Starting phenix.real_space_refine on Sun Aug 24 14:43:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwq_35062/08_2025/8hwq_35062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwq_35062/08_2025/8hwq_35062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwq_35062/08_2025/8hwq_35062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwq_35062/08_2025/8hwq_35062.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwq_35062/08_2025/8hwq_35062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwq_35062/08_2025/8hwq_35062.cif" } resolution = 3.58 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= 0.006 sd= 0.063 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 13587 2.51 5 N 3430 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20783 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "A" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "B" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "D" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "E" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "G" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Time building chain proxies: 4.44, per 1000 atoms: 0.21 Number of scatterers: 20783 At special positions: 0 Unit cell: (125.33, 124.5, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3654 8.00 N 3430 7.00 C 13587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 672.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 14 sheets defined 63.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'F' and resid 2 through 11 removed outlier: 4.049A pdb=" N GLU F 9 " --> pdb=" O HIS F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 104 through 122 removed outlier: 4.181A pdb=" N LYS F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 132 through 148 Processing helix chain 'F' and resid 159 through 168 removed outlier: 3.634A pdb=" N LYS F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 177 through 183 removed outlier: 3.734A pdb=" N ALA F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.515A pdb=" N ALA F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 230 removed outlier: 3.635A pdb=" N THR F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 282 removed outlier: 4.073A pdb=" N VAL F 277 " --> pdb=" O SER F 273 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 296 removed outlier: 4.256A pdb=" N VAL F 286 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.701A pdb=" N MET F 307 " --> pdb=" O SER F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 317 removed outlier: 4.124A pdb=" N LEU F 313 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 removed outlier: 3.673A pdb=" N VAL F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 3.537A pdb=" N LEU F 349 " --> pdb=" O LEU F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 367 removed outlier: 4.025A pdb=" N VAL F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'A' and resid 3 through 11 removed outlier: 4.077A pdb=" N GLU A 9 " --> pdb=" O HIS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 104 through 122 removed outlier: 4.173A pdb=" N LYS A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 159 through 168 removed outlier: 3.503A pdb=" N LYS A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 177 through 183 removed outlier: 3.785A pdb=" N ALA A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.538A pdb=" N ALA A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.749A pdb=" N THR A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 removed outlier: 4.078A pdb=" N VAL A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 4.267A pdb=" N VAL A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.711A pdb=" N MET A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 4.136A pdb=" N LEU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.755A pdb=" N VAL A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.543A pdb=" N LEU A 349 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.049A pdb=" N VAL A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 3 through 11 removed outlier: 4.067A pdb=" N GLU B 9 " --> pdb=" O HIS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 104 through 122 removed outlier: 4.202A pdb=" N LYS B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.521A pdb=" N LYS B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.739A pdb=" N ALA B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.566A pdb=" N ALA B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.617A pdb=" N THR B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 282 removed outlier: 4.010A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 4.287A pdb=" N VAL B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.700A pdb=" N MET B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 removed outlier: 4.138A pdb=" N LEU B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.848A pdb=" N VAL B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.537A pdb=" N LEU B 349 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.049A pdb=" N VAL B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 3 through 11 removed outlier: 4.090A pdb=" N GLU C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 104 through 122 removed outlier: 4.158A pdb=" N LYS C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 159 through 168 removed outlier: 3.500A pdb=" N LYS C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.745A pdb=" N ALA C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.588A pdb=" N ALA C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.622A pdb=" N THR C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 282 removed outlier: 4.080A pdb=" N VAL C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.263A pdb=" N VAL C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.700A pdb=" N MET C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 removed outlier: 4.138A pdb=" N LEU C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.659A pdb=" N VAL C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.547A pdb=" N LEU C 349 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 367 removed outlier: 4.024A pdb=" N VAL C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 3 through 11 removed outlier: 4.059A pdb=" N GLU D 9 " --> pdb=" O HIS D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 104 through 122 removed outlier: 4.178A pdb=" N LYS D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 132 through 148 Processing helix