Starting phenix.real_space_refine on Fri Jul 3 06:13:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dku_27491/07_2026/8dku_27491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dku_27491/07_2026/8dku_27491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dku_27491/07_2026/8dku_27491.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dku_27491/07_2026/8dku_27491.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dku_27491/07_2026/8dku_27491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dku_27491/07_2026/8dku_27491.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dku_27491/07_2026/8dku_27491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dku_27491/07_2026/8dku_27491.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2340 atoms to isotropic. 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 32 5.16 5 C 7089 2.51 5 N 1666 2.21 5 O 1857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10644 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'UBH': 1, 'UBO': 1, 'XXR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.37, per 1000 atoms: 0.22 Number of scatterers: 10644 At special positions: 0 Unit cell: (91.8, 100.44, 141.48, 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 32 16.00 O 1857 8.00 N 1666 7.00 C 7089 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 Links applied ?1-2 " XXR F 1 " - " UBO F 2 " ?1-3 " UBO F 2 " - " UBH F 3 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 241.9 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 11 sheets defined 49.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 removed outlier: 4.451A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 114 through 129 removed outlier: 5.060A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.666A pdb=" N THR A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.859A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.953A pdb=" N VAL A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.591A pdb=" N LYS A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.727A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 20 through 26 Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.605A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 83 removed outlier: 3.608A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix removed outlier: 3.792A pdb=" N ILE B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.659A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 4.046A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.712A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.746A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.639A pdb=" N THR B 183 " --> pdb=" O PHE B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.860A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 192 " --> pdb=" O LEU B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 192' Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.803A pdb=" N LEU B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 223 through 254 Proline residue: B 235 - end of helix removed outlier: 4.633A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 4.173A pdb=" N ARG C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 114 through 130 removed outlier: 5.092A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 167 through 171 removed outlier: 4.141A pdb=" N ALA C 170 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 174 through 188 removed outlier: 4.076A pdb=" N LYS C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 240 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 23 through 43 removed outlier: 3.835A pdb=" N TRP D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix removed outlier: 3.522A pdb=" N LEU D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.901A pdb=" N LEU D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 88 removed outlier: 3.693A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.840A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.053A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 101 through 129 removed outlier: 3.754A pdb=" N ILE D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 163 removed outlier: 4.166A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 removed outlier: 4.314A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.819A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 225 through 248 removed outlier: 3.737A pdb=" N GLY D 229 " --> pdb=" O TYR D 225 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 249 through 256 removed outlier: 4.543A pdb=" N ALA D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.660A pdb=" N GLU A 32 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 13 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.660A pdb=" N GLU A 32 