Starting phenix.real_space_refine on Sun Jul 21 16:40:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/07_2024/8wtz_37847.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/07_2024/8wtz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/07_2024/8wtz_37847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/07_2024/8wtz_37847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/07_2024/8wtz_37847.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtz_37847/07_2024/8wtz_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 Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "D GLU 490": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14930 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3695 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 12, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3650 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3695 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 12, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3654 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 12, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 4} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 8.02, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 5.37 Conformation dependent library (CDL) restraints added in 2.2 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: 1.38 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: 4.60 Time building geometry restraints manager: 5.89 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: 99.14 - 106.16: 287 106.16 - 113.17: 7920 113.17 - 120.19: 5854 120.19 - 127.21: 6364 127.21 - 134.23: 150 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 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.190 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.450 ------------------------------------------------------------------------------- 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 0.176 15275 Z= 0.347 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 *********************** 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 fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.554 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: 0.2582 time to fit residues: 91.5111 Evaluate side-chains 191 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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: 4.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.0170 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- 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** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15275 Z= 0.240 Angle : 0.615 17.247 20575 Z= 0.314 Chirality : 0.043 0.157 2266 Planarity : 0.005 0.054 2523 Dihedral : 9.627 87.604 2215 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 3.35 % Allowed : 19.29 % Favored : 77.36 % 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: 0.90 (0.20), residues: 1762 helix: 0.79 (0.15), residues: 1106 sheet: 0.57 (0.46), residues: 116 loop : 0.49 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 272 HIS 0.006 0.001 HIS C 445 PHE 0.020 0.001 PHE D 236 TYR 0.014 0.002 TYR D 82 ARG 0.009 0.000 ARG D 349 *********************** 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 234 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 181 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7584 (mp0) cc_final: 0.7146 (pm20) REVERT: C 222 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7847 (tp) REVERT: C 270 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7811 (p0) REVERT: C 337 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7472 (ttp-170) REVERT: C 344 MET cc_start: 0.7688 (mtt) cc_final: 0.7300 (mtt) REVERT: C 476 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7145 (mt) REVERT: D 267 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.6618 (mtm-85) REVERT: D 309 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7302 (mm) REVERT: D 469 HIS cc_start: 0.7681 (m90) cc_final: 0.7270 (m90) REVERT: A 183 GLU cc_start: 0.7339 (mp0) cc_final: 0.6715 (pm20) REVERT: A 270 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7855 (p0) REVERT: A 337 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7859 (ttp-170) REVERT: A 363 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6794 (m90) REVERT: A 445 HIS cc_start: 0.5785 (m-70) cc_final: 0.5399 (m-70) REVERT: A 476 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7081 (mt) REVERT: A 499 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7163 (mtpp) REVERT: B 267 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.6560 (mtm-85) REVERT: B 309 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7540 (mt) outliers start: 53 outliers final: 19 residues processed: 225 average time/residue: 0.2649 time to fit residues: 87.8899 Evaluate side-chains 194 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 337 ARG 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 D residue 131 LEU Chi-restraints excluded: chain D residue 267 ARG 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 D residue 424 PHE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 270 ASP 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 88 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 0.0980 chunk 158 optimal weight: 1.9990 chunk 54 optimal weight: 0.0000 chunk 128 optimal weight: 10.0000 