chain 'D' and resid 159 through 168 removed outlier: 3.514A pdb=" N LYS D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.739A pdb=" N ALA D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.508A pdb=" N ALA D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.625A pdb=" N THR D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 282 removed outlier: 4.064A pdb=" N VAL D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 296 removed outlier: 4.260A pdb=" N VAL D 286 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.713A pdb=" N MET D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.077A pdb=" N LEU D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.659A pdb=" N VAL D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.567A pdb=" N LEU D 349 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 removed outlier: 4.054A pdb=" N VAL D 365 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP D 367 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 3 through 11 removed outlier: 4.091A pdb=" N GLU E 9 " --> pdb=" O HIS E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 104 through 122 removed outlier: 4.187A pdb=" N LYS E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Proline residue: E 111 - end of helix Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 132 through 148 Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 159 through 168 removed outlier: 3.576A pdb=" N LYS E 163 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.767A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.616A pdb=" N ALA E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.620A pdb=" N THR E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 216 " --> pdb=" O ARG E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 296 removed outlier: 4.136A pdb=" N VAL E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Proline residue: E 285 - end of helix removed outlier: 3.522A pdb=" N ILE E 288 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.699A pdb=" N MET E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 317 removed outlier: 4.140A pdb=" N LEU E 313 " --> pdb=" O PRO E 309 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.731A pdb=" N VAL E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 349 removed outlier: 3.543A pdb=" N LEU E 349 " --> pdb=" O LEU E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 367 removed outlier: 4.054A pdb=" N VAL E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP E 367 " --> pdb=" O ASP E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'G' and resid 3 through 11 removed outlier: 4.047A pdb=" N GLU G 9 " --> pdb=" O HIS G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 104 through 122 removed outlier: 4.189A pdb=" N LYS G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Proline residue: G 111 - end of helix Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 159 through 168 removed outlier: 3.597A pdb=" N LYS G 163 " --> pdb=" O GLN G 159 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 167 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 174 Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.791A pdb=" N ALA G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 201 removed outlier: 3.631A pdb=" N ALA G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 230 removed outlier: 3.608A pdb=" N THR G 208 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 282 removed outlier: 4.050A pdb=" N VAL G 277 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 296 removed outlier: 4.242A pdb=" N VAL G 286 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE G 288 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 308 removed outlier: 3.698A pdb=" N MET G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 317 removed outlier: 4.152A pdb=" N LEU G 313 " --> pdb=" O PRO G 309 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.670A pdb=" N VAL G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 349 removed outlier: 3.546A pdb=" N LEU G 349 " --> pdb=" O LEU G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 367 removed outlier: 4.051A pdb=" N VAL G 365 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP G 367 " --> pdb=" O ASP G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'F' and resid 89 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.398A pdb=" N ILE A 259 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N CYS A 242 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.581A pdb=" N LYS A 102 " --> pdb=" O HIS A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 66 removed outlier: 4.445A pdb=" N ILE B 259 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N CYS B 242 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.663A pdb=" N LYS B 102 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.610A pdb=" N LYS C 102 " --> pdb=" O HIS C 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.614A pdb=" N LYS D 102 " --> pdb=" O HIS D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 64 through 66 removed outlier: 4.487A pdb=" N ILE E 259 " --> pdb=" O CYS E 242 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N CYS E 242 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.636A pdb=" N LYS E 102 " --> pdb=" O HIS E 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'G' and resid 89 through 91 removed outlier: 3.669A pdb=" N LYS G 102 " --> pdb=" O HIS G 90 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2751 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: 2.66 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6411 1.34 - 1.46: 4543 1.46 - 1.58: 10151 1.58 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 21273 Sorted by residual: bond pdb=" C VAL B 284 " pdb=" N PRO B 285 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.24e-02 6.50e+03 1.39e+00 bond pdb=" CA ILE G 323 " pdb=" CB ILE G 323 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.31e-02 5.83e+03 1.39e+00 bond pdb=" C VAL A 284 " pdb=" N PRO A 285 " ideal model delta sigma weight residual 1.337 1.352 -0.014 1.24e-02 6.50e+03 1.36e+00 bond pdb=" CA ILE D 323 " pdb=" CB ILE D 323 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.05e-02 9.07e+03 1.36e+00 bond pdb=" CB ASP A 81 " pdb=" CG ASP A 81 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.35e+00 ... (remaining 21268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 28444 2.37 - 4.73: 331 4.73 - 7.10: 90 7.10 - 9.47: 7 9.47 - 11.84: 3 