Starting phenix.real_space_refine on Fri Jun 13 11:51:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtz_37847/06_2025/8wtz_37847.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtz_37847/06_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_37847/06_2025/8wtz_37847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtz_37847/06_2025/8wtz_37847.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtz_37847/06_2025/8wtz_37847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtz_37847/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.48, per 1000 atoms: 0.63 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: 3.91 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: 1.59 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: 4.61 Time building geometry restraints manager: 4.57 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.570 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- 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 : 1.444 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: 0.2720 time to fit residues: 96.5318 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 : 1.701 ------------------------------------------------------------------------------- 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 = 73)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137426 restraints weight = 15224.349| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.10 r_work: 0.3361 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7923 (mp0) cc_final: 0.7053 (pm20) REVERT: C 222 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7380 (tp) REVERT: C 337 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6920 (ttp-170) REVERT: C 344 MET cc_start: 0.7248 (mtt) cc_final: 0.6968 (mtt) REVERT: C 370 SER cc_start: 0.6033 (OUTLIER) cc_final: 0.5777 (m) REVERT: C 476 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6841 (mt) REVERT: C 485 THR cc_start: 0.1670 (OUTLIER) cc_final: 0.1291 (m) REVERT: D 80 ARG cc_start: 0.6680 (mtp-110) cc_final: 0.6262 (mmp80) REVERT: D 267 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.6300 (mtm-85) REVERT: D 309 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7189 (mt) REVERT: D 420 HIS cc_start: 0.6358 (t-170) cc_final: 0.6114 (t-170) REVERT: A 183 GLU cc_start: 0.7709 (mp0) cc_final: 0.6771 (pm20) REVERT: A 337 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7576 (ttp-170) REVERT: A 363 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6913 (m90) REVERT: A 476 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7130 (mt) REVERT: A 499 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7235 (mtpp) REVERT: B 96 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7201 (t) REVERT: B 267 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.6168 (mtm-85) REVERT: B 309 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7398 (mt) outliers start: 48 outliers final: 14 residues processed: 218 average time/residue: 0.2784 time to fit residues: 89.6274 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 : 1.790 ------------------------------------------------------------------------------- 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: 5.9990 chunk 167 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.233092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133988 restraints weight = 15159.141| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.03 r_work: 0.3322 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15276 Z= 0.192 Angle : 0.613 17.933 20575 Z= 0.311 Chirality : 0.044 0.183 2266 Planarity : 0.005 0.057 2523 Dihedral : 8.649 59.916 2205 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.38 % Favored : 97.50 % Rotamer: Outliers : 3.10 % Allowed : 20.05 % Favored : 76.85 % 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: 0.94 (0.20), residues: 1762 helix: 0.81 (0.15), residues: 1134 sheet: 0.61 (0.46), residues: 116 loop : 0.51 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 272 HIS 0.004 0.001 HIS C 445 PHE 0.019 0.002 PHE D 236 TYR 0.016 0.002 TYR A 275 ARG 0.006 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 902) hydrogen bonds : angle 4.99417 ( 2532) covalent geometry : bond 0.00452 (15275) covalent geometry : angle 0.61327 (20575) Misc. bond : bond 0.00059 ( 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 225 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.8075 (mp0) cc_final: 0.7105 (pm20) REVERT: C 336 PHE cc_start: 0.6414 (t80) cc_final: 0.6105 (t80) REVERT: C 340 MET cc_start: 0.7857 (tpp) cc_final: 0.7636 (ttt) REVERT: C 344 MET cc_start: 0.7307 (mtt) cc_final: 0.6917 (mtt) REVERT: C 370 SER cc_start: 0.5990 (OUTLIER) cc_final: 0.5710 (m) REVERT: D 197 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7358 (mtt-85) REVERT: D 309 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7358 (mm) REVERT: D 343 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6819 (mp) REVERT: A 183 GLU cc_start: 0.7815 (mp0) cc_final: 0.6824 (pm20) REVERT: A 363 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6921 (m90) REVERT: B 309 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7381 (mt) REVERT: B 334 GLU cc_start: 0.6151 (tp30) cc_final: 