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 13 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 165 removed outlier: 6.280A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 49 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 212 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 51 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU A 214 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 53 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU A 221 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 259 removed outlier: 4.339A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 282 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 257 through 259 removed outlier: 4.339A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 327 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 276 removed outlier: 3.500A pdb=" N ASN A 372 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 276 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE A 374 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 363 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU A 349 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASN A 365 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL A 347 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 297 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN A 313 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 299 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY A 311 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 301 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 392 removed outlier: 3.697A pdb=" N LEU C 329 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR C 279 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER C 266 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 281 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 264 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU C 283 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL C 262 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP C 285 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.528A pdb=" N ILE C 2 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 84 through 86 removed outlier: 7.313A pdb=" N VAL C 85 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE C 163 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 197 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE C 165 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU C 50 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 313 removed outlier: 3.506A pdb=" N GLY C 298 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 341 through 342 469 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2806 1.33 - 1.45: 2038 1.45 - 1.57: 6026 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 10922 Sorted by residual: bond pdb=" C LYS A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.331 1.372 -0.041 1.21e-02 6.83e+03 1.15e+01 bond pdb=" C4 UBO F 2 " pdb=" O4 UBO F 2 " ideal model delta sigma weight residual 1.430 1.367 0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" N GLU D 132 " pdb=" CA GLU D 132 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.52e+00 bond pdb=" N ILE B 127 " pdb=" CA ILE B 127 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.17e-02 7.31e+03 7.35e+00 bond pdb=" N MET C 353 " pdb=" CA MET C 353 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.19e-02 7.06e+03 6.61e+00 ... (remaining 10917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 14562 2.27 - 4.54: 177 4.54 - 6.80: 27 6.80 - 9.07: 4 9.07 - 11.34: 3 Bond angle restraints: 14773 Sorted by residual: angle pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" C VAL D 22 " ideal model delta sigma weight residual 112.96 108.31 4.65 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C LEU B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta sigma weight residual 122.54 115.64 6.90 1.65e+00 3.67e-01 1.75e+01 angle pdb=" C5 UBO F 2 " pdb=" C4 UBO F 2 " pdb=" O4 UBO F 2 " ideal model delta sigma weight residual 111.37 100.03 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 109.94 115.80 -5.86 1.57e+00 4.06e-01 1.40e+01 angle pdb=" CA TYR C 360 " pdb=" C TYR C 360 " pdb=" O TYR C 360 " ideal model delta sigma weight residual 120.82 117.09 3.73 1.05e+00 9.07e-01 1.26e+01 ... (remaining 14768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 5674 16.78 - 33.57: 594 33.57 - 50.35: 108 50.35 - 67.13: 26 67.13 - 83.92: 8 Dihedral angle restraints: 6410 sinusoidal: 2630 harmonic: 3780 Sorted by residual: dihedral pdb=" CA TRP B 26 " pdb=" C TRP B 26 " pdb=" N TRP B 27 " pdb=" CA TRP B 27 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA HIS C 361 " pdb=" C HIS C 361 " pdb=" N TRP C 362 " pdb=" CA TRP C 362 