Starting phenix.real_space_refine on Sun Apr 5 03:22:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpi_47105/04_2026/9dpi_47105.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpi_47105/04_2026/9dpi_47105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dpi_47105/04_2026/9dpi_47105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpi_47105/04_2026/9dpi_47105.map" model { file = "/net/cci-nas-00/data/ceres_data/9dpi_47105/04_2026/9dpi_47105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpi_47105/04_2026/9dpi_47105.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.134 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 4 5.49 5 S 49 5.16 5 C 4912 2.51 5 N 1262 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7651 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2030 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1565 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 203, 1565 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1587 Chain: "F" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2079 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 243} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1889 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 243, 1889 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1922 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.33 Number of scatterers: 7651 At special positions: 0 Unit cell: (88.55, 151.8, 78.2, 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 49 16.00 P 4 15.00 O 1424 8.00 N 1262 7.00 C 4912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 324 " distance=2.04 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 324 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 431.6 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 41.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 169 through 177 removed outlier: 4.672A pdb=" N VAL D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 218 removed outlier: 3.605A pdb=" N PHE D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 335 through 355 removed outlier: 3.529A pdb=" N LEU D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 407 removed outlier: 3.701A pdb=" N ARG D 405 " --> pdb=" O TYR D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 445 removed outlier: 3.678A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 removed outlier: 3.686A pdb=" N LYS D 457 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 removed outlier: 3.718A pdb=" N SER C 88 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR C 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C 90 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 removed outlier: 4.078A pdb=" N ILE C 118 " --> pdb=" O PRO C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.994A pdb=" N LYS C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.507A pdb=" N TYR C 150 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 240 through 251 removed outlier: 3.724A pdb=" N PHE C 244 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 removed outlier: 3.932A pdb=" N ILE C 273 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 removed outlier: 3.888A pdb=" N GLY C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 355 Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 169 through 177 removed outlier: 4.339A pdb=" N VAL F 175 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 218 removed outlier: 3.596A pdb=" N PHE F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 332 through 334 No H-bonds generated for 'chain 'F' and resid 332 through 334' Processing helix chain 'F' and resid 335 through 355 removed outlier: 3.503A pdb=" N LEU F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 407 removed outlier: 3.708A pdb=" N ARG F 405 " --> pdb=" O TYR F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 445 removed outlier: 3.706A pdb=" N GLN F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 457 Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.618A pdb=" N SER E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR E 89 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 90 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 removed outlier: 4.110A pdb=" N ILE E 118 " --> pdb=" O PRO E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 128 through 139 removed outlier: 3.989A pdb=" N LYS E 136 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 159 removed outlier: 3.612A pdb=" N TYR E 150 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET E 152 " --> pdb=" O CYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 177 Processing helix chain 'E' and resid 205 through 214 removed outlier: 4.214A pdb=" N MET E 209 " --> pdb=" O PRO E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 removed outlier: 3.943A pdb=" N PHE E 244 " --> pdb=" O PRO E 240 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 