0.5937 (tp30) outliers start: 49 outliers final: 22 residues processed: 214 average time/residue: 0.2983 time to fit residues: 94.4798 Evaluate side-chains 194 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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: 0.8980 chunk 94 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 135 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.237268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138371 restraints weight = 15086.085| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.07 r_work: 0.3369 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3529 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= 0.126 Angle : 0.557 17.491 20575 Z= 0.279 Chirality : 0.042 0.167 2266 Planarity : 0.004 0.058 2523 Dihedral : 7.959 59.712 2200 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 3.16 % Allowed : 20.18 % Favored : 76.66 % 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: 1.22 (0.20), residues: 1762 helix: 1.09 (0.15), residues: 1142 sheet: 0.39 (0.43), residues: 126 loop : 0.54 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 85 HIS 0.005 0.001 HIS C 445 PHE 0.011 0.001 PHE B 236 TYR 0.011 0.001 TYR C 213 ARG 0.008 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 902) hydrogen bonds : angle 4.62768 ( 2532) covalent geometry : bond 0.00280 (15275) covalent geometry : angle 0.55726 (20575) Misc. bond : bond 0.00018 ( 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 216 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7938 (mm-30) REVERT: C 145 MET cc_start: 0.5475 (mmp) cc_final: 0.5171 (mmp) REVERT: C 183 GLU cc_start: 0.8039 (mp0) cc_final: 0.7065 (pm20) REVERT: C 344 MET cc_start: 0.7228 (mtt) cc_final: 0.6906 (mtt) REVERT: C 476 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6621 (mt) REVERT: D 139 ASP cc_start: 0.6507 (t0) cc_final: 0.6095 (t70) REVERT: D 309 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7389 (mm) REVERT: D 343 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6875 (mp) REVERT: D 349 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7763 (mtp180) REVERT: A 183 GLU cc_start: 0.7769 (mp0) cc_final: 0.6816 (pm20) REVERT: A 363 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6937 (m90) REVERT: B 309 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7336 (mt) REVERT: B 334 GLU cc_start: 0.6170 (tp30) cc_final: 0.5851 (tp30) REVERT: B 345 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.8147 (ttp-110) REVERT: B 349 ARG cc_start: 0.7476 (mtm180) cc_final: 0.7253 (mtm180) outliers start: 50 outliers final: 24 residues processed: 208 average time/residue: 0.2450 time to fit residues: 78.4898 Evaluate side-chains 190 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 476 ILE 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 349 ARG 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 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 139 ASP 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.235329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135687 restraints weight = 15329.206| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.09 r_work: 0.3323 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3772 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= 0.143 Angle : 0.562 17.454 20575 Z= 0.282 Chirality : 0.042 0.168 2266 Planarity : 0.004 0.058 2523 Dihedral : 7.751 59.971 2197 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 2.66 % Allowed : 20.94 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1762 helix: 1.15 (0.15), residues: 1132 sheet: 0.55 (0.44), residues: 114 loop : 0.58 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 272 HIS 0.004 0.001 HIS C 445 PHE 0.022 0.001 PHE C 88 TYR 0.013 0.001 TYR A 275 ARG 0.006 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 902) hydrogen bonds : angle 4.58636 ( 2532) covalent geometry : bond 0.00329 (15275) covalent geometry : angle 0.56204 (20575) Misc. bond : bond 0.00027 ( 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 211 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: C 145 MET cc_start: 0.5404 (mmp) cc_final: 0.5119 (mmp) REVERT: C 183 GLU cc_start: 0.8056 (mp0) cc_final: 0.7099 (pm20) REVERT: D 139 ASP cc_start: 0.6562 (t0) cc_final: 0.6148 (t70) REVERT: D 309 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7431 (mm) REVERT: D 343 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6991 (mp) REVERT: D 349 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7754 (mtp180) REVERT: A 183 GLU cc_start: 0.7806 (mp0) cc_final: 0.6847 (pm20) REVERT: A 363 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6877 (m90) REVERT: B 139 ASP cc_start: 0.6188 (t70) cc_final: 0.5903 (t70) REVERT: B 309 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7476 (mm) REVERT: B 349 ARG cc_start: 0.7498 (mtm180) cc_final: 0.7231 (mtm180) outliers start: 42 outliers final: 26 residues processed: 201 average time/residue: 0.2582 time to fit residues: 78.1766 Evaluate side-chains 192 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 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 B 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.236553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139544 