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 391 GLN C 413 ASN C 445 HIS C 482 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 482 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15275 Z= 0.181 Angle : 0.550 17.134 20575 Z= 0.278 Chirality : 0.041 0.155 2266 Planarity : 0.004 0.056 2523 Dihedral : 8.332 82.001 2209 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.27 % Favored : 97.62 % Rotamer: Outliers : 2.91 % Allowed : 19.92 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1762 helix: 1.23 (0.15), residues: 1118 sheet: 0.58 (0.45), residues: 116 loop : 0.46 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 85 HIS 0.005 0.001 HIS C 445 PHE 0.013 0.001 PHE B 236 TYR 0.012 0.001 TYR C 213 ARG 0.006 0.000 ARG D 365 *********************** 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 217 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7652 (mp0) cc_final: 0.7148 (pm20) REVERT: C 270 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7844 (p0) REVERT: C 340 MET cc_start: 0.7714 (ttp) cc_final: 0.7460 (ttt) REVERT: C 344 MET cc_start: 0.7647 (mtt) cc_final: 0.7293 (mtt) REVERT: C 445 HIS cc_start: 0.6647 (OUTLIER) cc_final: 0.6432 (t-170) REVERT: D 171 TRP cc_start: 0.8064 (m100) cc_final: 0.7833 (m100) REVERT: D 309 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7374 (mm) REVERT: D 343 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6980 (mp) REVERT: D 349 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7367 (mtm180) REVERT: D 469 HIS cc_start: 0.7658 (m90) cc_final: 0.7359 (m90) REVERT: D 480 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6619 (tp) REVERT: A 169 MET cc_start: 0.8430 (tpp) cc_final: 0.8176 (mmm) REVERT: A 183 GLU cc_start: 0.7343 (mp0) cc_final: 0.6734 (pm20) REVERT: A 270 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7895 (p0) REVERT: A 363 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6786 (m90) REVERT: B 309 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7485 (mm) REVERT: B 340 MET cc_start: 0.7979 (mmm) cc_final: 0.7704 (mmt) outliers start: 46 outliers final: 20 residues processed: 205 average time/residue: 0.2716 time to fit residues: 83.5873 Evaluate side-chains 188 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 270 ASP Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 445 HIS 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 480 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 270 ASP 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 96 SER Chi-restraints excluded: chain B residue 184 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 158 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 170 optimal weight: 0.0020 chunk 152 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15275 Z= 0.174 Angle : 0.531 16.873 20575 Z= 0.267 Chirality : 0.041 0.159 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.909 64.057 2204 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 3.54 % Allowed : 19.99 % Favored : 76.47 % 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: 1.58 (0.20), residues: 1762 helix: 1.44 (0.15), residues: 1118 sheet: 0.57 (0.44), residues: 116 loop : 0.54 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 85 HIS 0.011 0.001 HIS C 445 PHE 0.023 0.001 PHE C 88 TYR 0.011 0.001 TYR C 238 ARG 0.004 0.000 ARG B 365 *********************** 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 218 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 162 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: C 183 GLU cc_start: 0.7653 (mp0) cc_final: 0.6993 (pm20) REVERT: C 270 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7762 (p0) REVERT: C 344 MET cc_start: 0.7623 (mtt) cc_final: 0.7308 (mtt) REVERT: D 309 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7441 (mm) REVERT: D 343 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7121 (mp) REVERT: D 469 HIS cc_start: 0.7759 (m90) cc_final: 0.7448 (m90) REVERT: D 480 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6550 (tp) REVERT: A 169 MET cc_start: 0.8384 (tpp) cc_final: 0.8158 (mmm) REVERT: A 270 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7860 (p0) REVERT: A 499 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7336 (mttp) REVERT: B 309 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7502 (mt) REVERT: B 340 MET cc_start: 0.7957 (mmm) cc_final: 0.7684 (mmt) REVERT: B 345 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.7251 (tmm160) REVERT: B 381 ILE cc_start: 0.4152 (OUTLIER) cc_final: 0.3913 (mt) outliers start: 56 outliers final: 28 residues processed: 210 average time/residue: 0.2360 time to fit residues: 75.8244 Evaluate side-chains 192 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 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 270 ASP Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP 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 424 PHE Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 118 ASP 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 209 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 184 VAL 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 381 ILE 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 96 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 348 ASN D 482 GLN A 500 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15275 Z= 0.428 Angle : 0.656 18.071 20575 Z= 0.332 Chirality : 0.046 0.169 2266 Planarity : 0.005 0.060 2523 Dihedral : 8.736 59.990 2204 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.01 % Favored : 96.88 % Rotamer: Outliers : 3.42 % Allowed : 21.32 % 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: 1.05 (0.20), residues: 1762 helix: 1.01 (0.15), residues: 1104 sheet: 0.52 (0.43), residues: 116 loop : 0.34 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 272 HIS 0.005 0.001 HIS C 230 PHE 0.024 0.002 PHE C 88 TYR 0.021 0.002 TYR C 275 ARG 0.005 0.000 ARG D 349 *********************** 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 221 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: C 133 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: C 145 MET cc_start: 0.5722 (mmp) cc_final: 0.5374 (mmp) REVERT: C 183 GLU cc_start: 0.7702 (mp0) cc_final: 0.7142 (pm20) REVERT: C 270 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8031 (p0) REVERT: C 344 MET cc_start: 0.7742 (mtt) cc_final: 0.7515 (mtt) REVERT: D 309 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7605 (mm) REVERT: D 343 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6989 (mp) REVERT: D 480 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6361 (tp) REVERT: D 482 GLN cc_start: 0.5947 (mm110) cc_final: 0.5519 (mm110) REVERT: A 112 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: A 183 GLU cc_start: 0.7500 (mp0) cc_final: 0.6849 (pm20) REVERT: B 345 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.7221 (tmm160) REVERT: B 503 MET cc_start: 0.6202 (mmm) cc_final: 0.5605 (mpp) outliers start: 54 outliers final: 31 residues processed: 213 average time/residue: 0.2691 time to fit residues: 84.1913 Evaluate side-chains 198 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 133 PHE 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 214 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 380 ASP 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 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE 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 209 ILE Chi-restraints excluded: chain A residue 222 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 114 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 164 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN A 413 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15275 Z= 0.196 Angle : 0.559 17.729 20575 Z= 0.279 Chirality : 0.041 0.144 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.898 59.802 2201 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.27 % Favored : 97.62 % Rotamer: Outliers : 3.10 % Allowed : 21.88 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1762 helix: 1.34 (0.15), residues: 1104 sheet: 0.68 (0.44), residues: 116 loop : 0.40 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.004 0.001 HIS A 230 PHE 0.022 0.001 PHE C 88 TYR 0.011 0.001 TYR C 275 ARG 0.008 0.000 ARG B 349 *********************** 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 218 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 169 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: C 183 GLU cc_start: 0.7575 (mp0) cc_final: 0.7027 (pm20) REVERT: C 209 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7385 (mp) REVERT: C 270 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7837 (p0) REVERT: C 499 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7535 (mmtp) REVERT: D 309 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7542 (mm) REVERT: D 343 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.7065 (mp) REVERT: D 345 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.7099 (tmm160) REVERT: D 349 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7465 (mtp180) REVERT: D 480 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6497 (tp) REVERT: A 183 GLU cc_start: 0.7393 (mp0) cc_final: 0.6774 (pm20) REVERT: A 270 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7826 (p0) REVERT: B 309 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7536 (mt) REVERT: B 340 MET cc_start: 0.8165 (mmm) cc_final: 0.7892 (mmt) REVERT: B 345 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.7772 (ttm170) REVERT: B 503 MET cc_start: 0.6136 (mmm) cc_final: 0.5509 (mpp) outliers start: 49 outliers final: 24 residues processed: 209 average time/residue: 0.2477 time to fit residues: 79.3182 Evaluate side-chains 198 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 112 GLU 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 270 ASP Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 497 LEU 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 D residue 480 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 270 ASP 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 114 LEU Chi-restraints excluded: chain B residue 184 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 391 GLN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15275 Z= 0.199 Angle : 0.550 17.515 20575 Z= 0.275 Chirality : 0.041 0.142 2266 Planarity : 0.004 0.061 2523 Dihedral : 7.640 59.493 2201 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.28 % 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: 1.60 (0.20), residues: 1762 helix: 1.42 (0.15), residues: 1106 sheet: 1.07 (0.48), residues: 104 loop : 0.52 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.004 0.001 HIS A 230 