 (mpp) cc_final: 0.5891 (mmm) REVERT: A 183 GLU cc_start: 0.7390 (mp0) cc_final: 0.6745 (pm20) REVERT: B 171 TRP cc_start: 0.8330 (m100) cc_final: 0.8068 (m100) REVERT: B 269 ILE cc_start: 0.8419 (mt) cc_final: 0.7796 (mm) REVERT: B 379 GLN cc_start: 0.5072 (OUTLIER) cc_final: 0.4828 (mt0) REVERT: B 422 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6791 (mm-30) REVERT: B 423 PHE cc_start: 0.7019 (m-80) cc_final: 0.6790 (m-80) outliers start: 34 outliers final: 9 residues processed: 240 average time/residue: 0.2547 time to fit residues: 90.3143 Evaluate side-chains 191 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 379 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS C 482 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.236164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137438 restraints weight = 15224.349| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.10 r_work: 0.3344 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15276 Z= 0.163 Angle : 0.625 17.184 20575 Z= 0.322 Chirality : 0.044 0.156 2266 Planarity : 0.005 0.054 2523 Dihedral : 9.648 83.421 2215 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.38 % Favored : 97.50 % Rotamer: Outliers : 3.04 % Allowed : 19.29 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1762 helix: 0.63 (0.15), residues: 1130 sheet: 0.03 (0.44), residues: 136 loop : 0.73 (0.31), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 272 HIS 0.006 0.001 HIS C 445 PHE 0.021 0.001 PHE D 236 TYR 0.015 0.002 TYR D 82 ARG 0.008 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 902) hydrogen bonds : angle 5.20767 ( 2532) covalent geometry : bond 0.00365 (15275) covalent geometry : angle 0.62485 (20575) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7926 (mp0) cc_final: 0.7046 (pm20) REVERT: C 222 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7372 (tp) REVERT: C 337 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6908 (ttp-170) REVERT: C 344 MET cc_start: 0.7204 (mtt) cc_final: 0.6934 (mtt) REVERT: C 370 SER cc_start: 0.6033 (OUTLIER) cc_final: 0.5776 (m) REVERT: C 476 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6835 (mt) REVERT: C 485 THR cc_start: 0.1635 (OUTLIER) cc_final: 0.1266 (m) REVERT: D 80 ARG cc_start: 0.6686 (mtp-110) cc_final: 0.6267 (mmp80) REVERT: D 267 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6288 (mtm-85) REVERT: D 309 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7181 (mt) REVERT: D 420 HIS cc_start: 0.6348 (t-170) cc_final: 0.6103 (t-170) REVERT: A 183 GLU cc_start: 0.7709 (mp0) cc_final: 0.6766 (pm20) REVERT: A 337 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7570 (ttp-170) REVERT: A 363 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6921 (m90) REVERT: A 476 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7126 (mt) REVERT: A 499 LYS cc_start: 0.7687 (mmtt) cc_final: 0.7238 (mtpp) REVERT: A 503 MET cc_start: 0.7936 (mmt) cc_final: 0.7735 (mmt) REVERT: B 96 SER cc_start: 0.7895 (OUTLIER) cc_final: 0.7186 (t) REVERT: B 267 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6153 (mtm-85) REVERT: B 309 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7389 (mt) REVERT: B 422 GLU cc_start: 0.6419 (mm-30) cc_final: 0.6217 (mm-30) outliers start: 48 outliers final: 14 residues processed: 218 average time/residue: 0.3054 time to fit residues: 96.5534 Evaluate side-chains 193 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 485 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 102 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 482 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.234095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135385 restraints weight = 15149.680| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.04 r_work: 0.3334 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15276 Z= 0.174 Angle : 0.600 17.715 20575 Z= 0.304 Chirality : 0.043 0.168 2266 Planarity : 0.005 0.057 2523 Dihedral : 8.540 59.796 2205 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 3.16 % Allowed : 19.67 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1762 helix: 0.86 (0.15), residues: 1136 sheet: 0.60 (0.46), residues: 116 loop : 0.56 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 272 HIS 0.004 0.001 HIS C 445 PHE 0.018 0.001 PHE B 236 TYR 0.015 0.002 TYR A 275 ARG 0.006 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 902) hydrogen bonds : angle 4.93980 ( 2532) covalent geometry : bond 0.00407 (15275) covalent geometry : angle 0.59955 (20575) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.8049 (mp0) cc_final: 0.7086 (pm20) REVERT: C 336 PHE cc_start: 0.6385 (t80) cc_final: 0.6090 (t80) REVERT: C 340 MET cc_start: 0.7728 (tpp) cc_final: 0.7506 (ttt) REVERT: C 344 MET cc_start: 0.7276 (mtt) cc_final: 0.6887 (mtt) REVERT: C 370 SER cc_start: 0.5973 (OUTLIER) cc_final: 0.5688 (m) REVERT: D 309 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7301 (mm) REVERT: D 343 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6777 (mp) REVERT: D 349 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7425 (mtm-85) REVERT: A 183 GLU cc_start: 0.7770 (mp0) cc_final: 0.6782 (pm20) REVERT: A 363 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6903 (m90) REVERT: B 309 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7310 (mt) REVERT: B 334 GLU cc_start: 0.6194 (tp30) cc_final: 0.5994 (tp30) outliers start: 50 outliers final: 22 residues processed: 214 average time/residue: 0.2732 time to fit residues: 87.3836 Evaluate side-chains 192 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 111 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 135 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN A 500 GLN B 482 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.237578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138448 restraints weight = 15119.888| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.08 r_work: 0.3368 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15276 Z= 0.128 Angle : 0.553 17.322 20575 Z= 0.278 Chirality : 0.041 0.165 2266 Planarity : 0.004 0.058 2523 Dihedral : 7.914 59.894 2200 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.56 % Rotamer: Outliers : 3.10 % Allowed : 20.11 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1762 helix: 1.10 (0.15), residues: 1144 sheet: 0.36 (0.42), residues: 126 loop : 0.56 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 85 HIS 0.004 0.001 HIS C 445 PHE 0.011 0.001 PHE B 236 TYR 0.016 0.001 TYR A 372 ARG 0.007 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 902) hydrogen bonds : angle 4.62765 ( 2532) covalent geometry : bond 0.00285 (15275) covalent geometry : angle 0.55322 (20575) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: C 145 MET cc_start: 0.5451 (mmp) cc_final: 0.5176 (mmp) REVERT: C 183 GLU cc_start: 0.8042 (mp0) cc_final: 0.7066 (pm20) REVERT: C 344 MET cc_start: 0.7223 (mtt) cc_final: 0.6890 (mtt) REVERT: D 139 ASP cc_start: 0.6471 (t0) cc_final: 0.6048 (t70) REVERT: D 309 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7381 (mm) REVERT: D 343 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6889 (mp) REVERT: A 183 GLU cc_start: 0.7766 (mp0) cc_final: 0.6813 (pm20) REVERT: A 363 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6926 (m90) REVERT: B 309 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7490 (mt) REVERT: B 334 GLU cc_start: 0.6195 (tp30) cc_final: 0.5889 (tp30) REVERT: B 345 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.8112 (ttp-110) REVERT: B 349 ARG cc_start: 0.7463 (mtm180) cc_final: 0.7229 (mtm180) outliers start: 49 outliers final: 23 residues processed: 209 average time/residue: 0.2416 time to fit residues: 75.9970 Evaluate side-chains 185 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 126 optimal weight: 0.0040 chunk 167 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN B 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.237977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139349 restraints weight = 15320.351| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.10 r_work: 0.3367 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15276 Z= 0.118 Angle : 0.543 16.970 20575 Z= 0.272 Chirality : 0.041 0.168 2266 Planarity : 0.004 0.058 2523 Dihedral : 7.582 59.968 2197 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 2.78 % Allowed : 21.19 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1762 helix: 1.27 (0.15), residues: 1132 sheet: 0.25 (0.42), residues: 126 loop : 0.62 (0.31), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 272 HIS 0.004 0.001 HIS C 445 PHE 0.021 0.001 PHE C 88 TYR 0.012 0.001 TYR C 213 ARG 0.007 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 902) hydrogen bonds : angle 4.50107 ( 2532) covalent geometry : bond 0.00257 (15275) covalent geometry : angle 0.54253 (20575) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7750 (mm-30) REVERT: C 145 MET cc_start: 0.5399 (mmp) cc_final: 0.5134 (mmp) REVERT: C 183 GLU cc_start: 0.8013 (mp0) cc_final: 0.7062 (pm20) REVERT: D 139 ASP cc_start: 0.6481 (t0) cc_final: 0.6064 (t70) REVERT: D 309 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7353 (mm) REVERT: D 343 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6852 (mp) REVERT: A 363 HIS cc_start: 0.7211 (OUTLIER) cc_final: 0.6883 (m90) REVERT: B 309 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7351 (mm) REVERT: B 345 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.8031 (ttp-110) REVERT: B 349 ARG cc_start: 0.7423 (mtm180) cc_final: 0.7195 (mtm180) outliers start: 44 outliers final: 26 residues processed: 193 average time/residue: 0.2410 time to fit residues: 70.8819 Evaluate side-chains 188 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.237217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138222 restraints weight = 15185.281| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.06 r_work: 0.3358 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15276 Z= 0.127 Angle : 0.547 16.856 20575 Z= 0.273 Chirality : 0.041 0.144 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.478 59.717 2197 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 2.47 % Allowed : 21.95 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1762 helix: 1.32 (0.15), residues: 1130 sheet: 0.53 (0.44), residues: 114 loop : 0.68 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 272 HIS 0.016 0.001 HIS C 445 PHE 0.022 0.001 PHE C 88 TYR 0.010 0.001 TYR C 275 ARG 0.006 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 902) hydrogen bonds : angle 4.48034 ( 2532) covalent geometry : bond 0.00286 (15275) covalent geometry : angle 0.54705 (20575) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: C 145 MET cc_start: 0.5362 (mmp) cc_final: 0.5052 (mmp) REVERT: C 183 GLU cc_start: 0.7969 (mp0) cc_final: 0.7030 (pm20) REVERT: D 139 ASP cc_start: 0.6394 (t0) cc_final: 0.5662 (p0) REVERT: D 309 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7352 (mm) REVERT: D 343 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6809 (mp) REVERT: D 349 ARG cc_start: 0.8176 (mtm180) cc_final: 0.7934 (mtm180) REVERT: A 112 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: A 183 GLU cc_start: 0.7753 (mp0) cc_final: 0.6791 (pm20) REVERT: A 363 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6943 (m90) REVERT: B 139 ASP cc_start: 0.6162 (t70) cc_final: 0.5883 (t70) REVERT: B 309 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7340 (mm) REVERT: B 345 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.6701 (tmm160) REVERT: B 349 ARG cc_start: 0.7435 (mtm180) cc_final: 0.7088 (mtm180) REVERT: B 503 MET cc_start: 0.5798 (mmm) cc_final: 0.5401 (mpp) outliers start: 39 outliers final: 22 residues processed: 196 average time/residue: 0.2550 time to fit residues: 75.8534 Evaluate side-chains 190 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 120 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS D 482 GLN B 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.238120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139333 restraints weight = 15281.392| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.07 r_work: 0.3382 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15276 Z= 0.121 Angle : 0.551 16.708 20575 Z= 0.272 Chirality : 0.041 0.143 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.246 59.544 2197 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 2.53 % Allowed : 21.82 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.20), residues: 1762 helix: 1.39 (0.15), residues: 1132 sheet: 1.20 (0.55), residues: 74 loop : 0.68 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 171 HIS 0.004 0.001 HIS A 363 PHE 0.022 0.001 PHE C 88 TYR 0.010 0.001 TYR C 213 ARG 0.007 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 902) hydrogen bonds : angle 4.40712 ( 2532) covalent geometry : bond 0.00268 (15275) covalent geometry : angle 0.55100 (20575) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 MET cc_start: 0.5388 (mmp) cc_final: 0.5077 (mmp) REVERT: C 183 GLU cc_start: 0.7941 (mp0) cc_final: 0.7035 (pm20) REVERT: D 139 ASP cc_start: 0.6367 (t0) cc_final: 0.5646 (p0) REVERT: D 309 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7412 (mm) REVERT: D 343 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6910 (mp) REVERT: D 345 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.6671 (tmm160) REVERT: D 482 GLN cc_start: 0.5988 (mm110) cc_final: 0.5709 (mm-40) REVERT: A 112 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7830 (mm-30) REVERT: A 142 THR cc_start: 0.4592 (OUTLIER) cc_final: 0.4352 (p) REVERT: B 139 ASP cc_start: 0.6203 (t70) cc_final: 0.5912 (t70) REVERT: B 309 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7376 (mm) REVERT: B 345 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.6706 (tmm160) REVERT: B 349 ARG cc_start: 0.7365 (mtm180) cc_final: 0.7031 (mtm180) REVERT: B 503 MET cc_start: 0.5774 (mmm) cc_final: 0.5331 (mpp) outliers start: 40 outliers