273 removed outlier: 3.924A pdb=" N ILE E 273 " --> pdb=" O ALA E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 336 removed outlier: 3.874A pdb=" N GLY E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 355 Processing sheet with id=AA1, first strand: chain 'D' and resid 154 through 159 removed outlier: 3.689A pdb=" N LYS D 154 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 361 " --> pdb=" O GLU D 156 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE D 158 " --> pdb=" O TYR D 359 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR D 359 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 393 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA D 381 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU D 391 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL D 393 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N CYS D 431 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N CYS D 395 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR D 429 " --> pdb=" O CYS D 395 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASN D 397 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN D 427 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N MET D 425 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER D 330 " --> pdb=" O MET D 425 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN D 427 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL D 328 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR D 429 " --> pdb=" O GLN D 326 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN D 326 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 327 " --> pdb=" O TYR D 294 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE D 292 " --> pdb=" O TYR D 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 154 through 159 removed outlier: 3.689A pdb=" N LYS D 154 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 361 " --> pdb=" O GLU D 156 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE D 158 " --> pdb=" O TYR D 359 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR D 359 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 393 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA D 381 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU D 391 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL D 393 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N CYS D 431 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N CYS D 395 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR D 429 " --> pdb=" O CYS D 395 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASN D 397 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN D 427 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N MET D 425 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER D 330 " --> pdb=" O MET D 425 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN D 427 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL D 328 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR D 429 " --> pdb=" O GLN D 326 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN D 326 " --> pdb=" O THR D 429 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 449 through 451 removed outlier: 3.640A pdb=" N ILE D 450 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 183 through 185 removed outlier: 8.510A pdb=" N VAL C 184 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS C 164 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL C 79 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG C 163 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS C 81 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE C 80 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N MET C 260 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C 82 " --> pdb=" O MET C 260 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU C 257 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ILE C 285 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL C 259 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG C 282 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TRP C 320 " --> pdb=" O ARG C 282 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU C 284 " --> pdb=" O TRP C 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 154 through 159 removed outlier: 3.730A pdb=" N LYS F 154 " --> pdb=" O ASN F 363 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE F 361 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE F 158 " --> pdb=" O TYR F 359 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR F 359 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL F 393 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA F 381 " --> pdb=" O GLU F 391 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU F 391 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL F 393 " --> pdb=" O CYS F 431 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N