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN B 16 " pdb=" C ASN B 16 " pdb=" N ARG B 17 " pdb=" CA ARG B 17 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1465 0.070 - 0.139: 189 0.139 - 0.209: 1 0.209 - 0.279: 2 0.279 - 0.349: 2 Chirality restraints: 1659 Sorted by residual: chirality pdb=" C3 UBO F 2 " pdb=" C2 UBO F 2 " pdb=" C4 UBO F 2 " pdb=" O3 UBO F 2 " both_signs ideal model delta sigma weight residual False 2.39 2.74 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C5 UBH F 3 " pdb=" C4 UBH F 3 " pdb=" C6 UBH F 3 " pdb=" O5 UBH F 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.22 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2 XXR F 1 " pdb=" C1 XXR F 1 " pdb=" C3 XXR F 1 " pdb=" O2 XXR F 1 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1656 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 28 " -0.032 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A 29 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 274 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 275 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 275 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 275 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 95 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 96 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " 0.022 5.00e-02 4.00e+02 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 888 2.74 - 3.28: 10341 3.28 - 3.82: 16866 3.82 - 4.36: 19536 4.36 - 4.90: 35545 Nonbonded interactions: 83176 Sorted by model distance: nonbonded pdb=" OG SER C 114 " pdb=" OE1 GLU C 117 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 252 " pdb=" OD2 ASP A 364 " model vdw 2.259 3.040 nonbonded pdb=" O THR D 40 " pdb=" OG SER D 44 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLU C 186 " pdb=" NZ LYS C 190 " model vdw 2.272 3.120 nonbonded pdb=" O VAL B 36 " pdb=" OG1 THR B 40 " model vdw 2.282 3.040 ... (remaining 83171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.050 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.004 0.063 10924 Z= 0.200 Angle : 0.641 11.341 14779 Z= 0.353 Chirality : 0.045 0.349 1659 Planarity : 0.003 0.050 1814 Dihedral : 14.112 83.918 3994 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.24), residues: 1292 helix: 0.60 (0.22), residues: 603 sheet: -0.52 (0.42), residues: 177 loop : -2.02 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 3 TYR 0.014 0.001 TYR D 63 PHE 0.020 0.001 PHE B 179 TRP 0.014 0.002 TRP B 26 HIS 0.007 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.20 (10922) covalent geometry : angle 0.63480 / 0.35 (14773) hydrogen bonds : bond 0.14573 / 9.03 ( 462) hydrogen bonds : angle 5.96974 / 4.27 ( 1350) glycosidic custom : bond 0.04487 / 2.67 ( 2) glycosidic custom : angle 4.40534 / 2.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7826 (m-30) cc_final: 0.7459 (m-30) REVERT: B 11 ARG cc_start: 0.7711 (mtm110) cc_final: 0.6667 (mmt180) REVERT: B 13 GLU cc_start: 0.7440 (tp30) cc_final: 0.7166 (tp30) REVERT: C 263 ARG cc_start: 0.7399 (mtm110) cc_final: 0.7013 (mtm110) REVERT: D 110 GLU cc_start: 0.7595 (tp30) cc_final: 0.7221 (tp30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0868 time to fit residues: 24.9684 Evaluate side-chains 162 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 ASN C 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.190215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129790 restraints weight = 12718.509| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.57 r_work: 0.3387 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10924 Z= 0.156 Angle : 0.571 10.154 14779 Z= 0.295 Chirality : 0.043 0.156 1659 Planarity : 0.004 0.041 1814 Dihedral : 4.194 23.507 1436 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.69 % Allowed : 9.14 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1292 helix: 0.79 (0.22), residues: 599 sheet: -0.47 (0.42), residues: 176 loop : -1.95 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.019 0.001 TYR C 384 PHE 0.029 0.002 PHE B 92 TRP 0.019 0.002 TRP B 26 HIS 0.003 0.001 HIS C 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (10922) covalent geometry : angle 0.56991 / 0.30 (14773) hydrogen bonds : bond 0.04421 / 2.75 ( 462) hydrogen bonds : angle 4.68433 / 3.25 ( 1350) glycosidic custom : bond 0.00069 / 0.04 ( 2) glycosidic custom : angle 1.81653 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7836 (m-30) cc_final: 0.7393 (m-30) REVERT: A 122 LEU cc_start: 0.7383 (tt) cc_final: 0.7102 (tp) REVERT: A 372 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7309 (p0) REVERT: B 11 ARG cc_start: 0.7807 (mtm110) cc_final: 0.6478 (mmt180) REVERT: C 117 GLU cc_start: 0.8605 (mp0) cc_final: 0.8342 (mp0) REVERT: C 127 