Starting phenix.real_space_refine on Tue May 20 23:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwq_35062/05_2025/8hwq_35062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwq_35062/05_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_35062/05_2025/8hwq_35062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwq_35062/05_2025/8hwq_35062.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwq_35062/05_2025/8hwq_35062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwq_35062/05_2025/8hwq_35062.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.76, per 1000 atoms: 0.57 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: 4.93 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.14 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: 5.91 Time building geometry restraints manager: 5.80 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: 0.03 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.500 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (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 TRP 0.030 0.001 TRP G 297 HIS 0.004 0.001 HIS A 231 PHE 0.012 0.001 PHE G 40 TYR 0.012 0.001 TYR E 122 ARG 0.003 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.15657 ( 926) hydrogen bonds : angle 5.88734 ( 2751) covalent geometry : bond 0.00260 (21273) covalent geometry : angle 0.68366 (28875) *********************** 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 : 2.073 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: 0.2497 time to fit residues: 126.6636 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 : 2.120 ------------------------------------------------------------------------------- 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 212 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 105 optimal weight: 0.0970 chunk 65 optimal weight: 0.3980 chunk 128 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN E 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.219064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.156754 restraints weight = 30030.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155012 restraints weight = 22111.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156855 restraints weight = 17264.024| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.0904 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= 0.119 Angle : 0.617 11.455 28875 Z= 0.298 Chirality : 0.038 0.136 3388 Planarity : 0.004 0.035 3535 Dihedral : 4.642 56.638 2811 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.42 % Allowed : 30.39 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2534 helix: 0.46 (0.14), residues: 1477 sheet: None (None), residues: 0 loop : -2.96 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 297 HIS 0.005 0.001 HIS A 231 PHE 0.011 0.001 PHE F 240 TYR 0.009 0.001 TYR E 280 ARG 0.003 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 926) hydrogen bonds : angle 4.42398 ( 2751) covalent geometry : bond 0.00267 (21273) covalent geometry : angle 0.61733 (28875) *********************** 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 372 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7526 (pm20) cc_final: 0.7207 (pm20) REVERT: F 200 GLN cc_start: 0.8302 (mt0) cc_final: 0.7963 (mp10) REVERT: F 326 LEU cc_start: 0.8841 (tp) cc_final: 0.8461 (mm) REVERT: F 327 ASN cc_start: 0.8292 (m110) cc_final: 0.7957 (m110) REVERT: A 10 TYR cc_start: 0.7891 (m-80) cc_final: 0.7480 (m-80) REVERT: A 31 GLU cc_start: 0.7530 (pm20) cc_final: 0.7208 (pm20) REVERT: B 31 GLU cc_start: 0.7365 (pm20) cc_final: 0.7025 (pm20) REVERT: C 129 GLN cc_start: 0.8229 (mm110) cc_final: 0.7955 (mm110) REVERT: C 324 ASN cc_start: 0.7169 (m-40) cc_final: 0.6941 (m110) REVERT: C 327 ASN cc_start: 0.8395 (t0) cc_final: 0.8008 (m-40) REVERT: D 31 GLU cc_start: 0.7305 (pm20) cc_final: 0.6970 (pm20) REVERT: D 147 LEU cc_start: 0.7438 (pp) cc_final: 0.7232 (pp) REVERT: D 327 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8105 (m110) REVERT: E 31 GLU cc_start: 0.7326 (pm20) cc_final: 0.6985 (pm20) REVERT: E 129 GLN cc_start: 0.8169 (mm110) cc_final: 0.7800 (mm110) REVERT: E 161 MET cc_start: 0.3462 (mmm) cc_final: 0.3165 (mmt) REVERT: G 10 TYR