restraints weight = 15167.252| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.81 r_work: 0.3355 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15276 Z= 0.128 Angle : 0.558 17.203 20575 Z= 0.276 Chirality : 0.042 0.148 2266 Planarity : 0.004 0.060 2523 Dihedral : 7.552 59.809 2197 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.16 % Favored : 97.73 % Rotamer: Outliers : 2.85 % Allowed : 21.25 % Favored : 75.90 % 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: 1.44 (0.20), residues: 1762 helix: 1.26 (0.15), residues: 1130 sheet: 0.50 (0.44), residues: 114 loop : 0.63 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.016 0.001 HIS C 445 PHE 0.022 0.001 PHE C 88 TYR 0.011 0.001 TYR A 275 ARG 0.006 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 902) hydrogen bonds : angle 4.51408 ( 2532) covalent geometry : bond 0.00288 (15275) covalent geometry : angle 0.55779 (20575) Misc. bond : bond 0.00018 ( 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 209 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: C 145 MET cc_start: 0.5339 (mmp) cc_final: 0.5021 (mmp) REVERT: C 183 GLU cc_start: 0.7982 (mp0) cc_final: 0.7068 (pm20) REVERT: D 139 ASP cc_start: 0.6370 (t0) cc_final: 0.5649 (p0) REVERT: D 309 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7444 (mm) REVERT: D 343 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.7003 (mp) REVERT: D 345 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7982 (mtm-85) REVERT: D 349 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7653 (mtp180) REVERT: A 112 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: A 183 GLU cc_start: 0.7801 (mp0) cc_final: 0.6838 (pm20) REVERT: A 363 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6884 (m90) REVERT: B 139 ASP cc_start: 0.6173 (t70) cc_final: 0.5884 (t70) REVERT: B 309 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7431 (mt) REVERT: B 345 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.6600 (tmm160) REVERT: B 349 ARG cc_start: 0.7547 (mtm180) cc_final: 0.7177 (mtm180) REVERT: B 482 GLN cc_start: 0.5581 (mm110) cc_final: 0.5039 (mm-40) REVERT: B 503 MET cc_start: 0.5850 (mmm) cc_final: 0.5435 (mpp) outliers start: 45 outliers final: 24 residues processed: 202 average time/residue: 0.2402 time to fit residues: 74.0527 Evaluate side-chains 195 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 349 ARG 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 139 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 120 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 39 optimal weight: 0.0070 chunk 68 optimal weight: 0.0870 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 D 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 = 0.237973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139182 restraints weight = 15259.945| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.08 r_work: 0.3384 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4092 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= 0.117 Angle : 0.552 17.005 20575 Z= 0.273 Chirality : 0.041 0.144 2266 Planarity : 0.004 0.060 2523 Dihedral : 7.301 59.604 2197 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.16 % Favored : 97.73 % Rotamer: Outliers : 2.59 % Allowed : 21.38 % 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: 1.57 (0.20), residues: 1762 helix: 1.37 (0.15), residues: 1132 sheet: 0.51 (0.44), residues: 114 loop : 0.69 (0.31), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 171 HIS 0.004 0.001 HIS A 363 PHE 0.022 0.001 PHE C 88 TYR 0.011 0.001 TYR C 213 ARG 0.006 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 902) hydrogen bonds : angle 4.41092 ( 2532) covalent geometry : bond 0.00257 (15275) covalent geometry : angle 0.55156 (20575) Misc. bond : bond 0.00015 ( 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: 41 poor density : 169 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: C 145 MET cc_start: 0.5267 (mmp) cc_final: 0.4941 (mmp) REVERT: C 183 GLU cc_start: 0.7941 (mp0) cc_final: 0.7039 (pm20) REVERT: C 499 LYS cc_start: 0.7685 (mmmt) cc_final: 0.7360 (mmtp) REVERT: D 139 ASP cc_start: 0.6449 (t0) cc_final: 0.5747 (p0) REVERT: D 309 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7402 (mm) REVERT: D 343 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6991 (mp) REVERT: D 345 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.6648 (tmm160) REVERT: D 349 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7559 (mtm180) REVERT: D 482 GLN cc_start: 0.5964 (mm110) cc_final: 0.5670 (mm-40) REVERT: A 112 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: A 183 GLU cc_start: 0.7743 (mp0) cc_final: 0.6799 (pm20) REVERT: A 363 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.7002 (m90) REVERT: B 139 ASP cc_start: 0.6306 (t70) cc_final: 0.6018 (t70) REVERT: B 309 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7453 (mm) REVERT: B 345 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.6743 (tmm160) REVERT: B 349 ARG cc_start: 0.7450 (mtm180) cc_final: 0.7072 (mtm180) REVERT: B 503 MET cc_start: 0.5816 (mmm) cc_final: 0.5383 (mpp) outliers start: 41 outliers final: 