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8167 (pt0) REVERT: C 128 PHE cc_start: 0.7360 (t80) cc_final: 0.7102 (t80) REVERT: C 190 LYS cc_start: 0.7743 (mtmm) cc_final: 0.6977 (pptt) REVERT: C 289 LYS cc_start: 0.7333 (mmtm) cc_final: 0.7059 (mmtm) REVERT: D 110 GLU cc_start: 0.8093 (tp30) cc_final: 0.7685 (tp30) REVERT: D 243 TYR cc_start: 0.6520 (t80) cc_final: 0.6313 (t80) outliers start: 8 outliers final: 5 residues processed: 181 average time/residue: 0.0835 time to fit residues: 21.7788 Evaluate side-chains 172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 93 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 127 optimal weight: 0.0770 chunk 122 optimal weight: 0.2980 chunk 39 optimal weight: 0.0050 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.190779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130447 restraints weight = 12776.005| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.61 r_work: 0.3394 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10924 Z= 0.130 Angle : 0.526 10.417 14779 Z= 0.275 Chirality : 0.041 0.161 1659 Planarity : 0.003 0.039 1814 Dihedral : 4.109 21.911 1436 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.29 % Allowed : 11.72 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1292 helix: 0.91 (0.22), residues: 600 sheet: -0.35 (0.43), residues: 175 loop : -1.91 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 17 TYR 0.016 0.001 TYR C 384 PHE 0.027 0.001 PHE B 92 TRP 0.023 0.002 TRP B 26 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (10922) covalent geometry : angle 0.52576 / 0.27 (14773) hydrogen bonds : bond 0.03861 / 2.42 ( 462) hydrogen bonds : angle 4.38580 / 3.02 ( 1350) glycosidic custom : bond 0.00056 / 0.03 ( 2) glycosidic custom : angle 1.37694 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7980 (m-30) cc_final: 0.7533 (m-30) REVERT: A 122 LEU cc_start: 0.7400 (tt) cc_final: 0.7177 (tp) REVERT: B 8 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7704 (tp30) REVERT: B 11 ARG cc_start: 0.7778 (mtm110) cc_final: 0.6462 (mmt180) REVERT: B 224 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7715 (mp) REVERT: C 16 LYS cc_start: 0.7057 (tttt) cc_final: 0.6843 (tttp) REVERT: C 117 GLU cc_start: 0.8412 (mp0) cc_final: 0.8103 (mp0) REVERT: C 128 PHE cc_start: 0.7366 (t80) cc_final: 0.7069 (t80) REVERT: C 182 ARG cc_start: 0.8492 (ptm-80) cc_final: 0.8088 (ptt180) REVERT: C 190 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7016 (pptt) REVERT: C 236 MET cc_start: 0.7729 (ttp) cc_final: 0.7345 (tpp) REVERT: C 289 LYS cc_start: 0.7278 (mmtm) cc_final: 0.7056 (mmtm) REVERT: D 110 GLU cc_start: 0.8136 (tp30) cc_final: 0.7700 (tp30) REVERT: D 243 TYR cc_start: 0.6498 (t80) cc_final: 0.5984 (t80) outliers start: 15 outliers final: 11 residues processed: 186 average time/residue: 0.1037 time to fit residues: 27.8091 Evaluate side-chains 176 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 67 optimal weight: 0.0670 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.191822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132044 restraints weight = 12847.879| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.61 r_work: 0.3412 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10924 Z= 0.105 Angle : 0.500 11.305 14779 Z= 0.259 Chirality : 0.041 0.159 1659 Planarity : 0.003 0.038 1814 Dihedral : 3.973 21.023 1436 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.98 % Allowed : 13.88 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1292 helix: 0.94 (0.22), residues: 611 sheet: -0.24 (0.43), residues: 174 loop : -1.81 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 182 TYR 0.018 0.001 TYR D 243 PHE 0.027 0.001 PHE B 92 TRP 0.029 0.002 TRP B 26 HIS 0.005 0.001 HIS C 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (10922) covalent geometry : angle 0.49978 / 0.26 (14773) hydrogen bonds : bond 0.03442 / 2.16 ( 462) hydrogen bonds : angle 4.19236 / 2.88 ( 1350) glycosidic custom : bond 0.00058 / 0.03 ( 2) glycosidic custom : angle 1.19371 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7654 (m-80) cc_final: 0.7447 (m-80) REVERT: A 97 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7845 (pm20) REVERT: A 119 ASP cc_start: 0.8066 (m-30) cc_final: 0.7693 (m-30) REVERT: A 122 LEU cc_start: 0.7252 (tt) cc_final: 0.6921 (tp) REVERT: A 274 PHE cc_start: 0.7870 (m-80) cc_final: 0.7563 (m-10) REVERT: A 358 GLU cc_start: 0.7531 (tt0) cc_final: 0.7283 (tp30) REVERT: A 372 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7299 (p0) REVERT: B 8 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7659 (tp30) REVERT: B 224 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7619 (mp) REVERT: C 16 LYS cc_start: 0.7122 (tttt) cc_final: 0.6893 (tttp) REVERT: C 117 GLU cc_start: 