Bond angle restraints: 28875 Sorted by residual: angle pdb=" N VAL A 277 " pdb=" CA VAL A 277 " pdb=" C VAL A 277 " ideal model delta sigma weight residual 111.90 108.56 3.34 8.10e-01 1.52e+00 1.70e+01 angle pdb=" N VAL B 277 " pdb=" CA VAL B 277 " pdb=" C VAL B 277 " ideal model delta sigma weight residual 111.81 108.52 3.29 8.60e-01 1.35e+00 1.46e+01 angle pdb=" N VAL F 277 " pdb=" CA VAL F 277 " pdb=" C VAL F 277 " ideal model delta sigma weight residual 111.81 108.53 3.28 8.60e-01 1.35e+00 1.46e+01 angle pdb=" N VAL G 277 " pdb=" CA VAL G 277 " pdb=" C VAL G 277 " ideal model delta sigma weight residual 111.81 108.53 3.28 8.60e-01 1.35e+00 1.45e+01 angle pdb=" N VAL D 277 " pdb=" CA VAL D 277 " pdb=" C VAL D 277 " ideal model delta sigma weight residual 111.81 108.58 3.23 8.60e-01 1.35e+00 1.41e+01 ... (remaining 28870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 10233 14.98 - 29.96: 1845 29.96 - 44.94: 584 44.94 - 59.91: 160 59.91 - 74.89: 16 Dihedral angle restraints: 12838 sinusoidal: 5138 harmonic: 7700 Sorted by residual: dihedral pdb=" CA THR F 260 " pdb=" C THR F 260 " pdb=" N CYS F 261 " pdb=" CA CYS F 261 " ideal model delta harmonic sigma weight residual 180.00 149.56 30.44 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA THR C 260 " pdb=" C THR C 260 " pdb=" N CYS C 261 " pdb=" CA CYS C 261 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA THR G 260 " pdb=" C THR G 260 " pdb=" N CYS G 261 " pdb=" CA CYS G 261 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 12835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2089 0.031 - 0.062: 961 0.062 - 0.093: 257 0.093 - 0.124: 61 0.124 - 0.155: 20 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CB VAL E 234 " pdb=" CA VAL E 234 " pdb=" CG1 VAL E 234 " pdb=" CG2 VAL E 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CB VAL C 234 " pdb=" CA VAL C 234 " pdb=" CG1 VAL C 234 " pdb=" CG2 VAL C 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CB VAL A 234 " pdb=" CA VAL A 234 " pdb=" CG1 VAL A 234 " pdb=" CG2 VAL A 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 3385 not shown) Planarity restraints: 3535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 297 " 0.011 2.00e-02 2.50e+03 1.13e-02 3.19e+00 pdb=" CG TRP G 297 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP G 297 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP G 297 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 297 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 297 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 297 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 297 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 297 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 297 " 0.010 2.00e-02 2.50e+03 9.74e-03 2.37e+00 pdb=" CG TRP F 297 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP F 297 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP F 297 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 297 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 297 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 297 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 297 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 297 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP F 105 " -0.022 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO F 106 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO F 106 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 106 " -0.018 5.00e-02 4.00e+02 ... (remaining 3532 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4767 2.78 - 3.31: 19712 3.31 - 3.84: 32644 3.84 - 4.37: 36919 4.37 - 4.90: 63697 Nonbonded interactions: 157739 Sorted by model distance: nonbonded pdb=" OG SER C 113 " pdb=" OH TYR C 226 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 113 " pdb=" OH TYR A 226 " model vdw 2.257 3.040 nonbonded pdb=" OG SER E 113 " pdb=" OH TYR E 226 " model vdw 2.267 3.040 nonbonded pdb=" OG SER D 113 " pdb=" OH TYR D 226 " model vdw 2.270 3.040 nonbonded pdb=" OG SER F 113 " pdb=" OH TYR F 226 " model vdw 2.271 3.040 ... (remaining 157734 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.830 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.160 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 0.033 21273 Z= 0.131 Angle : 0.684 11.836 28875 Z= 0.362 Chirality : 0.038 0.155 3388 Planarity : 0.004 0.032 3535 Dihedral : 17.353 74.892 7798 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.35 % Favored : 93.37 % Rotamer: Outliers : 0.21 % Allowed : 33.02 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.29 (0.18), residues: 2534 helix: 0.59 (0.15), residues: 1414 sheet: None (None), residues: 0 loop : -2.91 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.012 0.001 TYR E 122 PHE 0.012 0.001 PHE G 40 TRP 0.030 0.001 TRP G 297 HIS 0.004 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00260 (21273) covalent geometry : angle 0.68366 (28875) hydrogen bonds : bond 0.15657 ( 926) hydrogen bonds : angle 5.88734 ( 2751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 297 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 200 GLN cc_start: 0.8272 (mt0) cc_final: 0.7962 (mp10) REVERT: F 318 MET cc_start: 0.5946 (tpp) cc_final: 0.5714 (mmt) REVERT: F 326 LEU cc_start: 0.8881 (tp) cc_final: 0.8498 (mm) REVERT: F 327 ASN cc_start: 0.8192 (m110) cc_final: 0.7982 (m-40) REVERT: A 10 TYR cc_start: 0.7881 (m-80) cc_final: 0.7573 (m-80) REVERT: A 12 LEU cc_start: 0.8051 (tp) cc_final: 0.7812 (tp) REVERT: B 318 MET cc_start: 0.6450 (tpp) cc_final: 0.5947 (mmt) REVERT: C 200 GLN cc_start: 0.7944 (mt0) cc_final: 0.7133 (mp10) REVERT: E 129 GLN cc_start: 0.8198 (mm110) cc_final: 0.7768 (mm110) REVERT: E 161 MET cc_start: 0.3409 (mmm) cc_final: 0.3111 (mmt) REVERT: G 10 TYR cc_start: 0.7644 (m-80) cc_final: 0.7216 (m-80) outliers start: 5 outliers final: 5 residues processed: 300 average time/residue: 0.1096 time to fit residues: 56.3654 Evaluate side-chains 273 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 268 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain G residue 166 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN E 324 ASN E 327 ASN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.212027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.148982 restraints weight = 30090.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147695 restraints weight = 23825.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148488 restraints weight = 17992.