cc_start: 0.7605 (m-80) cc_final: 0.7117 (m-80) REVERT: G 31 GLU cc_start: 0.7508 (pm20) cc_final: 0.7147 (pm20) REVERT: G 86 ASP cc_start: 0.8234 (m-30) cc_final: 0.7810 (m-30) REVERT: G 161 MET cc_start: 0.3588 (mmm) cc_final: 0.3263 (mmt) outliers start: 57 outliers final: 30 residues processed: 358 average time/residue: 0.2452 time to fit residues: 149.2431 Evaluate side-chains 333 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 302 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 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 133 VAL Chi-restraints excluded: chain A residue 206 VAL 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 C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 294 LEU 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 255 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 276 SER 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 133 VAL 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 96 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 226 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 40 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.219460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166142 restraints weight = 29544.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160106 restraints weight = 24271.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163244 restraints weight = 24116.480| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21273 Z= 0.111 Angle : 0.600 11.661 28875 Z= 0.287 Chirality : 0.039 0.278 3388 Planarity : 0.003 0.035 3535 Dihedral : 4.050 26.684 2800 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.65 % Allowed : 31.20 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2534 helix: 0.47 (0.15), residues: 1463 sheet: None (None), residues: 0 loop : -2.88 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 345 HIS 0.004 0.001 HIS A 231 PHE 0.009 0.001 PHE A 240 TYR 0.008 0.001 TYR E 280 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 926) hydrogen bonds : angle 4.16279 ( 2751) covalent geometry : bond 0.00239 (21273) covalent geometry : angle 0.59956 (28875) *********************** 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 352 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7499 (pm20) cc_final: 0.7147 (pm20) REVERT: F 237 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7816 (tp40) REVERT: F 327 ASN cc_start: 0.8370 (m110) cc_final: 0.8003 (m110) REVERT: A 10 TYR cc_start: 0.7888 (m-80) cc_final: 0.7521 (m-80) REVERT: A 31 GLU cc_start: 0.7426 (pm20) cc_final: 0.7097 (pm20) REVERT: B 10 TYR cc_start: 0.7788 (m-80) cc_final: 0.7516 (m-80) REVERT: B 31 GLU cc_start: 0.7352 (pm20) cc_final: 0.6987 (pm20) REVERT: C 129 GLN cc_start: 0.8187 (mm110) cc_final: 0.7961 (mm110) REVERT: D 31 GLU cc_start: 0.7316 (pm20) cc_final: 0.6955 (pm20) REVERT: D 318 MET cc_start: 0.4807 (tpt) cc_final: 0.4353 (mmt) REVERT: E 31 GLU cc_start: 0.7308 (pm20) cc_final: 0.6939 (pm20) REVERT: E 129 GLN cc_start: 0.8156 (mm110) cc_final: 0.7819 (mm110) REVERT: E 161 MET cc_start: 0.3612 (mmm) cc_final: 0.3265 (mmt) REVERT: E 327 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7619 (m-40) REVERT: G 10 TYR cc_start: 0.7685 (m-80) cc_final: 0.7271 (m-80) REVERT: G 31 GLU cc_start: 0.7471 (pm20) cc_final: 0.7079 (pm20) REVERT: G 86 ASP cc_start: 0.8508 (m-30) cc_final: 0.8053 (m-30) REVERT: G 161 MET cc_start: 0.3607 (mmm) cc_final: 0.3309 (mmt) REVERT: G 324 ASN cc_start: 0.7626 (t0) cc_final: 0.6998 (m-40) outliers start: 39 outliers final: 22 residues processed: 343 average time/residue: 0.2538 time to fit residues: 145.9243 Evaluate side-chains 323 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 324 ASN 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 206 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 275 SER 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 46 optimal weight: 2.9990 chunk 226 optimal weight: 0.0970 chunk 59 optimal weight: 0.0980 chunk 197 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 242 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 140 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 327 ASN C 336 ASN D 336 ASN E 336 ASN ** G 336 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 = 0.4581 r_free = 0.4581 target = 0.221272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.152850 restraints weight = 29692.