final: 21 residues processed: 199 average time/residue: 0.2575 time to fit residues: 76.5535 Evaluate side-chains 186 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 10.0000 chunk 154 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.234909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137367 restraints weight = 15069.063| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.99 r_work: 0.3296 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15276 Z= 0.170 Angle : 0.602 17.135 20575 Z= 0.298 Chirality : 0.043 0.236 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.555 59.647 2197 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.16 % Favored : 97.73 % Rotamer: Outliers : 2.21 % Allowed : 22.83 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1762 helix: 1.27 (0.15), residues: 1130 sheet: 0.55 (0.44), residues: 114 loop : 0.69 (0.31), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 171 HIS 0.005 0.001 HIS A 363 PHE 0.022 0.001 PHE C 88 TYR 0.016 0.002 TYR A 275 ARG 0.007 0.000 ARG B 365 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 902) hydrogen bonds : angle 4.52281 ( 2532) covalent geometry : bond 0.00402 (15275) covalent geometry : angle 0.60239 (20575) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 145 MET cc_start: 0.5323 (mmp) cc_final: 0.4999 (mmp) REVERT: C 183 GLU cc_start: 0.8016 (mp0) cc_final: 0.7050 (pm20) REVERT: C 499 LYS cc_start: 0.7560 (mmmt) cc_final: 0.7330 (mmtp) REVERT: D 126 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7406 (mp) REVERT: D 139 ASP cc_start: 0.6264 (t0) cc_final: 0.5642 (p0) REVERT: D 309 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7513 (mm) REVERT: D 343 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6732 (mp) REVERT: D 345 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.6962 (tmm160) REVERT: A 112 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7893 (mm-30) REVERT: A 142 THR cc_start: 0.4685 (p) cc_final: 0.4455 (p) REVERT: A 209 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7232 (mp) REVERT: A 499 LYS cc_start: 0.7610 (mmmm) cc_final: 0.7405 (mmtp) REVERT: B 139 ASP cc_start: 0.6195 (t70) cc_final: 0.5920 (t70) REVERT: B 309 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7405 (mt) REVERT: B 345 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.6785 (tmm160) REVERT: B 349 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7152 (mtm180) REVERT: B 503 MET cc_start: 0.5885 (mmm) cc_final: 0.5455 (mpp) outliers start: 35 outliers final: 20 residues processed: 195 average time/residue: 0.2760 time to fit residues: 81.6122 Evaluate side-chains 195 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 133 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 138 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.237177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138692 restraints weight = 15013.640| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.04 r_work: 0.3379 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15276 Z= 0.125 Angle : 0.573 17.057 20575 Z= 0.281 Chirality : 0.042 0.181 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.285 59.539 2197 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 1.83 % Allowed : 23.15 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1762 helix: 1.35 (0.15), residues: 1132 sheet: 0.55 (0.44), residues: 114 loop : 0.71 (0.31), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 171 HIS 0.003 0.001 HIS A 230 PHE 0.021 0.001 PHE C 88 TYR 0.011 0.001 TYR C 213 ARG 0.007 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 902) hydrogen bonds : angle 4.39094 ( 2532) covalent geometry : bond 0.00280 (15275) covalent geometry : angle 0.57323 (20575) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.562 Fit side-chains REVERT: C 145 MET cc_start: 0.5289 (mmp) cc_final: 0.4934 (mmp) REVERT: C 183 GLU cc_start: 0.7899 (mp0) cc_final: 0.6989 (pm20) REVERT: C 209 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7173 (mp) REVERT: C 499 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7372 (mmtp) REVERT: D 139 ASP cc_start: 0.6379 (t0) cc_final: 0.5754 (p0) REVERT: D 309 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7440 (mm) REVERT: D 345 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.6999 (tmm160) REVERT: D 349 ARG cc_start: 0.7325 (ptt180) cc_final: 0.7094 (ptt180) REVERT: D 482 GLN cc_start: 0.5906 (mm110) cc_final: 0.5677 (mm-40) REVERT: A 112 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: A 142 THR cc_start: 0.4783 (OUTLIER) cc_final: 0.4554 (p) REVERT: A 499 LYS cc_start: 0.7604 (mmmm) cc_final: 0.7386 (mmtp) REVERT: A 504 ASN cc_start: 0.8805 (t0) cc_final: 