CYS F 431 " --> pdb=" O VAL F 393 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N CYS F 395 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR F 429 " --> pdb=" O CYS F 395 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASN F 397 " --> pdb=" O ASN F 427 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASN F 427 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N MET F 425 " --> pdb=" O SER F 330 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER F 330 " --> pdb=" O MET F 425 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASN F 427 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL F 328 " --> pdb=" O ASN F 427 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N THR F 429 " --> pdb=" O GLN F 326 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN F 326 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 327 " --> pdb=" O TYR F 294 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 292 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 449 through 451 removed outlier: 3.602A pdb=" N ILE F 450 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 185 removed outlier: 6.319A pdb=" N ILE E 80 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N MET E 260 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E 82 " --> pdb=" O MET E 260 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU E 257 " --> pdb=" O LEU E 283 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ILE E 285 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL E 259 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TRP E 320 " --> pdb=" O ARG E 282 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU E 284 " --> pdb=" O TRP E 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 193 through 195 275 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2441 1.34 - 1.46: 1767 1.46 - 1.58: 3546 1.58 - 1.70: 8 1.70 - 1.82: 70 Bond restraints: 7832 Sorted by residual: bond pdb=" CA PRO D 461 " pdb=" C PRO D 461 " ideal model delta sigma weight residual 1.517 1.509 0.008 6.70e-03 2.23e+04 1.45e+00 bond pdb=" CA GLY E 336 " pdb=" C GLY E 336 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.33e+00 bond pdb=" CB ASP C 95 " pdb=" CG ASP C 95 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CG LEU D 173 " pdb=" CD1 LEU D 173 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 bond pdb=" C HIS C 127 " pdb=" N PRO C 128 " ideal model delta sigma weight residual 1.332 1.341 -0.009 8.20e-03 1.49e+04 1.26e+00 ... (remaining 7827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 10464 2.66 - 5.32: 137 5.32 - 7.98: 16 7.98 - 10.64: 1 10.64 - 13.30: 1 Bond angle restraints: 10619 Sorted by residual: angle pdb=" CA LEU C 344 " pdb=" CB LEU C 344 " pdb=" CG LEU C 344 " ideal model delta sigma weight residual 116.30 129.60 -13.30 3.50e+00 8.16e-02 1.44e+01 angle pdb=" C ASP E 170 " pdb=" N THR E 171 " pdb=" CA THR E 171 " ideal model delta sigma weight residual 122.61 127.97 -5.36 1.56e+00 4.11e-01 1.18e+01 angle pdb=" C ASP C 170 " pdb=" N THR C 171 " pdb=" CA THR C 171 " ideal model delta sigma weight residual 122.61 127.31 -4.70 1.56e+00 4.11e-01 9.07e+00 angle pdb=" N GLU C 129 " pdb=" CA GLU C 129 " pdb=" C GLU C 129 " ideal model delta sigma weight residual 109.81 116.36 -6.55 2.21e+00 2.05e-01 8.77e+00 angle pdb=" N THR E 171 " pdb=" CA THR E 171 " pdb=" C THR E 171 " ideal model delta sigma weight residual 112.47 116.06 -3.59 1.24e+00 6.50e-01 8.37e+00 ... (remaining 10614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 4229 20.83 - 41.66: 453 41.66 - 62.49: 95 62.49 - 83.32: 17 83.32 - 104.15: 7 Dihedral angle restraints: 4801 sinusoidal: 1992 harmonic: 2809 Sorted by residual: dihedral pdb=" CA CYS C 324 " pdb=" C CYS C 324 " pdb=" N ASP C 325 " pdb=" CA ASP C 325 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA CYS E 324 " pdb=" C CYS E 324 " pdb=" N ASP E 325 " pdb=" CA ASP E 325 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" O1A AR6 E 401 " pdb=" O3A AR6 E 401 " pdb=" PA AR6 E 401 " pdb=" PB AR6 E 401 " ideal model delta sinusoidal sigma weight residual -82.51 21.64 -104.15 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 4798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 771 0.039 - 0.079: 304 0.079 - 0.118: 86 0.118 - 0.158: 23 0.158 - 0.197: 3 Chirality restraints: 1187 Sorted by residual: chirality pdb=" CB THR D 429 " pdb=" CA THR D 429 " pdb=" OG1 THR D 429 " pdb=" CG2 THR D 429 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA GLU C 129 " pdb=" N GLU C 129 " pdb=" C GLU C 129 " pdb=" CB GLU C 129 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA THR E 171 " pdb=" N THR E 171 " pdb=" C THR E 171 " pdb=" CB THR E 171 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 1184 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 127 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO C 128 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 274 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 275 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 275 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 275 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 274 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO F 275 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 275 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 275 " 0.030 5.00e-02 4.00e+02 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 3995 2.99 - 3.47: 7858 3.47 - 3.95: 12231 3.95 - 4.42: 14161 4.42 - 4.90: 22285 Nonbonded interactions: 60530 Sorted by model distance: nonbonded pdb=" O ASP D 334 " pdb=" OD1 ASN D 335 " model vdw 2.519 3.040 nonbonded pdb=" N GLU C 179 " pdb=" OE1 GLU C 179 " model vdw 2.534 3.120 nonbonded pdb=" N VAL D 177 " pdb=" N ASP D 178 " model vdw 2.602 2.560 nonbonded pdb=" O ASP F 161 " pdb=" OD1 ASP F 161 " model vdw 2.611 3.040 nonbonded pdb=" N ASP E 325 " pdb=" OD1 ASP E 325 " model vdw 2.615 3.120 ... (remaining 60525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 137 through 364 or resid 372 through 475)) } 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=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7834 Z= 0.153 Angle : 0.745 13.300 10623 Z= 0.393 Chirality : 0.047 0.197 1187 Planarity : 0.005 0.062 1345 Dihedral : 17.666 104.149 2971 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.19 % Allowed : 27.41 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.28), residues: 931 helix: -0.78 (0.27), residues: 345 sheet: -1.70 (0.41), residues: 157 loop : -0.44 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 78 TYR 0.016 0.001 TYR D 168 PHE 0.024 0.002 PHE C 251 TRP 0.027 0.002 TRP E 337 HIS 0.006 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7832) covalent geometry : angle 0.74466 (10619) SS BOND : bond 0.00511 ( 2) SS BOND : angle 1.05557 ( 4) hydrogen bonds : bond 0.17014 ( 262) hydrogen bonds : angle 8.22625 ( 777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 337 TRP cc_start: 0.7317 (m-90) cc_final: 0.6329 (m-90) REVERT: F 178 ASP cc_start: 0.7171 (t0) cc_final: 0.6765 (t0) REVERT: F 405 ARG cc_start: 0.7465 (ttm110) cc_final: 0.6553 (mmt180) REVERT: E 260 MET cc_start: 0.7399 (ttm) cc_final: 0.6676 (ttt) REVERT: E 325 ASP cc_start: 0.6844 (m-30) cc_final: 0.6418 (m-30) outliers start: 18 outliers final: 16 residues processed: 177 average time/residue: 0.0776 time to fit residues: 19.2023 Evaluate side-chains 170 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.236729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.183996 restraints weight = 189318.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.189348 restraints weight = 47782.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.185239 restraints weight = 37932.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.184221 restraints weight = 38521.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.183732 restraints weight = 36095.741| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7834 Z= 0.217 Angle : 0.718 9.876 10623 Z= 0.364 Chirality : 0.049 0.170 1187 Planarity : 0.005 0.061 1345 Dihedral : 9.761 102.423 1153 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 6.21 % Allowed : 22.90 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.27), residues: 931 helix: -1.01 (0.26), residues: 359 sheet: -1.51 (0.41), residues: 166 loop : -0.54 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 78 TYR 0.015 0.002 TYR F 220 PHE 0.027 0.003 PHE E 269 TRP 0.023 0.002 TRP E 337 HIS 0.006 0.001 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 7832) covalent geometry : angle 0.71738 (10619) SS BOND : bond 0.00520 ( 2) SS BOND : angle 1.31283 ( 4) hydrogen bonds : bond 0.04430 ( 262) hydrogen bonds : angle 5.85354 ( 777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 ASP cc_start: 0.7323 (t0) cc_final: 0.6827 (t70) REVERT: D 431 CYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7561 (p) REVERT: F 178 ASP cc_start: 0.7324 (t0) cc_final: 0.6944 (t0) REVERT: F 416 MET cc_start: 0.7897 (tmm) cc_final: 0.7693 (ppp) REVERT: E 325 ASP cc_start: 0.7539 (m-30) cc_final: 0.7117 (m-30) outliers start: 51 outliers final: 28 residues processed: 197 average time/residue: 0.0721 time to fit residues: 20.1849 Evaluate side-chains 182 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.233214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.195118 restraints weight = 120281.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.197954 restraints weight = 47640.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.196997 restraints weight = 39216.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.197216 restraints weight = 40555.