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.157425 restraints weight = 16212.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158884 restraints weight = 11848.181| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21273 Z= 0.103 Angle : 0.583 10.916 28875 Z= 0.277 Chirality : 0.037 0.138 3388 Planarity : 0.003 0.034 3535 Dihedral : 3.916 23.848 2800 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.03 % Allowed : 30.99 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2534 helix: 0.43 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 345 HIS 0.003 0.000 HIS A 231 PHE 0.009 0.001 PHE F 240 TYR 0.012 0.001 TYR B 289 ARG 0.003 0.000 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 926) hydrogen bonds : angle 3.97205 ( 2751) covalent geometry : bond 0.00224 (21273) covalent geometry : angle 0.58285 (28875) *********************** 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 359 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 2.184 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7410 (pm20) cc_final: 0.7002 (pm20) REVERT: F 237 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: F 327 ASN cc_start: 0.8343 (m110) cc_final: 0.7882 (m110) REVERT: A 31 GLU cc_start: 0.7434 (pm20) cc_final: 0.7037 (pm20) REVERT: B 10 TYR cc_start: 0.7840 (m-80) cc_final: 0.7557 (m-80) REVERT: B 31 GLU cc_start: 0.7295 (pm20) cc_final: 0.6887 (pm20) REVERT: C 86 ASP cc_start: 0.8067 (m-30) cc_final: 0.7377 (m-30) REVERT: C 129 GLN cc_start: 0.8179 (mm110) cc_final: 0.7909 (mm110) REVERT: D 318 MET cc_start: 0.4977 (tpt) cc_final: 0.4513 (mmt) REVERT: D 327 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.8052 (m110) REVERT: E 31 GLU cc_start: 0.7361 (pm20) cc_final: 0.6921 (pm20) REVERT: E 129 GLN cc_start: 0.8165 (mm110) cc_final: 0.7732 (mm110) REVERT: E 161 MET cc_start: 0.3569 (mmm) cc_final: 0.2764 (mmm) REVERT: E 327 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7661 (m110) REVERT: G 10 TYR cc_start: 0.7746 (m-80) cc_final: 0.7280 (m-80) REVERT: G 86 ASP cc_start: 0.8089 (m-30) cc_final: 0.7442 (m-30) REVERT: G 324 ASN cc_start: 0.7638 (t0) cc_final: 0.6976 (m-40) outliers start: 48 outliers final: 34 residues processed: 350 average time/residue: 0.2414 time to fit residues: 143.2418 Evaluate side-chains 334 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 336 ASN 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 158 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 158 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 49 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 336 ASN D 336 ASN E 327 ASN E 336 ASN ** G 336 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 = 0.4535 r_free = 0.4535 target = 0.215922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147824 restraints weight = 29700.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147702 restraints weight = 21345.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149249 restraints weight = 14805.113| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21273 Z= 0.166 Angle : 0.627 9.198 28875 Z= 0.303 Chirality : 0.040 0.149 3388 Planarity : 0.004 0.035 3535 Dihedral : 4.135 28.533 2800 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.43 % Allowed : 31.37 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2534 helix: 0.38 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.90 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 345 HIS 0.007 0.001 HIS C 231 PHE 0.015 0.001 PHE C 269 TYR 0.016 0.001 TYR D 280 ARG 0.003 0.000 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 926) hydrogen bonds : angle 4.00724 ( 2751) covalent geometry : bond 0.00386 (21273) covalent geometry : angle 0.62749 (28875) *********************** 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 382 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 301 time to evaluate : 2.146 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7668 (pm20) cc_final: 0.7278 (pm20) REVERT: F 327 ASN cc_start: 0.8429 (m110) cc_final: 