0.8423 (mp0) cc_final: 0.8110 (mp0) REVERT: C 182 ARG cc_start: 0.8455 (ptm-80) cc_final: 0.7986 (ptt-90) REVERT: C 190 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7048 (pptt) REVERT: C 236 MET cc_start: 0.7731 (ttp) cc_final: 0.7341 (tpp) REVERT: C 289 LYS cc_start: 0.7234 (mmtm) cc_final: 0.6948 (mmtm) outliers start: 23 outliers final: 16 residues processed: 193 average time/residue: 0.0959 time to fit residues: 26.8784 Evaluate side-chains 183 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 HIS C 215 HIS D 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125860 restraints weight = 12811.412| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.59 r_work: 0.3336 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10924 Z= 0.238 Angle : 0.594 12.051 14779 Z= 0.308 Chirality : 0.044 0.153 1659 Planarity : 0.004 0.042 1814 Dihedral : 4.231 20.733 1436 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.33 % Allowed : 14.74 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.24), residues: 1292 helix: 0.63 (0.22), residues: 614 sheet: -0.61 (0.40), residues: 188 loop : -1.81 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 166 TYR 0.019 0.001 TYR B 63 PHE 0.025 0.002 PHE C 128 TRP 0.028 0.002 TRP B 26 HIS 0.003 0.001 HIS C 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.24 (10922) covalent geometry : angle 0.59363 / 0.31 (14773) hydrogen bonds : bond 0.04613 / 2.90 ( 462) hydrogen bonds : angle 4.34311 / 2.98 ( 1350) glycosidic custom : bond 0.00217 / 0.13 ( 2) glycosidic custom : angle 1.50243 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7854 (m-80) cc_final: 0.7534 (m-80) REVERT: A 119 ASP cc_start: 0.8085 (m-30) cc_final: 0.7860 (m-30) REVERT: A 274 PHE cc_start: 0.8039 (m-80) cc_final: 0.7669 (m-10) REVERT: B 8 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7660 (tp30) REVERT: C 117 GLU cc_start: 0.8410 (mp0) cc_final: 0.8028 (mp0) REVERT: C 182 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.8047 (ptt180) REVERT: C 190 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7062 (pptt) REVERT: C 236 MET cc_start: 0.7775 (ttp) cc_final: 0.7348 (tpp) REVERT: C 289 LYS cc_start: 0.7373 (mmtm) cc_final: 0.6831 (mmtm) REVERT: D 110 GLU cc_start: 0.8249 (tp30) cc_final: 0.7774 (tp30) outliers start: 27 outliers final: 21 residues processed: 187 average time/residue: 0.0943 time to fit residues: 25.6383 Evaluate side-chains 183 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 65 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN C 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.190328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134232 restraints weight = 12852.507| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.88 r_work: 0.3361 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10924 Z= 0.115 Angle : 0.514 10.733 14779 Z= 0.267 Chirality : 0.041 0.157 1659 Planarity : 0.003 0.040 1814 Dihedral : 4.025 18.750 1436 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.07 % Allowed : 15.43 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.24), residues: 1292 helix: 0.86 (0.22), residues: 612 sheet: -0.48 (0.41), residues: 186 loop : -1.82 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 182 TYR 0.014 0.001 TYR B 63 PHE 0.026 0.001 PHE B 92 TRP 0.024 0.002 TRP B 26 HIS 0.003 0.001 HIS C 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10922) covalent geometry : angle 0.51344 / 0.27 (14773) hydrogen bonds : bond 0.03538 / 2.20 ( 462) hydrogen bonds : angle 4.17115 / 2.86 ( 1350) glycosidic custom : bond 0.00067 / 0.04 ( 2) glycosidic custom : angle 1.18869 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7814 (m-80) cc_final: 0.7458 (m-80) REVERT: A 137 LYS cc_start: 0.8025 (mppt) cc_final: 0.7802 (mptt) REVERT: A 274 PHE cc_start: 0.7865 (m-80) cc_final: 0.7629 (m-10) REVERT: A 358 GLU cc_start: 0.7226 (tp30) cc_final: 0.6954 (tp30) REVERT: A 372 ASN cc_start: 0.7568 (OUTLIER) cc_final: 0.7192 (p0) REVERT: B 8 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7654 (tp30) REVERT: C 117 GLU cc_start: 0.8418 (mp0) cc_final: 0.8094 (mp0) REVERT: C 190 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7375 (pptt) REVERT: C 236 MET cc_start: 0.7836 (ttp) cc_final: 0.7365 (tpp) REVERT: C 289 LYS cc_start: 0.7364 (mmtm) cc_final: 0.6792 (mmtm) outliers start: 24 outliers final: 18 residues processed: 183 average time/residue: 0.0885 time to fit residues: 23.9739 Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.190879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130885 restraints weight = 12814.234| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.61 r_work: 0.3391 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10924 Z= 0.114 Angle : 0.522 12.894 14779 Z= 