21 residues processed: 198 average time/residue: 0.2575 time to fit residues: 76.7825 Evaluate side-chains 188 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 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 349 ARG 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 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 476 ILE Chi-restraints excluded: chain A residue 507 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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 B 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.234623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134286 restraints weight = 15041.192| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.06 r_work: 0.3321 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4248 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= 0.168 Angle : 0.599 17.449 20575 Z= 0.296 Chirality : 0.043 0.162 2266 Planarity : 0.004 0.060 2523 Dihedral : 7.630 59.814 2197 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 2.59 % Allowed : 22.14 % Favored : 75.27 % 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: 1.46 (0.20), residues: 1762 helix: 1.26 (0.15), residues: 1130 sheet: 0.53 (0.44), residues: 114 loop : 0.67 (0.31), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 171 HIS 0.005 0.001 HIS A 363 PHE 0.022 0.001 PHE C 88 TYR 0.017 0.001 TYR A 275 ARG 0.007 0.000 ARG B 365 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 902) hydrogen bonds : angle 4.53927 ( 2532) covalent geometry : bond 0.00398 (15275) covalent geometry : angle 0.59903 (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 212 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: C 145 MET cc_start: 0.5338 (mmp) cc_final: 0.5008 (mmp) REVERT: C 183 GLU cc_start: 0.7972 (mp0) cc_final: 0.7080 (pm20) REVERT: C 209 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7179 (mp) REVERT: C 499 LYS cc_start: 0.7725 (mmmt) cc_final: 0.7325 (mmtp) REVERT: D 126 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7317 (mp) REVERT: D 139 ASP cc_start: 0.6412 (t0) cc_final: 0.5768 (p0) REVERT: D 309 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7496 (mm) REVERT: D 343 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6798 (mp) REVERT: D 345 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.6831 (tmm160) REVERT: D 349 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7506 (mtm180) REVERT: A 112 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: A 183 GLU cc_start: 0.7804 (mp0) cc_final: 0.6846 (pm20) REVERT: A 209 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7318 (mp) REVERT: B 139 ASP cc_start: 0.6330 (t70) cc_final: 0.6032 (t70) REVERT: B 309 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7336 (mt) REVERT: B 345 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.6634 (tmm160) REVERT: B 349 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7354 (mtm180) REVERT: B 503 MET cc_start: 0.5923 (mmm) cc_final: 0.5487 (mpp) outliers start: 41 outliers final: 23 residues processed: 198 average time/residue: 0.2508 time to fit residues: 75.5542 Evaluate side-chains 196 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 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 284 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 349 ARG 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 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 476 ILE Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 284 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 133 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** 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 = 0.4512 r_free = 0.4512 target = 0.235962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137166 restraints weight = 15010.268| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.03 r_work: 0.3379 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15276 Z= 0.132 Angle : 0.572 17.376 20575 Z= 0.282 Chirality : 0.042 0.147 2266 Planarity : 0.004 0.060 2523 Dihedral : 7.413 59.653 2197 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 2.15 % Allowed : 22.64 % Favored : 75.21 % 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: 1.33 (0.15), residues: 1132 sheet: 0.53 (0.44), residues: 114 loop : 0.68 (0.31), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 171 HIS 0.004 0.001 HIS C 230 PHE 0.021 0.001 PHE C 88 TYR 0.011 0.001 TYR A 275 ARG 0.007 0.000 ARG B 365 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 902) hydrogen bonds : angle 4.43690 ( 2532) covalent geometry : bond 0.00300 (15275) covalent geometry : angle 0.57207 (20575) Misc. bond : bond 0.00020 ( 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 205 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: C 145 MET cc_start: 0.5308 (mmp) cc_final: 0.4944 (mmp) REVERT: C 183 GLU cc_start: 0.7918 (mp0) cc_final: 0.6975 (pm20) REVERT: C 209 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7190 (mp) REVERT: C 499 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7345 (mmtp) REVERT: D 139 ASP cc_start: 0.6379 (t0) cc_final: 0.5777 (p0) REVERT: D 309 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7477 (mm) REVERT: D 345 