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.197141 restraints weight = 37077.756| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7834 Z= 0.153 Angle : 0.657 11.192 10623 Z= 0.329 Chirality : 0.047 0.189 1187 Planarity : 0.005 0.063 1345 Dihedral : 9.347 99.503 1146 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.26 % Allowed : 24.24 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.27), residues: 931 helix: -0.78 (0.27), residues: 357 sheet: -1.46 (0.42), residues: 167 loop : -0.48 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 78 TYR 0.010 0.001 TYR F 410 PHE 0.020 0.002 PHE E 269 TRP 0.022 0.001 TRP E 337 HIS 0.006 0.001 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7832) covalent geometry : angle 0.65698 (10619) SS BOND : bond 0.00643 ( 2) SS BOND : angle 0.98268 ( 4) hydrogen bonds : bond 0.03857 ( 262) hydrogen bonds : angle 5.51284 ( 777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 ASP cc_start: 0.7201 (t0) cc_final: 0.6832 (t70) REVERT: D 415 LYS cc_start: 0.8678 (mppt) cc_final: 0.8164 (mttp) REVERT: C 126 LYS cc_start: 0.6430 (mmmt) cc_final: 0.5796 (tmmt) REVERT: C 172 LEU cc_start: 0.7264 (tp) cc_final: 0.7031 (mt) REVERT: F 178 ASP cc_start: 0.7201 (t0) cc_final: 0.6760 (t0) REVERT: F 431 CYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7830 (p) REVERT: E 325 ASP cc_start: 0.5998 (m-30) cc_final: 0.5590 (m-30) outliers start: 35 outliers final: 24 residues processed: 185 average time/residue: 0.0751 time to fit residues: 19.7701 Evaluate side-chains 176 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 335 ASN ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN E 167 GLN ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.233198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.194848 restraints weight = 95128.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.197791 restraints weight = 46170.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.196013 restraints weight = 37248.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.196495 restraints weight = 38363.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.196287 restraints weight = 35243.799| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7834 Z= 0.142 Angle : 0.640 9.531 10623 Z= 0.322 Chirality : 0.046 0.205 1187 Planarity : 0.005 0.065 1345 Dihedral : 9.091 97.351 1142 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.24 % Allowed : 23.26 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.27), residues: 931 helix: -0.71 (0.27), residues: 356 sheet: -1.48 (0.42), residues: 169 loop : -0.40 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 78 TYR 0.011 0.001 TYR F 410 PHE 0.018 0.002 PHE C 124 TRP 0.024 0.001 TRP E 337 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7832) covalent geometry : angle 0.63944 (10619) SS BOND : bond 0.00406 ( 2) SS BOND : angle 1.41169 ( 4) hydrogen bonds : bond 0.03488 ( 262) hydrogen bonds : angle 5.25318 ( 777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 172 ASP cc_start: 0.7887 (p0) cc_final: 0.7552 (p0) REVERT: D 178 ASP cc_start: 0.7318 (t0) cc_final: 0.6848 (t70) REVERT: D 415 LYS cc_start: 0.8678 (mppt) cc_final: 0.8112 (mttp) REVERT: D 444 TYR cc_start: 0.8178 (m-80) cc_final: 0.7754 (m-80) REVERT: C 126 LYS cc_start: 0.6708 (mmmt) cc_final: 0.6054 (tmmt) REVERT: C 153 ARG cc_start: 0.7371 (mtp85) cc_final: 0.6818 (mtp85) REVERT: C 338 LYS cc_start: 0.7950 (tptt) cc_final: 0.7743 (tptt) REVERT: F 178 ASP cc_start: 0.7383 (t0) cc_final: 0.7005 (t70) REVERT: F 431 CYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7937 (p) REVERT: E 325 ASP cc_start: 0.5988 (m-30) cc_final: 0.5601 (m-30) outliers start: 43 outliers final: 27 residues processed: 193 average time/residue: 0.0799 time to fit residues: 21.2233 Evaluate side-chains 173 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 0.0370 chunk 26 optimal weight: 0.0020 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 335 ASN D 443 ASN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.241701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.188414 restraints weight = 129893.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.193267 restraints weight = 44771.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.190048 restraints weight = 37118.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.190261 restraints weight = 36691.