PHE 0.022 0.001 PHE C 88 TYR 0.013 0.001 TYR C 275 ARG 0.006 0.000 ARG B 365 *********************** 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 206 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: C 183 GLU cc_start: 0.7523 (mp0) cc_final: 0.7015 (pm20) REVERT: C 209 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7431 (mp) REVERT: C 270 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7820 (p0) REVERT: C 340 MET cc_start: 0.7687 (mmm) cc_final: 0.6901 (tpt) REVERT: C 499 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7559 (mmtp) REVERT: D 309 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7477 (mm) REVERT: D 343 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6976 (mp) REVERT: D 345 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.6917 (tmm160) REVERT: D 480 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6456 (tp) REVERT: A 112 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: A 144 ARG cc_start: 0.5113 (mtp85) cc_final: 0.4813 (mtp85) REVERT: A 183 GLU cc_start: 0.7406 (mp0) cc_final: 0.6783 (pm20) REVERT: A 209 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7540 (mp) REVERT: A 270 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7805 (p0) REVERT: B 309 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7518 (mt) REVERT: B 503 MET cc_start: 0.6121 (mmm) cc_final: 0.5029 (mpp) outliers start: 41 outliers final: 22 residues processed: 196 average time/residue: 0.2575 time to fit residues: 76.0353 Evaluate side-chains 191 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP 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 270 ASP Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 497 LEU 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 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 270 ASP 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 114 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 504 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15275 Z= 0.199 Angle : 0.554 17.341 20575 Z= 0.275 Chirality : 0.041 0.174 2266 Planarity : 0.004 0.059 2523 Dihedral : 7.544 59.744 2201 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.33 % Rotamer: Outliers : 2.66 % Allowed : 22.20 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.20), residues: 1762 helix: 1.46 (0.15), residues: 1106 sheet: 1.12 (0.48), residues: 104 loop : 0.57 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 171 HIS 0.004 0.001 HIS A 230 PHE 0.022 0.001 PHE C 88 TYR 0.013 0.001 TYR A 213 ARG 0.007 0.000 ARG B 365 *********************** 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 215 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 173 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: C 183 GLU cc_start: 0.7523 (mp0) cc_final: 0.6871 (pm20) REVERT: C 209 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7408 (mp) REVERT: C 270 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7813 (p0) REVERT: C 344 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7728 (mtt) REVERT: C 499 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7516 (mmtp) REVERT: D 309 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7476 (mm) REVERT: D 345 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.6771 (tmm160) REVERT: D 349 ARG cc_start: 0.7588 (mtp180) cc_final: 0.7288 (mtm180) REVERT: D 480 ILE cc_start: 0.6481 (OUTLIER) cc_final: 0.6269 (tp) REVERT: D 482 GLN cc_start: 0.6099 (mm110) cc_final: 0.5811 (mm-40) REVERT: A 112 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: A 144 ARG cc_start: 0.5193 (mtp85) cc_final: 0.4890 (mtp85) REVERT: A 183 GLU cc_start: 0.7411 (mp0) cc_final: 0.6849 (pm20) REVERT: A 209 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 270 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7813 (p0) REVERT: A 504 ASN cc_start: 0.8951 (m110) cc_final: 0.8717 (t0) REVERT: B 309 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7519 (mt) REVERT: B 503 MET cc_start: 0.6120 (mmm) cc_final: 0.5039 (mpp) outliers start: 42 outliers final: 25 residues processed: 205 average time/residue: 0.2477 time to fit residues: 77.5847 Evaluate side-chains 196 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP 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 270 ASP Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 497 LEU 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 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 270 ASP 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 114 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 162 optimal weight: 10.0000 chunk 148 optimal weight: 0.2980 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15275 Z= 0.184 Angle : 0.549 17.038 20575 Z= 0.272 Chirality : 0.041 0.144 2266 Planarity : 0.004 0.061 2523 Dihedral : 7.365 59.983 2201 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 2.66 % Allowed : 22.39 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.20), residues: 1762 helix: 1.56 (0.15), residues: 1106 sheet: 1.19 (0.49), residues: 104 loop : 0.59 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 171 HIS 0.004 0.001 HIS C 230 PHE 0.022 0.001 PHE C 88 TYR 0.012 0.001 TYR A 213 ARG 0.007 0.000 ARG B 365 *********************** 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 209 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7503 (mp0) cc_final: 