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149029 restraints weight = 16129.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.149092 restraints weight = 13436.948| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21273 Z= 0.227 Angle : 0.699 10.461 28875 Z= 0.345 Chirality : 0.042 0.157 3388 Planarity : 0.004 0.037 3535 Dihedral : 5.029 55.955 2811 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.11 % Allowed : 30.48 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: -1.65 (0.17), residues: 2534 helix: 0.09 (0.14), residues: 1533 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 212 TYR 0.018 0.002 TYR F 280 PHE 0.020 0.002 PHE B 269 TRP 0.013 0.002 TRP G 297 HIS 0.008 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00526 (21273) covalent geometry : angle 0.69936 (28875) hydrogen bonds : bond 0.04238 ( 926) hydrogen bonds : angle 4.61019 ( 2751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 298 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7751 (pm20) cc_final: 0.7443 (pm20) REVERT: F 126 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7904 (tp) REVERT: F 200 GLN cc_start: 0.8215 (mt0) cc_final: 0.8003 (mp10) REVERT: F 326 LEU cc_start: 0.8830 (tp) cc_final: 0.8448 (mm) REVERT: F 327 ASN cc_start: 0.8359 (m-40) cc_final: 0.8107 (m110) REVERT: A 10 TYR cc_start: 0.7964 (m-80) cc_final: 0.7623 (m-80) REVERT: A 31 GLU cc_start: 0.7679 (pm20) cc_final: 0.7388 (pm20) REVERT: B 31 GLU cc_start: 0.7623 (pm20) cc_final: 0.7311 (pm20) REVERT: C 324 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6941 (m110) REVERT: C 327 ASN cc_start: 0.8434 (t0) cc_final: 0.8056 (m110) REVERT: D 31 GLU cc_start: 0.7438 (pm20) cc_final: 0.7136 (pm20) REVERT: E 31 GLU cc_start: 0.7599 (pm20) cc_final: 0.7260 (pm20) REVERT: E 161 MET cc_start: 0.3703 (mmm) cc_final: 0.3383 (mmt) REVERT: G 10 TYR cc_start: 0.7696 (m-80) cc_final: 0.7238 (m-80) REVERT: G 31 GLU cc_start: 0.7663 (pm20) cc_final: 0.7327 (pm20) REVERT: G 161 MET cc_start: 0.3667 (mmm) cc_final: 0.3352 (mmt) outliers start: 97 outliers final: 46 residues processed: 366 average time/residue: 0.0977 time to fit residues: 61.9568 Evaluate side-chains 339 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 25 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 chunk 181 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 211 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN D 327 ASN E 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.214420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152876 restraints weight = 30075.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.150628 restraints weight = 26259.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151592 restraints weight = 20388.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152064 restraints weight = 17502.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152390 restraints weight = 14635.422| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21273 Z= 0.144 Angle : 0.621 9.880 28875 Z= 0.300 Chirality : 0.039 0.146 3388 Planarity : 0.004 0.036 3535 Dihedral : 4.431 31.941 2802 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.92 % Allowed : 32.43 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.56 (0.17), residues: 2534 helix: 0.16 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.94 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 201 TYR 0.013 0.001 TYR E 280 PHE 0.014 0.001 PHE F 240 TRP 0.008 0.001 TRP F 297 HIS 0.004 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00333 (21273) covalent geometry : angle 0.62108 (28875) hydrogen bonds : bond 0.03410 ( 926) hydrogen bonds : angle 4.30679 ( 2751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7688 (pm20) cc_final: 0.7368 (pm20) REVERT: F 37 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7582 (tp) REVERT: F 86 ASP cc_start: 0.8342 (m-30) cc_final: 0.8066 (m-30) REVERT: F 326 LEU cc_start: 0.8786 (tp) cc_final: 0.8430 (mm) REVERT: F 327 ASN cc_start: 0.8248 (m-40) cc_final: 0.7950 (m110) REVERT: A 10 TYR cc_start: 0.7941 (m-80) cc_final: 0.7569 (m-80) REVERT: A 31 GLU cc_start: 0.7637 (pm20) cc_final: 0.7308 (pm20) REVERT: A 37 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7534 (tp) REVERT: B 31 GLU cc_start: 0.7614 (pm20) cc_final: 0.7253 (pm20) REVERT: C 327 ASN cc_start: 0.8301 (t0) cc_final: 0.8029 (m-40) REVERT: D 31 GLU cc_start: 0.7454 (pm20) cc_final: 0.7138 (pm20) REVERT: D 37 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7665 (tp) REVERT: D 318 MET cc_start: 0.4928 (tpt) cc_final: 0.4511 (mmt) REVERT: E 31 GLU cc_start: 0.7553 (pm20) cc_final: 0.7192 (pm20) REVERT: G 10 TYR cc_start: 0.7803 (m-80) cc_final: 0.7366 (m-80) REVERT: G 31 GLU cc_start: 0.7515 (pm20) cc_final: 0.7167 (pm20) REVERT: G 86 ASP cc_start: 0.8296 (m-30) cc_final: 0.7971 (m-30) outliers start: 69 outliers final: 37 residues processed: 361 average time/residue: 0.1019 time to fit residues: 63.6369 Evaluate side-chains 330 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 41 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN E 324 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 HIS ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.212982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150498 restraints weight = 29851.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.149023 restraints weight = 23324.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149835 restraints weight = 17383.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150486 restraints weight = 15428.