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.189596 restraints weight = 34186.020| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7834 Z= 0.130 Angle : 0.637 10.844 10623 Z= 0.315 Chirality : 0.046 0.190 1187 Planarity : 0.005 0.065 1345 Dihedral : 8.927 96.790 1140 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.87 % Allowed : 22.78 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.28), residues: 931 helix: -0.62 (0.27), residues: 354 sheet: -1.48 (0.42), residues: 167 loop : -0.39 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 242 TYR 0.012 0.001 TYR C 150 PHE 0.019 0.002 PHE C 124 TRP 0.022 0.001 TRP E 337 HIS 0.004 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7832) covalent geometry : angle 0.63647 (10619) SS BOND : bond 0.00444 ( 2) SS BOND : angle 1.57721 ( 4) hydrogen bonds : bond 0.03367 ( 262) hydrogen bonds : angle 5.20239 ( 777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 ASP cc_start: 0.7299 (t0) cc_final: 0.6813 (t70) REVERT: D 350 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7186 (mm-30) REVERT: D 431 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7759 (p) REVERT: D 444 TYR cc_start: 0.8025 (m-80) cc_final: 0.7689 (m-80) REVERT: C 126 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6496 (tmmt) REVERT: C 144 LYS cc_start: 0.7501 (tttp) cc_final: 0.7248 (tptm) REVERT: C 338 LYS cc_start: 0.8555 (tptt) cc_final: 0.8292 (tptt) REVERT: F 178 ASP cc_start: 0.7203 (t0) cc_final: 0.6793 (t70) REVERT: F 431 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7978 (p) REVERT: E 192 THR cc_start: 0.6847 (OUTLIER) cc_final: 0.6586 (t) REVERT: E 325 ASP cc_start: 0.7275 (m-30) cc_final: 0.6938 (m-30) outliers start: 40 outliers final: 25 residues processed: 186 average time/residue: 0.0704 time to fit residues: 18.5770 Evaluate side-chains 172 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.231685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.176558 restraints weight = 142113.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.181419 restraints weight = 46639.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.177490 restraints weight = 36716.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.177484 restraints weight = 38378.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.176996 restraints weight = 34486.766| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7834 Z= 0.239 Angle : 0.710 9.277 10623 Z= 0.358 Chirality : 0.050 0.220 1187 Planarity : 0.005 0.068 1345 Dihedral : 9.133 96.927 1138 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.12 % Allowed : 23.14 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.27), residues: 931 helix: -0.74 (0.26), residues: 364 sheet: -1.68 (0.42), residues: 167 loop : -0.47 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 153 TYR 0.017 0.002 TYR D 224 PHE 0.025 0.002 PHE E 244 TRP 0.023 0.002 TRP E 337 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 7832) covalent geometry : angle 0.70905 (10619) SS BOND : bond 0.00418 ( 2) SS BOND : angle 1.48163 ( 4) hydrogen bonds : bond 0.03950 ( 262) hydrogen bonds : angle 5.23972 ( 777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 172 ASP cc_start: 0.7897 (p0) cc_final: 0.7674 (p0) REVERT: D 178 ASP cc_start: 0.7477 (t0) cc_final: 0.7033 (t70) REVERT: D 203 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7796 (tp) REVERT: D 431 CYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7755 (p) REVERT: C 126 LYS cc_start: 0.7283 (mmmt) cc_final: 0.6469 (tmmt) REVERT: C 144 LYS cc_start: 0.7595 (tttp) cc_final: 0.7110 (tptm) REVERT: C 170 ASP cc_start: 0.8240 (p0) cc_final: 0.7967 (p0) REVERT: C 337 TRP cc_start: 0.7718 (m-90) cc_final: 0.6685 (m-90) REVERT: C 338 LYS cc_start: 0.8668 (tptt) cc_final: 0.8443 (tptt) REVERT: F 178 ASP cc_start: 0.7431 (t0) cc_final: 0.6988 (t70) REVERT: F 203 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7734 (tp) REVERT: F 335 ASN cc_start: 0.8001 (t0) cc_final: 0.7472 (p0) REVERT: F 431 CYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7752 (p) REVERT: E 156 LYS cc_start: 0.7098 (tttt) cc_final: 0.6791 (pttp) REVERT: E 182 ASP cc_start: 0.6671 (m-30) cc_final: 0.5496 (p0) REVERT: E 192 THR cc_start: 0.7063 (OUTLIER) cc_final: 0.6774 (t) REVERT: E 325 ASP cc_start: 0.7394 (m-30) cc_final: 0.7146 (m-30) outliers start: 42 outliers final: 28 residues processed: 189 average time/residue: 0.0693 time to fit residues: 18.5596 Evaluate side-chains 184 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 41 optimal weight: 0.6980 chunk 90 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.232666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.195546 restraints weight = 120531.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.198221 restraints weight = 46719.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.195928 restraints weight = 37938.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.196278 restraints weight = 38222.