0.6865 (pm20) REVERT: C 209 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7415 (mp) REVERT: C 270 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7798 (p0) REVERT: C 344 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7786 (mtt) REVERT: C 431 MET cc_start: 0.3782 (mtt) cc_final: 0.3265 (mtm) REVERT: C 499 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7474 (mmtp) REVERT: D 309 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7476 (mt) REVERT: D 345 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.7004 (tmm160) REVERT: D 349 ARG cc_start: 0.7460 (mtp180) cc_final: 0.7161 (mtm180) REVERT: D 480 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6327 (tp) REVERT: D 482 GLN cc_start: 0.6284 (mm110) cc_final: 0.5956 (mm-40) REVERT: A 112 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: A 144 ARG cc_start: 0.5249 (mtp85) cc_final: 0.4971 (mtp85) REVERT: A 209 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7515 (mp) REVERT: A 270 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7794 (p0) REVERT: A 504 ASN cc_start: 0.8975 (m110) cc_final: 0.8718 (t0) REVERT: B 309 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7549 (mm) REVERT: B 340 MET cc_start: 0.8297 (tpp) cc_final: 0.8000 (mmt) REVERT: B 345 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.7753 (ttm170) REVERT: B 503 MET cc_start: 0.6156 (mmm) cc_final: 0.5089 (mpp) outliers start: 42 outliers final: 24 residues processed: 196 average time/residue: 0.2459 time to fit residues: 73.2153 Evaluate side-chains 195 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 497 LEU 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 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 343 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 96 SER Chi-restraints excluded: chain B residue 114 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 161 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15275 Z= 0.209 Angle : 0.566 17.032 20575 Z= 0.280 Chirality : 0.041 0.144 2266 Planarity : 0.004 0.061 2523 Dihedral : 7.404 59.901 2199 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.38 % Favored : 97.50 % Rotamer: Outliers : 2.47 % Allowed : 22.33 % 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: 1.74 (0.20), residues: 1762 helix: 1.52 (0.15), residues: 1106 sheet: 1.17 (0.48), residues: 104 loop : 0.59 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 171 HIS 0.004 0.001 HIS A 230 PHE 0.022 0.001 PHE C 88 TYR 0.014 0.001 TYR A 275 ARG 0.009 0.000 ARG B 349 ********************** 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 208 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 183 GLU cc_start: 0.7510 (mp0) cc_final: 0.6874 (pm20) REVERT: C 209 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7437 (mp) REVERT: C 270 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7815 (p0) REVERT: C 340 MET cc_start: 0.7852 (mmm) cc_final: 0.6928 (tpt) REVERT: C 499 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7482 (mmtp) REVERT: D 309 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7494 (mm) REVERT: D 345 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.6815 (tmm160) REVERT: D 349 ARG cc_start: 0.7404 (mtp180) cc_final: 0.7144 (mtm180) REVERT: D 480 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6404 (tp) REVERT: D 482 GLN cc_start: 0.6299 (mm110) cc_final: 0.5965 (mm-40) REVERT: A 112 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: A 144 ARG cc_start: 0.5132 (mtp85) cc_final: 0.4860 (mtp85) REVERT: A 209 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7591 (mp) REVERT: A 270 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7795 (p0) REVERT: A 504 ASN cc_start: 0.8967 (m110) cc_final: 0.8710 (t0) REVERT: B 139 ASP cc_start: 0.6186 (t70) cc_final: 0.5902 (t70) REVERT: B 309 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7561 (mm) REVERT: B 345 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.7787 (ttm170) REVERT: B 503 MET cc_start: 0.6182 (mmm) cc_final: 0.5134 (mpp) outliers start: 39 outliers final: 26 residues processed: 199 average time/residue: 0.2484 time to fit residues: 75.9709 Evaluate side-chains 200 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain D residue 184 VAL 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 319 LEU Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 114 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.0030 chunk 42 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.235725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142132 restraints weight = 15058.821| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.87 r_work: 0.3308 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15275 Z= 0.210 Angle : 0.571 17.079 20575 Z= 0.282 Chirality : 0.041 0.144 2266 Planarity : 0.004 0.061 2523 Dihedral : 7.388 59.847 2199 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 2.53 % Allowed : 22.52 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.20), residues: 1762 helix: 1.52 (0.15), residues: 1106 sheet: 1.19 (0.48), residues: 104 loop : 0.60 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 171 HIS 0.004 0.001 HIS A 230 PHE 0.022 0.001 PHE C 88 TYR 0.013 0.001 TYR A 275 ARG 0.007 0.000 ARG B 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.26 seconds wall clock time: 61 minutes 33.12 seconds (3693.12 seconds total)