0.7996 (m110) REVERT: A 31 GLU cc_start: 0.7698 (pm20) cc_final: 0.7323 (pm20) REVERT: A 75 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7415 (mmt90) REVERT: B 10 TYR cc_start: 0.7883 (m-80) cc_final: 0.7599 (m-80) REVERT: B 31 GLU cc_start: 0.7553 (pm20) cc_final: 0.7147 (pm20) REVERT: C 31 GLU cc_start: 0.7551 (pm20) cc_final: 0.7144 (pm20) REVERT: C 86 ASP cc_start: 0.8327 (m-30) cc_final: 0.7936 (m-30) REVERT: D 31 GLU cc_start: 0.7444 (pm20) cc_final: 0.7076 (pm20) REVERT: D 318 MET cc_start: 0.5020 (tpt) cc_final: 0.4578 (mmt) REVERT: E 31 GLU cc_start: 0.7582 (pm20) cc_final: 0.7141 (pm20) REVERT: E 129 GLN cc_start: 0.8156 (mm110) cc_final: 0.7908 (mm110) REVERT: G 31 GLU cc_start: 0.7583 (pm20) cc_final: 0.7171 (pm20) REVERT: G 86 ASP cc_start: 0.8272 (m-30) cc_final: 0.7984 (m-30) outliers start: 81 outliers final: 51 residues processed: 363 average time/residue: 0.2415 time to fit residues: 149.2129 Evaluate side-chains 344 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain F residue 158 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 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 305 TYR 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 158 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 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 158 VAL Chi-restraints excluded: chain D residue 267 SER 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 127 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 276 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 160 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 181 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.218220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150841 restraints weight = 29585.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152217 restraints weight = 19753.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153423 restraints weight = 13583.465| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21273 Z= 0.110 Angle : 0.588 8.572 28875 Z= 0.279 Chirality : 0.038 0.132 3388 Planarity : 0.003 0.036 3535 Dihedral : 3.961 23.334 2800 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.95 % Allowed : 32.98 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2534 helix: 0.50 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 345 HIS 0.003 0.001 HIS C 231 PHE 0.011 0.001 PHE C 240 TYR 0.012 0.001 TYR G 122 ARG 0.001 0.000 ARG E 262 Details of bonding type rmsd hydrogen bonds : bond 0.02829 ( 926) hydrogen bonds : angle 3.89540 ( 2751) covalent geometry : bond 0.00251 (21273) covalent geometry : angle 0.58828 (28875) *********************** 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 353 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 2.381 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7610 (pm20) cc_final: 0.7236 (pm20) REVERT: F 318 MET cc_start: 0.6009 (tpp) cc_final: 0.5518 (tpp) REVERT: F 327 ASN cc_start: 0.8375 (m110) cc_final: 0.7962 (m110) REVERT: A 31 GLU cc_start: 0.7615 (pm20) cc_final: 0.7245 (pm20) REVERT: A 147 LEU cc_start: 0.7457 (pp) cc_final: 0.7215 (pp) REVERT: B 10 TYR cc_start: 0.7990 (m-80) cc_final: 0.7674 (m-80) REVERT: B 31 GLU cc_start: 0.7450 (pm20) cc_final: 0.7074 (pm20) REVERT: C 31 GLU cc_start: 0.7529 (pm20) cc_final: 0.7169 (pm20) REVERT: C 86 ASP cc_start: 0.8192 (m-30) cc_final: 0.7630 (m-30) REVERT: D 10 TYR cc_start: 0.7978 (m-80) cc_final: 0.7736 (m-80) REVERT: D 31 GLU cc_start: 0.7415 (pm20) cc_final: 0.7068 (pm20) REVERT: D 147 LEU cc_start: 0.7349 (pp) cc_final: 0.7124 (pp) REVERT: D 318 MET cc_start: 0.5054 (tpt) cc_final: 0.4767 (mmt) REVERT: E 31 GLU cc_start: 0.7539 (pm20) cc_final: 0.7175 (pm20) REVERT: E 129 GLN cc_start: 0.8140 (mm110) cc_final: 0.7893 (mm110) REVERT: E 161 MET cc_start: 0.1937 (mmt) cc_final: 0.1285 (mmm) REVERT: E 283 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7026 (mp) REVERT: G 10 TYR cc_start: 0.7743 (m-80) cc_final: 0.7245 (m-80) REVERT: G 31 GLU cc_start: 0.7563 (pm20) cc_final: 0.7160 (pm20) outliers start: 46 outliers final: 31 residues processed: 344 average time/residue: 0.2386 time to fit residues: 138.5815 Evaluate side-chains 330 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 305 TYR Chi-restraints excluded: chain F residue 324 ASN 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 B residue 80 VAL Chi-restraints excluded: chain B residue 158 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 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 127 LEU 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 133 VAL Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 198 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.216289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150660 restraints weight = 29614.