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.196109 restraints weight = 35405.349| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7834 Z= 0.134 Angle : 0.673 10.811 10623 Z= 0.330 Chirality : 0.047 0.193 1187 Planarity : 0.005 0.065 1345 Dihedral : 8.960 95.881 1138 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.26 % Allowed : 24.85 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.28), residues: 931 helix: -0.59 (0.27), residues: 365 sheet: -1.56 (0.42), residues: 168 loop : -0.31 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 153 TYR 0.012 0.001 TYR D 168 PHE 0.022 0.002 PHE E 214 TRP 0.020 0.001 TRP E 337 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7832) covalent geometry : angle 0.67243 (10619) SS BOND : bond 0.00426 ( 2) SS BOND : angle 1.50099 ( 4) hydrogen bonds : bond 0.03430 ( 262) hydrogen bonds : angle 5.06439 ( 777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 ASP cc_start: 0.7200 (t0) cc_final: 0.6714 (t70) REVERT: D 203 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7497 (tp) REVERT: D 350 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7325 (mm-30) REVERT: D 431 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7695 (p) REVERT: D 444 TYR cc_start: 0.8147 (m-80) cc_final: 0.7838 (m-80) REVERT: C 337 TRP cc_start: 0.6881 (m-90) cc_final: 0.6112 (m-90) REVERT: C 338 LYS cc_start: 0.8176 (tptt) cc_final: 0.7976 (tptt) REVERT: F 178 ASP cc_start: 0.7127 (t0) cc_final: 0.6785 (t70) REVERT: F 431 CYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7835 (p) REVERT: F 444 TYR cc_start: 0.8149 (m-80) cc_final: 0.7874 (m-80) REVERT: E 325 ASP cc_start: 0.6504 (m-30) cc_final: 0.6272 (m-30) outliers start: 35 outliers final: 24 residues processed: 179 average time/residue: 0.0726 time to fit residues: 18.3550 Evaluate side-chains 168 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.0870 chunk 40 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.239009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.185847 restraints weight = 134981.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.191099 restraints weight = 46121.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.186976 restraints weight = 37479.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.187109 restraints weight = 37960.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.186603 restraints weight = 35007.030| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7834 Z= 0.132 Angle : 0.701 14.576 10623 Z= 0.338 Chirality : 0.048 0.226 1187 Planarity : 0.005 0.066 1345 Dihedral : 8.723 96.270 1137 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.65 % Allowed : 25.46 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.28), residues: 931 helix: -0.52 (0.27), residues: 353 sheet: -1.53 (0.42), residues: 163 loop : -0.36 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 153 TYR 0.010 0.001 TYR F 359 PHE 0.023 0.002 PHE C 124 TRP 0.021 0.001 TRP E 337 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7832) covalent geometry : angle 0.70015 (10619) SS BOND : bond 0.00927 ( 2) SS BOND : angle 2.01897 ( 4) hydrogen bonds : bond 0.03347 ( 262) hydrogen bonds : angle 5.00963 ( 777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 ASP cc_start: 0.7424 (t0) cc_final: 0.6977 (t70) REVERT: D 203 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7578 (tp) REVERT: D 350 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7250 (mm-30) REVERT: D 431 CYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7782 (p) REVERT: C 153 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7119 (mtp85) REVERT: C 172 LEU cc_start: 0.7389 (mp) cc_final: 0.7176 (mp) REVERT: F 178 ASP cc_start: 0.7213 (t0) cc_final: 0.6804 (t70) REVERT: F 431 CYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7809 (p) REVERT: E 235 PHE cc_start: 0.6774 (m-80) cc_final: 0.6434 (m-80) outliers start: 30 outliers final: 23 residues processed: 164 average time/residue: 0.0665 time to fit residues: 15.9923 Evaluate side-chains 164 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.230326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.191030 restraints weight = 143022.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.194752 restraints weight = 46398.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.192386 restraints weight = 37523.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.192867 restraints weight = 39021.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.192603 restraints weight = 35410.830| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7834 Z= 0.163 Angle : 0.724 14.211 10623 Z= 0.352 Chirality : 0.049 0.215 1187 Planarity : 0.005 0.066 1345 Dihedral : 8.725 95.856 1137 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.38 % Allowed : 24.85 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.28), residues: 931 helix: -0.49 (0.27), residues: 364 sheet: -1.62 (0.41), residues: 173 loop : -0.34 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 242 TYR 0.014 0.002 TYR D 168 PHE 0.022 0.002 PHE C 124 TRP 0.019 0.001 TRP E 337 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7832) covalent geometry : angle 0.72321 (10619) SS BOND : bond 0.01068 ( 2) SS BOND : angle 2.15848 ( 4) hydrogen bonds : bond 0.03458 ( 262) hydrogen bonds : angle 4.99350 ( 