0.270 Chirality : 0.041 0.158 1659 Planarity : 0.003 0.039 1814 Dihedral : 4.000 20.753 1436 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.90 % Allowed : 16.12 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1292 helix: 0.92 (0.22), residues: 611 sheet: -0.40 (0.41), residues: 186 loop : -1.82 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 17 TYR 0.013 0.001 TYR B 63 PHE 0.025 0.001 PHE B 92 TRP 0.036 0.002 TRP B 26 HIS 0.004 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (10922) covalent geometry : angle 0.52177 / 0.27 (14773) hydrogen bonds : bond 0.03440 / 2.14 ( 462) hydrogen bonds : angle 4.11746 / 2.83 ( 1350) glycosidic custom : bond 0.00060 / 0.03 ( 2) glycosidic custom : angle 1.19970 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7809 (m-80) cc_final: 0.7475 (m-80) REVERT: A 137 LYS cc_start: 0.8032 (mppt) cc_final: 0.7811 (mptt) REVERT: A 274 PHE cc_start: 0.7841 (m-80) cc_final: 0.7617 (m-10) REVERT: A 358 GLU cc_start: 0.7258 (tp30) cc_final: 0.6974 (tp30) REVERT: B 8 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7685 (tp30) REVERT: B 11 ARG cc_start: 0.7789 (mtm110) cc_final: 0.6446 (mmt180) REVERT: B 172 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7042 (tp) REVERT: C 117 GLU cc_start: 0.8447 (mp0) cc_final: 0.8186 (mp0) REVERT: C 190 LYS cc_start: 0.7799 (mtmm) cc_final: 0.7059 (pptt) REVERT: C 236 MET cc_start: 0.7836 (ttp) cc_final: 0.7366 (tpp) REVERT: C 289 LYS cc_start: 0.7307 (mmtm) cc_final: 0.6770 (mmtm) REVERT: D 247 LYS cc_start: 0.8039 (tppt) cc_final: 0.7606 (tppt) outliers start: 22 outliers final: 19 residues processed: 183 average time/residue: 0.0943 time to fit residues: 25.2291 Evaluate side-chains 181 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 ASN D 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.188663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130434 restraints weight = 12847.185| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.80 r_work: 0.3349 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10924 Z= 0.165 Angle : 0.559 13.958 14779 Z= 0.288 Chirality : 0.042 0.156 1659 Planarity : 0.003 0.039 1814 Dihedral : 4.097 18.195 1436 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.24 % Allowed : 16.21 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1292 helix: 0.77 (0.22), residues: 614 sheet: -0.53 (0.41), residues: 186 loop : -1.80 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 17 TYR 0.015 0.001 TYR D 63 PHE 0.025 0.002 PHE B 92 TRP 0.035 0.002 TRP B 26 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.16 (10922) covalent geometry : angle 0.55817 / 0.29 (14773) hydrogen bonds : bond 0.04018 / 2.52 ( 462) hydrogen bonds : angle 4.17417 / 2.86 ( 1350) glycosidic custom : bond 0.00081 / 0.05 ( 2) glycosidic custom : angle 1.35148 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7869 (m-80) cc_final: 0.7463 (m-80) REVERT: A 119 ASP cc_start: 0.7994 (m-30) cc_final: 0.7753 (m-30) REVERT: A 137 LYS cc_start: 0.7971 (mppt) cc_final: 0.7714 (mptt) REVERT: A 274 PHE cc_start: 0.7853 (m-80) cc_final: 0.7582 (m-10) REVERT: A 358 GLU cc_start: 0.7303 (tp30) cc_final: 0.7026 (tp30) REVERT: A 372 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6963 (p0) REVERT: B 8 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7647 (tp30) REVERT: B 172 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7216 (tp) REVERT: C 117 GLU cc_start: 0.8459 (mp0) cc_final: 0.8118 (mp0) REVERT: C 190 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7115 (pptt) REVERT: C 236 MET cc_start: 0.7834 (ttp) cc_final: 0.7309 (tpp) REVERT: C 289 LYS cc_start: 0.7352 (mmtm) cc_final: 0.6847 (mmtm) REVERT: C 323 LEU cc_start: 0.7244 (mt) cc_final: 0.7043 (mt) REVERT: D 247 LYS cc_start: 0.7916 (tppt) cc_final: 0.7393 (tppt) outliers start: 26 outliers final: 20 residues processed: 182 average time/residue: 0.0883 time to fit residues: 23.7831 Evaluate side-chains 184 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.190506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.133635 restraints weight = 12801.781| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.80 r_work: 0.3382 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10924 Z= 0.112 Angle : 0.529 13.939 14779 Z= 0.272 Chirality : 0.041 0.158 1659 Planarity : 0.003 0.038 1814 Dihedral : 4.000 18.798 1436 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.24 % Allowed : 16.64 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.24), residues: 1292 helix: 0.92 (0.22), residues: 612 sheet: -0.48 (0.41), residues: 186 loop : -1.82 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 80 TYR 0.013 0.001 TYR B 63 PHE 0.025 0.001 PHE B 92 TRP 0.032 0.002 TRP B 26 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (10922) covalent geometry : angle 0.52807 / 0.27 (14773) hydrogen bonds : bond 0.03439 / 2.14 ( 462) hydrogen bonds : angle 4.07989 / 2.79 ( 1350) glycosidic custom : bond 0.00065 / 0.04 ( 2) glycosidic custom : angle 1.20925 / 0.