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150682 restraints weight = 13060.118| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21273 Z= 0.151 Angle : 0.629 8.941 28875 Z= 0.304 Chirality : 0.040 0.343 3388 Planarity : 0.004 0.037 3535 Dihedral : 4.371 33.102 2800 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.69 % Allowed : 31.88 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.48 (0.17), residues: 2534 helix: 0.22 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.87 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 29 TYR 0.013 0.001 TYR E 280 PHE 0.014 0.001 PHE A 240 TRP 0.024 0.001 TRP A 345 HIS 0.004 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00351 (21273) covalent geometry : angle 0.62922 (28875) hydrogen bonds : bond 0.03232 ( 926) hydrogen bonds : angle 4.19792 ( 2751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 296 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7749 (pm20) cc_final: 0.7430 (pm20) REVERT: F 37 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7621 (tp) REVERT: F 86 ASP cc_start: 0.8337 (m-30) cc_final: 0.8085 (m-30) REVERT: F 326 LEU cc_start: 0.8767 (tp) cc_final: 0.8406 (mm) REVERT: F 327 ASN cc_start: 0.8273 (m-40) cc_final: 0.7980 (m110) REVERT: A 10 TYR cc_start: 0.7924 (m-80) cc_final: 0.7491 (m-80) REVERT: A 31 GLU cc_start: 0.7581 (pm20) cc_final: 0.7272 (pm20) REVERT: A 35 ASP cc_start: 0.6949 (m-30) cc_final: 0.6735 (t0) REVERT: A 37 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7575 (tp) REVERT: B 31 GLU cc_start: 0.7682 (pm20) cc_final: 0.7333 (pm20) REVERT: D 31 GLU cc_start: 0.7521 (pm20) cc_final: 0.7218 (pm20) REVERT: D 37 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7633 (tp) REVERT: D 283 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7074 (mp) REVERT: D 318 MET cc_start: 0.4882 (tpt) cc_final: 0.4437 (mmt) REVERT: E 31 GLU cc_start: 0.7679 (pm20) cc_final: 0.7328 (pm20) REVERT: E 283 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7188 (mp) REVERT: G 10 TYR cc_start: 0.7807 (m-80) cc_final: 0.7372 (m-80) REVERT: G 31 GLU cc_start: 0.7584 (pm20) cc_final: 0.7254 (pm20) REVERT: G 86 ASP cc_start: 0.8306 (m-30) cc_final: 0.8030 (m-30) outliers start: 87 outliers final: 59 residues processed: 368 average time/residue: 0.0969 time to fit residues: 61.3495 Evaluate side-chains 352 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 15 optimal weight: 30.0000 chunk 187 optimal weight: 0.7980 chunk 237 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 HIS G 336 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.214849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151842 restraints weight = 29814.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147245 restraints weight = 23606.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.150024 restraints weight = 19024.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150146 restraints weight = 15678.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150551 restraints weight = 13642.536| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21273 Z= 0.119 Angle : 0.603 8.182 28875 Z= 0.289 Chirality : 0.039 0.161 3388 Planarity : 0.004 0.036 3535 Dihedral : 4.226 29.987 2800 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.97 % Allowed : 33.11 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.17), residues: 2534 helix: 0.31 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.87 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.012 0.001 TYR E 280 PHE 0.013 0.001 PHE A 240 TRP 0.021 0.001 TRP G 345 HIS 0.005 0.001 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00273 (21273) covalent geometry : angle 0.60312 (28875) hydrogen bonds : bond 0.02984 ( 926) hydrogen bonds : angle 4.07669 ( 2751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 299 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7701 (pm20) cc_final: 0.7359 (pm20) REVERT: F 37 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7548 (tp) REVERT: F 86 ASP cc_start: 0.8230 (m-30) cc_final: 0.7929 (m-30) REVERT: F 318 MET cc_start: 0.5858 (tpp) cc_final: 0.5445 (tpp) REVERT: F 326 LEU cc_start: 0.8892 (tp) cc_final: 0.8425 (mm) REVERT: F 327 ASN cc_start: 0.8370 (m-40) cc_final: 0.8024 (m110) REVERT: A 10 TYR cc_start: 0.7921 (m-80) cc_final: 0.7463 (m-80) REVERT: A 31 GLU cc_start: 0.7594 (pm20) cc_final: 0.7262 (pm20) REVERT: A 37 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7532 (tp) REVERT: B 10 TYR cc_start: 0.7743 (m-80) cc_final: 0.7474 (m-80) REVERT: B 31 GLU cc_start: 0.7623 (pm20) cc_final: 0.7257 (pm20) REVERT: C 31 GLU cc_start: 0.7552 (pm20) cc_final: 0.7220 (pm20) REVERT: C 86 ASP cc_start: 0.8189 (m-30) cc_final: 0.7669 (m-30) REVERT: D 9 GLU cc_start: 0.8195 (mp0) cc_final: 0.7706 (mp0) REVERT: D 31 GLU cc_start: 0.7505 (pm20) cc_final: 0.7178 (pm20) REVERT: D 147 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7258 (pp) REVERT: D 283 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7037 (mp) REVERT: D 318 MET cc_start: 0.5044 (tpt) cc_final: 0.4528 (mmt) REVERT: E 31 GLU cc_start: 0.7655 (pm20) cc_final: 0.7301 (pm20) REVERT: E 139 ASP cc_start: 0.7752 (m-30) cc_final: 0.7550 (t0) REVERT: E 283 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7047 (mp) REVERT: G 10 TYR cc_start: 0.7810 (m-80) cc_final: 0.7458 (m-80) REVERT: G 31 GLU cc_start: 0.7548 (pm20) cc_final: 0.7201 (pm20) outliers start: 70 outliers final: 48 residues processed: 360 average time/residue: 0.0975 time to fit residues: 60.0247 Evaluate side-chains 339 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 286 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 229 HIS Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 229 HIS Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 179 optimal weight: 30.0000 chunk 217 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 336 ASN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.213782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.152609 restraints weight = 29624.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.151150 restraints weight = 24489.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151998 restraints weight = 18956.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152482 restraints weight = 16255.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152636 restraints weight = 13642.612| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21273 Z= 0.142 Angle : 0.616 7.768 28875 Z= 0.297 Chirality : 0.039 0.149 3388 Planarity : 0.004 0.036 3535 Dihedral : 4.249 31.147 2800 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.43 % Allowed : 33.70 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.33 (0.17), residues: 2534 helix: 0.39 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.91 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 29 TYR 0.015 0.001 TYR E 280 PHE 0.014 0.001 PHE A 240 TRP 0.020 0.001 TRP G 345 HIS 0.004 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00332 (21273) covalent geometry : angle 0.61647 (28875) hydrogen bonds : bond 0.03018 ( 926) hydrogen bonds : angle 4.02905 ( 2751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 291 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: F 10 TYR cc_start: 0.8027 (m-80) cc_final: 0.7682 (m-80) REVERT: F 31 GLU cc_start: 0.7780 (pm20) cc_final: 0.7482 (pm20) REVERT: F 37 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7607 (tp) REVERT: F 318 MET cc_start: 0.6003 (tpp) cc_final: 0.5562 (tpp) REVERT: F 326 LEU cc_start: 0.8717 (tp) cc_final: 0.8384 (mm) REVERT: F 327 ASN cc_start: 0.8334 (m-40) cc_final: 0.8027 (m110) REVERT: A 10 TYR cc_start: 0.7963 (m-80) cc_final: 0.7498 (m-80) REVERT: A 31 GLU cc_start: 0.7692 (pm20) cc_final: 0.7408 (pm20) REVERT: A 37 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7565 (tp) REVERT: A 147 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7369 (pp) REVERT: B 10 TYR cc_start: 0.7918 (m-80) cc_final: 0.7655 (m-80) REVERT: B 31 GLU cc_start: 0.7757 (pm20) cc_final: 0.7427 (pm20) REVERT: B 37 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7749 (tp) REVERT: B 147 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7405 (pp) REVERT: C 31 GLU cc_start: 0.7737 (pm20) cc_final: 0.7436 (pm20) REVERT: D 31 GLU cc_start: 0.7601 (pm20) cc_final: 0.7333 (pm20) REVERT: D 37 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7686 (tp) REVERT: D 147 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7437 (pp) REVERT: D 283 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7147 (mp) REVERT: E 37 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7644 (tp) REVERT: E 147 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7363 (pp) REVERT: E 161 MET cc_start: 0.2083 (mmt) cc_final: 0.1380 (mmm) REVERT: E 283 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.6961 (mp) REVERT: G 10 TYR cc_start: 0.7909 (m-80) cc_final: 0.7401 (m-80) REVERT: G 31 GLU cc_start: 0.7706 (pm20) cc_final: 0.7373 (pm20) outliers start: 81 outliers final: 59 residues processed: 358 average time/residue: 0.1015 time to fit residues: 62.5191 Evaluate side-chains 354 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 284 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 324 ASN Chi-restraints excluded: chain G residue 336 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 87 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 179 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 200 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.205834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143569 restraints weight = 30094.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138983 restraints weight = 23178.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140319 restraints weight = 20472.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141010 restraints weight = 16246.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141136 restraints weight = 14657.144| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 21273 Z= 0.325 Angle : 0.809 8.638 28875 Z= 0.401 Chirality : 0.047 0.243 3388 Planarity : 0.005 0.060 3535 Dihedral : 5.041 39.095 2800 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.45 % Allowed : 33.15 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -1.90 (0.17), residues: 2534 helix: -0.11 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -3.05 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 212 TYR 0.034 0.003 TYR G 226 PHE 0.023 0.002 PHE B 269 TRP 0.017 0.002 TRP G 345 HIS 0.006 0.001 HIS F 91 Details of bonding type rmsd covalent geometry : bond 0.00749 (21273) covalent geometry : angle 0.80889 (28875) hydrogen bonds : bond 0.04188 ( 926) hydrogen bonds : angle 4.53422 ( 2751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 303 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: F 10 TYR cc_start: 0.8108 (m-80) cc_final: 0.7723 (m-80) REVERT: F 30 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7823 (mt) REVERT: F 31 GLU cc_start: 0.7913 (pm20) cc_final: 0.7610 (pm20) REVERT: F 37 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7660 (tp) REVERT: F 73 SER cc_start: 0.8600 (t) cc_final: 0.8334 (p) REVERT: F 318 MET cc_start: 0.5975 (tpp) cc_final: 0.5564 (tpp) REVERT: F 326 LEU cc_start: 0.8986 (tp) cc_final: 0.8540 (mm) REVERT: F 327 ASN cc_start: 0.8445 (m-40) cc_final: 0.8213 (m110) REVERT: A 9 GLU cc_start: 0.8179 (mp0) cc_final: 0.7964 (mp0) REVERT: A 31 GLU cc_start: 0.7913 (pm20) cc_final: 0.7589 (pm20) REVERT: A 37 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7735 (tp) REVERT: A 75 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7348 (mmt90) REVERT: A 147 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7313 (pp) REVERT: A 280 TYR cc_start: 0.8707 (m-80) cc_final: 0.8504 (m-80) REVERT: B 10 TYR cc_start: 0.7932 (m-80) cc_final: 0.7682 (m-80) REVERT: B 31 GLU cc_start: 0.7913 (pm20) cc_final: 0.7572 (pm20) REVERT: B 37 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7654 (tp) REVERT: B 280 TYR cc_start: 0.8652 (m-80) cc_final: 0.8358 (m-80) REVERT: C 210 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7729 (mp) REVERT: C 327 ASN cc_start: 0.8354 (t0) cc_final: 0.8135 (m110) REVERT: D 37 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7816 (tp) REVERT: D 80 VAL cc_start: 0.7402 (OUTLIER) cc_final: 0.7087 (t) REVERT: D 147 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7387 (pp) REVERT: E 37 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7670 (tp) REVERT: E 147 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7276 (pp) REVERT: E 283 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6695 (mp) REVERT: G 73 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8497 (p) outliers start: 105 outliers final: 64 residues processed: 386 average time/residue: 0.0969 time to fit residues: 64.2181 Evaluate side-chains 372 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 295 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 48 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 86 optimal weight: 0.0030 chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS F 200 GLN A 5 HIS ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN D 5 HIS D 213 ASN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 HIS ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 HIS ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 ASN G 336 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.210055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.147669 restraints weight = 29901.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145062 restraints weight = 23117.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146699 restraints weight = 19425.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147119 restraints weight = 15855.