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149649 restraints weight = 21724.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151157 restraints weight = 15481.954| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2194 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= 0.137 Angle : 0.605 7.910 28875 Z= 0.288 Chirality : 0.039 0.139 3388 Planarity : 0.004 0.034 3535 Dihedral : 3.989 25.977 2800 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.03 % Allowed : 33.11 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2534 helix: 0.54 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 345 HIS 0.004 0.001 HIS C 231 PHE 0.011 0.001 PHE C 269 TYR 0.014 0.001 TYR G 122 ARG 0.002 0.000 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 926) hydrogen bonds : angle 3.90859 ( 2751) covalent geometry : bond 0.00322 (21273) covalent geometry : angle 0.60463 (28875) *********************** 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 334 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: F 10 TYR cc_start: 0.7978 (m-80) cc_final: 0.7637 (m-80) REVERT: F 31 GLU cc_start: 0.7684 (pm20) cc_final: 0.7331 (pm20) REVERT: F 318 MET cc_start: 0.6079 (tpp) cc_final: 0.5740 (tpp) REVERT: F 327 ASN cc_start: 0.8347 (m110) cc_final: 0.7931 (m110) REVERT: A 31 GLU cc_start: 0.7664 (pm20) cc_final: 0.7307 (pm20) REVERT: A 147 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7244 (pp) REVERT: B 10 TYR cc_start: 0.8029 (m-80) cc_final: 0.7705 (m-80) REVERT: B 31 GLU cc_start: 0.7602 (pm20) cc_final: 0.7227 (pm20) REVERT: C 31 GLU cc_start: 0.7588 (pm20) cc_final: 0.7232 (pm20) REVERT: C 86 ASP cc_start: 0.8492 (m-30) cc_final: 0.8028 (m-30) REVERT: D 10 TYR cc_start: 0.8030 (m-80) cc_final: 0.7738 (m-80) REVERT: D 31 GLU cc_start: 0.7474 (pm20) cc_final: 0.7132 (pm20) REVERT: D 147 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7253 (pp) REVERT: D 318 MET cc_start: 0.5007 (tpt) cc_final: 0.4724 (mmt) REVERT: E 31 GLU cc_start: 0.7687 (pm20) cc_final: 0.7324 (pm20) REVERT: E 129 GLN cc_start: 0.8105 (mm110) cc_final: 0.7854 (mm-40) REVERT: E 147 LEU cc_start: 0.7484 (pp) cc_final: 0.7275 (pp) REVERT: E 161 MET cc_start: 0.2080 (mmt) cc_final: 0.1416 (mmm) REVERT: E 283 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.6998 (mp) REVERT: G 10 TYR cc_start: 0.7820 (m-80) cc_final: 0.7294 (m-80) REVERT: G 31 GLU cc_start: 0.7531 (pm20) cc_final: 0.7149 (pm20) outliers start: 48 outliers final: 38 residues processed: 325 average time/residue: 0.2433 time to fit residues: 134.0636 Evaluate side-chains 325 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 174 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 133 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 133 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN 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 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 305 TYR 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 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 275 SER 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 179 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 = 0.4507 r_free = 0.4507 target = 0.213176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141855 restraints weight = 29687.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146300 restraints weight = 15951.