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.6646 (tmm160) REVERT: D 349 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7578 (mtm180) REVERT: D 482 GLN cc_start: 0.6101 (mm110) cc_final: 0.5833 (mm-40) REVERT: A 112 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: A 183 GLU cc_start: 0.7758 (mp0) cc_final: 0.6829 (pm20) REVERT: A 209 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7287 (mp) REVERT: B 139 ASP cc_start: 0.6429 (t70) cc_final: 0.6139 (t70) REVERT: B 309 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7356 (mt) REVERT: B 503 MET cc_start: 0.5923 (mmm) cc_final: 0.5476 (mpp) outliers start: 34 outliers final: 18 residues processed: 192 average time/residue: 0.2624 time to fit residues: 75.8666 Evaluate side-chains 190 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 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 349 ARG Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 424 PHE 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 209 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 507 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 160 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.235033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135595 restraints weight = 15079.052| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.04 r_work: 0.3340 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4464 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= 0.148 Angle : 0.588 17.446 20575 Z= 0.290 Chirality : 0.042 0.142 2266 Planarity : 0.004 0.060 2523 Dihedral : 7.451 59.747 2197 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 1.83 % Allowed : 22.77 % Favored : 75.40 % 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: 1.49 (0.20), residues: 1762 helix: 1.28 (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 0.019 0.001 TRP B 171 HIS 0.004 0.001 HIS A 230 PHE 0.021 0.001 PHE C 88 TYR 0.013 0.001 TYR A 275 ARG 0.007 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 902) hydrogen bonds : angle 4.46546 ( 2532) covalent geometry : bond 0.00343 (15275) covalent geometry : angle 0.58841 (20575) Misc. bond : bond 0.00023 ( 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 200 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.551 Fit side-chains revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: C 145 MET cc_start: 0.5188 (mmp) cc_final: 0.4807 (mmp) REVERT: C 183 GLU cc_start: 0.7940 (mp0) cc_final: 0.7025 (pm20) REVERT: C 209 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7196 (mp) REVERT: C 499 LYS cc_start: 0.7670 (mmmt) cc_final: 0.7408 (mmtp) REVERT: D 139 ASP cc_start: 0.6396 (t0) cc_final: 0.5795 (p0) REVERT: D 309 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7508 (mm) REVERT: D 343 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6684 (mp) REVERT: D 345 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.6845 (tmm160) REVERT: D 482 GLN cc_start: 0.5957 (mm110) cc_final: 0.5633 (mm-40) REVERT: A 112 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: A 183 GLU cc_start: 0.7767 (mp0) cc_final: 0.6843 (pm20) REVERT: A 209 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7325 (mp) REVERT: B 139 ASP cc_start: 0.6464 (t70) cc_final: 0.6167 (t70) REVERT: B 309 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7421 (mm) REVERT: B 503 MET cc_start: 0.5910 (mmm) cc_final: 0.5467 (mpp) outliers start: 29 outliers final: 18 residues processed: 192 average time/residue: 0.2495 time to fit residues: 72.7056 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 : 1.516 ------------------------------------------------------------------------------- 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 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 424 PHE 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 209 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 507 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 170 optimal weight: 30.0000 chunk 167 optimal weight: 0.0060 chunk 86 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 33 optimal weight: 0.0270 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.237181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142721 restraints weight = 15079.700| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.14 r_work: 0.3305 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15276 Z= 0.124 Angle : 0.582 17.254 20575 Z= 0.284 Chirality : 0.042 0.144 2266 Planarity : 0.004 0.060 2523 Dihedral : 7.252 59.712 2197 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.27 % Favored : 97.62 % Rotamer: Outliers : 1.90 % Allowed : 22.71 % Favored : 75.40 % 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: 1.60 (0.20), residues: 1762 helix: 1.37 (0.15), residues: 1132 sheet: 0.64 (0.47), residues: 104 loop : 0.72 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 C 213 ARG 0.011 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 902) hydrogen bonds : angle 4.38723 ( 2532) covalent geometry : bond 0.00279 (15275) covalent geometry : angle 0.58158 (20575) Misc. bond : bond 0.00017 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11170.34 seconds wall clock time: 193 minutes 46.77 seconds (11626.77 seconds total)