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147282 restraints weight = 13892.494| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21273 Z= 0.162 Angle : 0.662 7.886 28875 Z= 0.321 Chirality : 0.041 0.266 3388 Planarity : 0.004 0.058 3535 Dihedral : 4.612 33.525 2800 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.52 % Allowed : 34.46 % Favored : 62.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -1.70 (0.17), residues: 2534 helix: 0.15 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -3.05 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 212 TYR 0.025 0.002 TYR G 122 PHE 0.016 0.001 PHE F 240 TRP 0.018 0.001 TRP G 345 HIS 0.004 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00385 (21273) covalent geometry : angle 0.66153 (28875) hydrogen bonds : bond 0.03245 ( 926) hydrogen bonds : angle 4.22910 ( 2751) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 309 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7835 (pm20) cc_final: 0.7562 (pm20) REVERT: F 37 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7567 (tp) REVERT: F 283 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6837 (mp) REVERT: F 318 MET cc_start: 0.5951 (tpp) cc_final: 0.5410 (tpp) REVERT: F 326 LEU cc_start: 0.8890 (tp) cc_final: 0.8460 (mm) REVERT: F 327 ASN cc_start: 0.8374 (m-40) cc_final: 0.8129 (m110) REVERT: A 31 GLU cc_start: 0.7818 (pm20) cc_final: 0.7545 (pm20) REVERT: A 37 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7565 (tp) REVERT: A 75 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7228 (mmt90) REVERT: A 147 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7317 (pp) REVERT: A 280 TYR cc_start: 0.8514 (m-80) cc_final: 0.8301 (m-80) REVERT: B 10 TYR cc_start: 0.7922 (m-80) cc_final: 0.7547 (m-80) REVERT: B 31 GLU cc_start: 0.7740 (pm20) cc_final: 0.7417 (pm20) REVERT: B 37 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7578 (tp) REVERT: B 147 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7402 (pp) REVERT: C 30 LEU cc_start: 0.7883 (mm) cc_final: 0.7656 (mm) REVERT: C 31 GLU cc_start: 0.7824 (pm20) cc_final: 0.7526 (pm20) REVERT: C 210 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7621 (mp) REVERT: D 31 GLU cc_start: 0.7768 (pm20) cc_final: 0.7487 (pm20) REVERT: D 37 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7598 (tp) REVERT: D 147 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7459 (pp) REVERT: D 283 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.6830 (mp) REVERT: E 37 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7514 (tp) REVERT: E 147 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7256 (pp) REVERT: E 283 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6730 (mp) REVERT: G 30 LEU cc_start: 0.7884 (mm) cc_final: 0.7615 (mm) REVERT: G 31 GLU cc_start: 0.7832 (pm20) cc_final: 0.7503 (pm20) REVERT: G 283 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.6752 (mp) outliers start: 83 outliers final: 58 residues processed: 372 average time/residue: 0.1008 time to fit residues: 64.5128 Evaluate side-chains 371 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 299 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 324 ASN Chi-restraints excluded: chain G residue 336 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 236 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS F 200 GLN A 5 HIS A 336 ASN B 5 HIS ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 HIS C 327 ASN D 5 HIS D 152 ASN D 336 ASN E 5 HIS E 152 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 HIS G 324 ASN G 336 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.212735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151608 restraints weight = 29611.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149808 restraints weight = 22702.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151004 restraints weight = 18114.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151445 restraints weight = 15331.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151500 restraints weight = 13174.499| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21273 Z= 0.118 Angle : 0.631 8.686 28875 Z= 0.304 Chirality : 0.040 0.312 3388 Planarity : 0.004 0.038 3535 Dihedral : 4.355 30.134 2800 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.63 % Allowed : 35.44 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.46 (0.17), residues: 2534 helix: 0.36 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -2.99 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 212 TYR 0.026 0.001 TYR E 151 PHE 0.015 0.001 PHE C 240 TRP 0.027 0.001 TRP C 297 HIS 0.003 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00270 (21273) covalent geometry : angle 0.63104 (28875) hydrogen bonds : bond 0.02922 ( 926) hydrogen bonds : angle 4.05327 ( 2751) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 297 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7682 (pm20) cc_final: 0.7424 (pm20) REVERT: F 37 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7510 (tp) REVERT: F 283 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6758 (mp) REVERT: F 318 MET cc_start: 0.5963 (tpp) cc_final: 0.5414 (tpp) REVERT: F 326 LEU cc_start: 0.8827 (tp) cc_final: 0.8424 (mm) REVERT: F 327 ASN cc_start: 0.8298 (m-40) cc_final: 0.8094 (m110) REVERT: A 31 GLU cc_start: 0.7775 (pm20) cc_final: 0.7495 (pm20) REVERT: A 37 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7453 (tp) REVERT: A 75 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.7202 (mmt90) REVERT: A 147 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7383 (pp) REVERT: B 10 TYR cc_start: 0.7830 (m-80) cc_final: 0.7533 (m-80) REVERT: B 31 GLU cc_start: 0.7727 (pm20) cc_final: 0.7426 (pm20) REVERT: B 37 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7615 (tp) REVERT: B 147 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7442 (pp) REVERT: C 31 GLU cc_start: 0.7746 (pm20) cc_final: 0.7468 (pm20) REVERT: C 210 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7549 (mp) REVERT: D 31 GLU cc_start: 0.7673 (pm20) cc_final: 0.7416 (pm20) REVERT: D 37 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7611 (tp) REVERT: D 147 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7395 (pp) REVERT: D 283 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.6820 (mp) REVERT: E 37 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7518 (tp) REVERT: E 147 