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149213 restraints weight = 11104.335| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21273 Z= 0.170 Angle : 0.637 7.878 28875 Z= 0.307 Chirality : 0.040 0.147 3388 Planarity : 0.004 0.035 3535 Dihedral : 4.206 27.892 2800 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.46 % Allowed : 32.98 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2534 helix: 0.45 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.88 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 345 HIS 0.005 0.001 HIS C 231 PHE 0.015 0.001 PHE E 240 TYR 0.019 0.002 TYR G 122 ARG 0.009 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 926) hydrogen bonds : angle 4.02399 ( 2751) covalent geometry : bond 0.00396 (21273) covalent geometry : angle 0.63728 (28875) *********************** 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 340 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 2.377 Fit side-chains REVERT: F 10 TYR cc_start: 0.7988 (m-80) cc_final: 0.7665 (m-80) REVERT: F 31 GLU cc_start: 0.7751 (pm20) cc_final: 0.7434 (pm20) REVERT: F 318 MET cc_start: 0.6126 (tpp) cc_final: 0.5781 (tpp) REVERT: F 327 ASN cc_start: 0.8349 (m110) cc_final: 0.7981 (m110) REVERT: A 31 GLU cc_start: 0.7775 (pm20) cc_final: 0.7448 (pm20) REVERT: A 35 ASP cc_start: 0.6964 (m-30) cc_final: 0.6736 (t0) REVERT: A 147 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7270 (pp) REVERT: B 10 TYR cc_start: 0.8059 (m-80) cc_final: 0.7757 (m-80) REVERT: B 31 GLU cc_start: 0.7736 (pm20) cc_final: 0.7376 (pm20) REVERT: C 30 LEU cc_start: 0.8120 (mm) cc_final: 0.7915 (mm) REVERT: C 31 GLU cc_start: 0.7801 (pm20) cc_final: 0.7469 (pm20) REVERT: C 86 ASP cc_start: 0.8342 (m-30) cc_final: 0.7988 (m-30) REVERT: D 10 TYR cc_start: 0.8082 (m-80) cc_final: 0.7841 (m-80) REVERT: D 31 GLU cc_start: 0.7608 (pm20) cc_final: 0.7281 (pm20) REVERT: D 75 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7701 (mmt-90) REVERT: D 147 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7178 (pp) REVERT: D 318 MET cc_start: 0.4882 (tpt) cc_final: 0.4575 (mmt) REVERT: E 30 LEU cc_start: 0.8012 (mm) cc_final: 0.7723 (mm) REVERT: E 31 GLU cc_start: 0.7769 (pm20) cc_final: 0.7401 (pm20) REVERT: E 129 GLN cc_start: 0.8219 (mm110) cc_final: 0.7944 (mm-40) REVERT: E 147 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7237 (pp) REVERT: E 161 MET cc_start: 0.2363 (mmt) cc_final: 0.0882 (tpt) REVERT: E 283 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6737 (mp) REVERT: G 31 GLU cc_start: 0.7764 (pm20) cc_final: 0.7404 (pm20) outliers start: 58 outliers final: 46 residues processed: 330 average time/residue: 0.2456 time to fit residues: 137.6260 Evaluate side-chains 324 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 2.541 ------------------------------------------------------------------------------- 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 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 38 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 174 PHE 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 133 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 133 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN 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 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 147 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 248 LEU 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 120 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR 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 220 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.215976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150401 restraints weight = 29539.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.149844 restraints weight = 20685.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.151454 restraints weight = 14437.132| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2650 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= 0.114 Angle : 0.605 8.263 28875 Z= 0.288 Chirality : 0.039 0.255 3388 Planarity : 0.004 0.040 3535 Dihedral : 4.026 24.437 2800 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.03 % Allowed : 33.57 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2534 helix: 0.54 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.88 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 345 HIS 0.003 0.001 HIS A 231 PHE 0.012 0.001 PHE A 54 TYR 0.015 0.001 TYR