0.8254 (t0) REVERT: B 87 MET cc_start: 0.7504 (tpp) cc_final: 0.7278 (tpp) REVERT: B 139 ASP cc_start: 0.6378 (t70) cc_final: 0.6089 (t70) REVERT: B 309 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7365 (mt) REVERT: B 345 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.6896 (tmm160) REVERT: B 349 ARG cc_start: 0.7493 (mtm180) cc_final: 0.7142 (mtm180) REVERT: B 503 MET cc_start: 0.5840 (mmm) cc_final: 0.5384 (mpp) outliers start: 29 outliers final: 16 residues processed: 192 average time/residue: 0.2480 time to fit residues: 72.2885 Evaluate side-chains 187 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 160 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 118 optimal weight: 1.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.236479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137296 restraints weight = 15075.790| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.04 r_work: 0.3369 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15276 Z= 0.133 Angle : 0.587 16.956 20575 Z= 0.287 Chirality : 0.042 0.150 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.264 59.586 2197 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 1.58 % Allowed : 23.53 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1762 helix: 1.34 (0.15), residues: 1132 sheet: 0.61 (0.47), residues: 104 loop : 0.73 (0.31), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 171 HIS 0.004 0.001 HIS A 230 PHE 0.021 0.001 PHE C 88 TYR 0.012 0.001 TYR A 275 ARG 0.007 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 902) hydrogen bonds : angle 4.41148 ( 2532) covalent geometry : bond 0.00306 (15275) covalent geometry : angle 0.58688 (20575) Misc. bond : bond 0.00020 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3524 Ramachandran restraints generated. 1762 Oldfield, 0 Emsley, 1762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: C 145 MET cc_start: 0.5302 (mmp) cc_final: 0.4925 (mmp) REVERT: C 183 GLU cc_start: 0.7910 (mp0) cc_final: 0.6994 (pm20) REVERT: C 209 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7186 (mp) REVERT: D 87 MET cc_start: 0.7545 (tpp) cc_final: 0.7297 (tpp) REVERT: D 139 ASP cc_start: 0.6420 (t0) cc_final: 0.5769 (p0) REVERT: D 309 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7413 (mm) REVERT: D 345 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.6980 (tmm160) REVERT: D 349 ARG cc_start: 0.7398 (ptt180) cc_final: 0.7025 (ptt180) REVERT: D 351 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8307 (mmtp) REVERT: D 482 GLN cc_start: 0.5924 (mm110) cc_final: 0.5613 (mm-40) REVERT: A 112 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: A 142 THR cc_start: 0.4823 (OUTLIER) cc_final: 0.4588 (p) REVERT: A 499 LYS cc_start: 0.7566 (mmmm) cc_final: 0.7343 (mmtp) REVERT: B 87 MET cc_start: 0.7611 (tpp) cc_final: 0.7373 (tpp) REVERT: B 139 ASP cc_start: 0.6377 (t70) cc_final: 0.6082 (t70) REVERT: B 309 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7409 (mm) REVERT: B 345 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.6881 (tmm160) REVERT: B 349 ARG cc_start: 0.7501 (mtm180) cc_final: 0.7135 (mtm180) REVERT: B 503 MET cc_start: 0.5773 (mmm) cc_final: 0.5317 (mpp) outliers start: 25 outliers final: 16 residues processed: 184 average time/residue: 0.2438 time to fit residues: 67.7601 Evaluate side-chains 186 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 167 optimal weight: 0.3980 chunk 86 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS D 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.236865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137474 restraints weight = 15107.774| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.05 r_work: 0.3370 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15276 Z= 0.134 Angle : 0.590 16.891 20575 Z= 0.288 Chirality : 0.042 0.144 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.221 59.531 2197 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.16 % Favored : 97.73 % Rotamer: Outliers : 1.77 % Allowed : 23.28 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1762 helix: 1.33 (0.15), residues: 1134 sheet: 0.56 (0.47), residues: 104 loop : 0.76 (0.31), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 171 HIS 0.004 0.001 HIS A 230 PHE 0.021 0.001 PHE C 88 TYR 0.011 0.001 TYR A 275 ARG 0.007 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 902) hydrogen bonds : angle 4.38866 ( 2532) covalent geometry : bond 0.00307 (15275) covalent geometry : angle 0.58996 (20575) Misc. bond : bond 0.00022 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10563.20 seconds wall clock time: 182 minutes 36.05 seconds (10956.05 seconds total)