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7210 (pp) REVERT: E 283 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6720 (mp) REVERT: G 31 GLU cc_start: 0.7750 (pm20) cc_final: 0.7455 (pm20) REVERT: G 283 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6704 (mp) outliers start: 62 outliers final: 42 residues processed: 347 average time/residue: 0.1012 time to fit residues: 60.1749 Evaluate side-chains 343 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 324 ASN Chi-restraints excluded: chain G residue 336 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 185 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 232 optimal weight: 40.0000 chunk 251 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 215 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 219 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS F 200 GLN A 5 HIS A 152 ASN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 HIS B 152 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 HIS ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 HIS ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 HIS ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 HIS G 166 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.207760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145137 restraints weight = 29970.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142425 restraints weight = 23362.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142912 restraints weight = 20188.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143820 restraints weight = 15830.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.144025 restraints weight = 14130.647| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21273 Z= 0.240 Angle : 0.717 8.554 28875 Z= 0.352 Chirality : 0.044 0.256 3388 Planarity : 0.004 0.047 3535 Dihedral : 4.659 34.995 2800 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.63 % Allowed : 35.40 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -1.65 (0.17), residues: 2534 helix: 0.12 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.98 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 334 TYR 0.027 0.002 TYR A 151 PHE 0.017 0.002 PHE A 240 TRP 0.016 0.001 TRP C 297 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00562 (21273) covalent geometry : angle 0.71748 (28875) hydrogen bonds : bond 0.03481 ( 926) hydrogen bonds : angle 4.21046 ( 2751) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: F 10 TYR cc_start: 0.8025 (m-80) cc_final: 0.7639 (m-80) REVERT: F 30 LEU cc_start: 0.7811 (mm) cc_final: 0.7567 (mm) REVERT: F 31 GLU cc_start: 0.7741 (pm20) cc_final: 0.7471 (pm20) REVERT: F 37 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7695 (tp) REVERT: F 73 SER cc_start: 0.8587 (t) cc_final: 0.8317 (p) REVERT: F 283 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.6740 (mp) REVERT: F 318 MET cc_start: 0.5936 (tpp) cc_final: 0.5371 (tpp) REVERT: F 326 LEU cc_start: 0.8857 (tp) cc_final: 0.8449 (mm) REVERT: F 327 ASN cc_start: 0.8395 (m-40) cc_final: 0.8195 (m110) REVERT: A 37 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7668 (tp) REVERT: A 75 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7389 (mmt90) REVERT: A 139 ASP cc_start: 0.8134 (m-30) cc_final: 0.7879 (t0) REVERT: A 147 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7380 (pp) REVERT: A 280 TYR cc_start: 0.8574 (m-80) cc_final: 0.8354 (m-80) REVERT: B 10 TYR cc_start: 0.7906 (m-80) cc_final: 0.7586 (m-80) REVERT: B 31 GLU cc_start: 0.7823 (pm20) cc_final: 0.7495 (pm20) REVERT: B 37 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7643 (tp) REVERT: B 147 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7477 (pp) REVERT: C 210 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7611 (mp) REVERT: D 31 GLU cc_start: 0.7868 (pm20) cc_final: 0.7574 (pm20) REVERT: D 37 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7730 (tp) REVERT: D 80 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7171 (t) REVERT: D 147 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7434 (pp) REVERT: D 283 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.6872 (mp) REVERT: E 37 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7564 (tp) REVERT: E 147 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7221 (pp) REVERT: E 161 MET cc_start: 0.2161 (mmt) cc_final: 0.0835 (tpt) REVERT: E 283 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.6653 (mp) REVERT: G 30 LEU cc_start: 0.7904 (mm) cc_final: 0.7643 (mm) REVERT: G 31 GLU cc_start: 0.7888 (pm20) cc_final: 0.7571 (pm20) outliers start: 62 outliers final: 45 residues processed: 345 average time/residue: 0.1003 time to fit residues: 59.5265 Evaluate side-chains 352 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 80 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 196 optimal weight: 0.2980 chunk 94 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS F 200 GLN A 5 HIS A 336 ASN B 5 HIS B 160 HIS ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 HIS D 5 HIS D 336 ASN E 5 HIS E 213 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 HIS G 336 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.213583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.149610 restraints weight = 29139.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.148036 restraints weight = 21234.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149517 restraints weight = 14655.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.150301 restraints weight = 12404.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150377 restraints weight = 11177.109| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21273 Z= 0.117 Angle : 0.639 8.110 28875 Z= 0.307 Chirality : 0.040 0.261 3388 Planarity : 0.004 0.048 3535 Dihedral : 4.289 27.262 2800 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.25 % Allowed : 35.65 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.17), residues: 2534 helix: 0.37 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.92 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 212 TYR 0.027 0.001 TYR F 151 PHE 0.014 0.001 PHE C 240 TRP 0.018 0.001 TRP G 345 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00265 (21273) covalent geometry : angle 0.63877 (28875) hydrogen bonds : bond 0.02840 ( 926) hydrogen bonds : angle 4.02790 ( 2751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.44 seconds wall clock time: 51 minutes 3.27 seconds (3063.27 seconds total)