B 122 ARG 0.008 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.02815 ( 926) hydrogen bonds : angle 3.92029 ( 2751) covalent geometry : bond 0.00260 (21273) covalent geometry : angle 0.60474 (28875) *********************** 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 333 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 2.219 Fit side-chains REVERT: F 10 TYR cc_start: 0.7957 (m-80) cc_final: 0.7600 (m-80) REVERT: F 31 GLU cc_start: 0.7671 (pm20) cc_final: 0.7355 (pm20) REVERT: F 75 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7903 (tpp80) REVERT: F 318 MET cc_start: 0.6076 (tpp) cc_final: 0.5710 (tpp) REVERT: F 327 ASN cc_start: 0.8215 (m110) cc_final: 0.7898 (m110) REVERT: A 31 GLU cc_start: 0.7723 (pm20) cc_final: 0.7415 (pm20) REVERT: A 147 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7241 (pp) REVERT: A 369 MET cc_start: 0.5133 (pmm) cc_final: 0.4926 (pmm) REVERT: B 10 TYR cc_start: 0.8055 (m-80) cc_final: 0.7720 (m-80) REVERT: B 31 GLU cc_start: 0.7663 (pm20) cc_final: 0.7314 (pm20) REVERT: C 31 GLU cc_start: 0.7729 (pm20) cc_final: 0.7421 (pm20) REVERT: C 86 ASP cc_start: 0.8184 (m-30) cc_final: 0.7666 (m-30) REVERT: D 10 TYR cc_start: 0.8051 (m-80) cc_final: 0.7771 (m-80) REVERT: D 31 GLU cc_start: 0.7502 (pm20) cc_final: 0.7204 (pm20) REVERT: D 75 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7432 (mmt-90) REVERT: D 147 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7245 (pp) REVERT: D 318 MET cc_start: 0.5017 (tpt) cc_final: 0.4688 (mmt) REVERT: E 30 LEU cc_start: 0.7922 (mm) cc_final: 0.7634 (mm) REVERT: E 31 GLU cc_start: 0.7759 (pm20) cc_final: 0.7414 (pm20) REVERT: E 129 GLN cc_start: 0.8224 (mm110) cc_final: 0.7972 (mm-40) REVERT: E 161 MET cc_start: 0.2327 (mmt) cc_final: 0.0800 (tpt) REVERT: E 283 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.6803 (mp) REVERT: G 31 GLU cc_start: 0.7642 (pm20) cc_final: 0.7315 (pm20) outliers start: 48 outliers final: 41 residues processed: 321 average time/residue: 0.2461 time to fit residues: 133.0438 Evaluate side-chains 326 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 282 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain F residue 260 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 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 174 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 133 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 133 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain D residue 80 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 258 LEU 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 127 LEU Chi-restraints excluded: chain E residue 248 LEU 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 38 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 267 SER 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 128 optimal weight: 0.7980 chunk 139 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 241 optimal weight: 0.0470 chunk 41 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.212530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145102 restraints weight = 29702.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145507 restraints weight = 19624.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.146228 restraints weight = 13662.447| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21273 Z= 0.175 Angle : 0.653 8.706 28875 Z= 0.315 Chirality : 0.041 0.236 3388 Planarity : 0.004 0.039 3535 Dihedral : 4.215 28.881 2800 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.25 % Allowed : 33.45 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2534 helix: 0.44 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.89 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 345 HIS 0.005 0.001 HIS C 231 PHE 0.014 0.001 PHE C 269 TYR 0.022 0.002 TYR B 122 ARG 0.008 0.000 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 926) hydrogen bonds : angle 3.98599 ( 2751) covalent geometry : bond 0.00411 (21273) covalent geometry : angle 0.65347 (28875) ********************** 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 336 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 2.384 Fit side-chains REVERT: F 10 TYR cc_start: 