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7850 (m-80) cc_final: 0.7421 (m-80) REVERT: A 137 LYS cc_start: 0.8023 (mppt) cc_final: 0.7802 (mptt) REVERT: A 274 PHE cc_start: 0.7810 (m-80) cc_final: 0.7573 (m-10) REVERT: A 358 GLU cc_start: 0.7293 (tp30) cc_final: 0.7028 (tp30) REVERT: A 372 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6802 (p0) REVERT: B 8 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7660 (tp30) REVERT: B 11 ARG cc_start: 0.7781 (mtm110) cc_final: 0.6448 (mmt180) REVERT: B 172 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7013 (tp) REVERT: C 117 GLU cc_start: 0.8428 (mp0) cc_final: 0.8109 (mp0) REVERT: C 190 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7113 (pptt) REVERT: C 236 MET cc_start: 0.7832 (ttp) cc_final: 0.7301 (tpp) REVERT: C 285 ASP cc_start: 0.6591 (m-30) cc_final: 0.6338 (m-30) REVERT: C 289 LYS cc_start: 0.7361 (mmtm) cc_final: 0.6838 (mmtm) REVERT: C 323 LEU cc_start: 0.7168 (mt) cc_final: 0.6957 (mt) outliers start: 26 outliers final: 21 residues processed: 183 average time/residue: 0.0934 time to fit residues: 25.1759 Evaluate side-chains 183 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 107 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 37 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN D 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.191165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134769 restraints weight = 12809.972| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.77 r_work: 0.3375 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10924 Z= 0.106 Angle : 0.515 13.705 14779 Z= 0.265 Chirality : 0.041 0.159 1659 Planarity : 0.003 0.038 1814 Dihedral : 3.940 18.094 1436 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.98 % Allowed : 16.98 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1292 helix: 0.97 (0.22), residues: 612 sheet: -0.42 (0.41), residues: 184 loop : -1.80 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 182 TYR 0.012 0.001 TYR B 63 PHE 0.025 0.001 PHE B 92 TRP 0.032 0.002 TRP B 26 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10922) covalent geometry : angle 0.51443 / 0.26 (14773) hydrogen bonds : bond 0.03328 / 2.07 ( 462) hydrogen bonds : angle 4.03438 / 2.76 ( 1350) glycosidic custom : bond 0.00066 / 0.04 ( 2) glycosidic custom : angle 1.18263 / 0.69 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7846 (m-80) cc_final: 0.7419 (m-80) REVERT: A 137 LYS cc_start: 0.7969 (mppt) cc_final: 0.7723 (mptt) REVERT: A 358 GLU cc_start: 0.7285 (tp30) cc_final: 0.7021 (tp30) REVERT: B 8 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7637 (tp30) REVERT: B 172 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.7065 (tp) REVERT: C 117 GLU cc_start: 0.8440 (mp0) cc_final: 0.8131 (mp0) REVERT: C 190 LYS cc_start: 0.7819 (mtmm) cc_final: 0.7116 (pptt) REVERT: C 236 MET cc_start: 0.7867 (ttp) cc_final: 0.7304 (tpp) REVERT: C 285 ASP cc_start: 0.6533 (m-30) cc_final: 0.6299 (m-30) REVERT: C 289 LYS cc_start: 0.7362 (mmtm) cc_final: 0.6932 (mmtm) outliers start: 23 outliers final: 22 residues processed: 183 average time/residue: 0.0923 time to fit residues: 24.8411 Evaluate side-chains 183 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 48 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 273 ASN A 372 ASN D 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.190969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129531 restraints weight = 12753.842| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.72 r_work: 0.3376 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10924 Z= 0.102 Angle : 0.520 14.008 14779 Z= 0.267 Chirality : 0.041 0.160 1659 Planarity : 0.003 0.037 1814 Dihedral : 3.873 18.174 1436 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.81 % Allowed : 17.50 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1292 helix: 1.06 (0.22), residues: 612 sheet: -0.34 (0.42), residues: 186 loop : -1.76 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 182 TYR 0.011 0.001 TYR B 63 PHE 0.023 0.001 PHE B 92 TRP 0.031 0.002 TRP B 26 HIS 0.005 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (10922) covalent geometry : angle 0.51959 / 0.27 (14773) hydrogen bonds : bond 0.03136 / 1.95 ( 462) hydrogen bonds : angle 3.96690 / 2.72 ( 1350) glycosidic custom : bond 0.00071 / 0.04 ( 2) glycosidic custom : angle 1.14162 / 0.66 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2657.78 seconds wall clock time: 46 minutes 18.79 seconds (2778.79 seconds total)