777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 ASP cc_start: 0.7454 (t0) cc_final: 0.7073 (t70) REVERT: D 203 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7639 (tp) REVERT: D 350 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 431 CYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7812 (p) REVERT: C 153 ARG cc_start: 0.7215 (mtp85) cc_final: 0.6747 (mtp85) REVERT: C 172 LEU cc_start: 0.7239 (mp) cc_final: 0.6958 (mp) REVERT: C 337 TRP cc_start: 0.6926 (m-90) cc_final: 0.6425 (m-90) REVERT: F 178 ASP cc_start: 0.7346 (t0) cc_final: 0.6968 (t70) REVERT: F 203 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7642 (tp) REVERT: F 350 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7230 (mm-30) REVERT: F 431 CYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7927 (p) outliers start: 36 outliers final: 28 residues processed: 171 average time/residue: 0.0742 time to fit residues: 18.0193 Evaluate side-chains 175 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 416 MET Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.234220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.196057 restraints weight = 145170.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.202774 restraints weight = 48016.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.198253 restraints weight = 42200.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.198230 restraints weight = 39271.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.197825 restraints weight = 36597.207| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7834 Z= 0.125 Angle : 0.702 13.816 10623 Z= 0.342 Chirality : 0.048 0.236 1187 Planarity : 0.005 0.065 1345 Dihedral : 8.597 95.566 1137 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.41 % Allowed : 26.07 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.28), residues: 931 helix: -0.35 (0.27), residues: 361 sheet: -1.59 (0.41), residues: 174 loop : -0.30 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 242 TYR 0.010 0.001 TYR D 168 PHE 0.022 0.002 PHE C 124 TRP 0.016 0.001 TRP F 159 HIS 0.004 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7832) covalent geometry : angle 0.70107 (10619) SS BOND : bond 0.00667 ( 2) SS BOND : angle 2.14612 ( 4) hydrogen bonds : bond 0.03278 ( 262) hydrogen bonds : angle 4.92413 ( 777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 ASP cc_start: 0.7409 (t0) cc_final: 0.6990 (t70) REVERT: D 203 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7568 (tp) REVERT: D 350 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7200 (mm-30) REVERT: C 143 PHE cc_start: 0.7030 (m-80) cc_final: 0.6819 (m-80) REVERT: C 153 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6648 (mtp85) REVERT: C 172 LEU cc_start: 0.7023 (mp) cc_final: 0.6795 (mp) REVERT: C 337 TRP cc_start: 0.6841 (m-90) cc_final: 0.6627 (m-90) REVERT: F 178 ASP cc_start: 0.7148 (t0) cc_final: 0.6805 (t70) REVERT: F 350 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7319 (mm-30) REVERT: F 405 ARG cc_start: 0.7440 (ttm110) cc_final: 0.6200 (mmt180) REVERT: F 431 CYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7967 (p) outliers start: 28 outliers final: 22 residues processed: 171 average time/residue: 0.0704 time to fit residues: 17.3490 Evaluate side-chains 167 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 417 MET Chi-restraints excluded: chain F residue 431 CYS Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 0.0370 chunk 69 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.232172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.194745 restraints weight = 95262.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.197008 restraints weight = 45877.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.195596 restraints weight = 36911.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.195969 restraints weight = 37977.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.195845 restraints weight = 34658.660| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7834 Z= 0.140 Angle : 0.701 13.409 10623 Z= 0.341 Chirality : 0.048 0.208 1187 Planarity : 0.005 0.065 1345 Dihedral : 8.577 95.524 1137 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.29 % Allowed : 26.31 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.28), residues: 931 helix: -0.28 (0.27), residues: 354 sheet: -1.55 (0.41), residues: 173 loop : -0.24 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 242 TYR 0.012 0.001 TYR D 168 PHE 0.021 0.002 PHE C 124 TRP 0.016 0.001 TRP E 337 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7832) covalent geometry : angle 0.70056 (10619) SS BOND : bond 0.00544 ( 2) SS BOND : angle 1.88300 ( 4) hydrogen bonds : bond 0.03333 ( 262) hydrogen bonds : angle 4.93546 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.63 seconds wall clock time: 26 minutes 4.37 seconds (1564.37 seconds total)