0.7994 (m-80) cc_final: 0.7610 (m-80) REVERT: F 31 GLU cc_start: 0.7765 (pm20) cc_final: 0.7422 (pm20) REVERT: F 318 MET cc_start: 0.6076 (tpp) cc_final: 0.5727 (tpp) REVERT: A 31 GLU cc_start: 0.7809 (pm20) cc_final: 0.7474 (pm20) REVERT: A 147 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7192 (pp) REVERT: B 10 TYR cc_start: 0.8084 (m-80) cc_final: 0.7693 (m-80) REVERT: B 31 GLU cc_start: 0.7742 (pm20) cc_final: 0.7382 (pm20) REVERT: C 30 LEU cc_start: 0.8118 (mm) cc_final: 0.7902 (mm) REVERT: C 31 GLU cc_start: 0.7844 (pm20) cc_final: 0.7516 (pm20) REVERT: C 86 ASP cc_start: 0.8304 (m-30) cc_final: 0.7963 (m-30) REVERT: D 10 TYR cc_start: 0.8016 (m-80) cc_final: 0.7774 (m-80) REVERT: D 31 GLU cc_start: 0.7637 (pm20) cc_final: 0.7327 (pm20) REVERT: D 37 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7637 (tp) REVERT: D 75 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7836 (tpp80) REVERT: D 147 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7121 (pp) REVERT: D 318 MET cc_start: 0.5141 (tpt) cc_final: 0.4772 (mmt) REVERT: E 30 LEU cc_start: 0.8024 (mm) cc_final: 0.7711 (mm) REVERT: E 31 GLU cc_start: 0.7834 (pm20) cc_final: 0.7474 (pm20) REVERT: E 129 GLN cc_start: 0.8222 (mm110) cc_final: 0.7969 (mm-40) REVERT: E 161 MET cc_start: 0.2346 (mmt) cc_final: 0.0860 (tpt) REVERT: E 283 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6765 (mp) REVERT: G 31 GLU cc_start: 0.7827 (pm20) cc_final: 0.7469 (pm20) outliers start: 53 outliers final: 47 residues processed: 325 average time/residue: 0.2505 time to fit residues: 138.0341 Evaluate side-chains 329 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 278 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 158 VAL Chi-restraints excluded: chain F residue 260 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 38 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 174 PHE Chi-restraints excluded: chain A residue 267 SER 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 133 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 133 VAL Chi-restraints excluded: chain C residue 139 ASP 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 127 LEU 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 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 127 LEU 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 38 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 305 TYR 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 111 optimal weight: 0.0030 chunk 13 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 159 optimal weight: 0.0030 chunk 29 optimal weight: 3.9990 chunk 211 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 162 optimal weight: 0.0370 overall best weight: 0.1678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS A 336 ASN B 5 HIS ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 HIS ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 HIS D 336 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 HIS G 336 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.218034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152556 restraints weight = 29763.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151788 restraints weight = 21667.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153603 restraints weight = 14457.094| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21273 Z= 0.107 Angle : 0.610 8.608 28875 Z= 0.289 Chirality : 0.038 0.241 3388 Planarity : 0.004 0.036 3535 Dihedral : 3.901 21.926 2800 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.10 % Allowed : 34.76 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 2534 helix: 0.77 (0.15), residues: 1470 sheet: None (None), residues: 0 loop : -2.79 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 345 HIS 0.003 0.001 HIS A 231 PHE 0.010 0.001 PHE G 240 TYR 0.018 0.001 TYR B 122 ARG 0.009 0.000 ARG G 334 Details of bonding type rmsd hydrogen bonds : bond 0.02688 ( 926) hydrogen bonds : angle 3.87980 ( 2751) covalent geometry : bond 0.00234 (21273) covalent geometry : angle 0.60962 (28875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6191.88 seconds wall clock time: 109 minutes 43.94 seconds (6583.94 seconds total)