Starting phenix.real_space_refine on Tue Apr 29 09:51:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ebm_9026/04_2025/6ebm_9026_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ebm_9026/04_2025/6ebm_9026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ebm_9026/04_2025/6ebm_9026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ebm_9026/04_2025/6ebm_9026.map" model { file = "/net/cci-nas-00/data/ceres_data/6ebm_9026/04_2025/6ebm_9026_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ebm_9026/04_2025/6ebm_9026_neut.cif" } resolution = 4.0 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= -0.000 sd= 0.002 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 36 5.16 5 C 5636 2.51 5 N 1392 2.21 5 O 1468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8532 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2133 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 189 Chain: "D" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2133 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 189 Chain: "F" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2133 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 189 Chain: "H" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2133 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 189 Time building chain proxies: 5.62, per 1000 atoms: 0.66 Number of scatterers: 8532 At special positions: 0 Unit cell: (104.375, 104.375, 90.18, 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 36 16.00 O 1468 8.00 N 1392 7.00 C 5636 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: 2.19 Conformation dependent library (CDL) restraints added in 995.7 milliseconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.821A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.577A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 184 removed outlier: 3.814A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 4.160A pdb=" N GLN B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 removed outlier: 3.661A pdb=" N CYS B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.713A pdb=" N PHE B 250 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 253 through 276 removed outlier: 3.536A pdb=" N ILE B 257 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Proline residue: B 265 - end of helix removed outlier: 3.713A pdb=" N ASN B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.659A pdb=" N ILE B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.959A pdb=" N GLN B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 346 removed outlier: 3.684A pdb=" N LEU B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 369 removed outlier: 3.772A pdb=" N TRP B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.514A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 414 removed outlier: 3.503A pdb=" N ILE B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'D' and resid 121 through 131 removed outlier: 3.585A pdb=" N MET D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.559A pdb=" N LEU D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 184 removed outlier: 3.789A pdb=" N ALA D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 174 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 removed outlier: 4.221A pdb=" N GLN D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 243 removed outlier: 3.644A pdb=" N CYS D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.669A pdb=" N PHE D 250 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE D 251 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 276 removed outlier: 3.588A pdb=" N ILE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP D 259 " --> pdb=" O MET D 255 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Proline residue: D 265 - end of helix removed outlier: 3.710A pdb=" N ASN D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.676A pdb=" N ILE D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.930A pdb=" N GLN D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 346 removed outlier: 3.703A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 336 " --> pdb=" O PHE D 332 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 369 removed outlier: 3.764A pdb=" N TRP D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 369 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 removed outlier: 3.503A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 392 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 414 removed outlier: 3.506A pdb=" N ILE D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'F' and resid 121 through 131 removed outlier: 3.581A pdb=" N MET F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.532A pdb=" N TRP F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 184 removed outlier: 3.822A pdb=" N ALA F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 210 removed outlier: 4.082A pdb=" N GLN F 207 " --> pdb=" O HIS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 243 removed outlier: 3.774A pdb=" N CYS F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 239 " --> pdb=" O PHE F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 252 removed outlier: 3.651A pdb=" N PHE F 250 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR F 252 " --> pdb=" O GLY F 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 247 through 252' Processing helix chain 'F' and resid 253 through 275 removed outlier: 3.548A pdb=" N ILE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP F 259 " --> pdb=" O MET F 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.628A pdb=" N ILE F 294 " --> pdb=" O GLN F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 306 Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.924A pdb=" N GLN F 311 " --> pdb=" O SER F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 346 removed outlier: 3.640A pdb=" N LEU F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 336 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 369 removed outlier: 3.769A pdb=" N TRP F 363 " --> pdb=" O ASP F 359 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 365 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 399 removed outlier: 3.566A pdb=" N LEU F 389 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 414 removed outlier: 3.514A pdb=" N ILE F 405 " --> pdb=" O PRO F 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' Processing helix chain 'H' and resid 121 through 131 removed outlier: 3.583A pdb=" N MET H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.512A pdb=" N TRP H 150 " --> pdb=" O GLN H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 184 removed outlier: 3.814A pdb=" N ALA H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU H 174 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR H 184 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 210 removed outlier: 3.987A pdb=" N GLN H 207 " --> pdb=" O HIS H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 243 removed outlier: 3.723A pdb=" N CYS H 229 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL H 239 " --> pdb=" O PHE H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.614A pdb=" N PHE H 250 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE H 251 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 252 " --> pdb=" O GLY H 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 247 through 252' Processing helix chain 'H' and resid 253 through 276 removed outlier: 4.456A pdb=" N ASP H 259 " --> pdb=" O MET H 255 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE H 263 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) Proline residue: H 265 - end of helix removed outlier: 3.753A pdb=" N ASN H 276 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 296 removed outlier: 3.654A pdb=" N ILE H 294 " --> pdb=" O GLN H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 306 Processing helix chain 'H' and resid 307 through 319 removed outlier: 3.955A pdb=" N GLN H 311 " --> pdb=" O SER H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 346 removed outlier: 3.699A pdb=" N LEU H 327 " --> pdb=" O GLU H 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA H 345 " --> pdb=" O ALA H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 369 removed outlier: 3.774A pdb=" N TRP H 363 " --> pdb=" O ASP H 359 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 365 " --> pdb=" O PHE H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 399 removed outlier: 3.575A pdb=" N LEU H 389 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS H 390 " --> pdb=" O VAL H 386 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 391 " --> pdb=" O GLY H 387 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE H 392 " --> pdb=" O SER H 388 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 414 removed outlier: 3.651A pdb=" N ASN H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS H 414 " --> pdb=" O ASN H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 417 No H-bonds generated for 'chain 'H' and resid 415 through 417' 482 hydrogen bonds defined for protein. 1359 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: 1.95 Time building geometry restraints manager: 2.56 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: 2663 1.34 - 1.46: 2174 1.46 - 1.58: 3847 1.58 - 1.70: 0 1.70 - 1.81: 56 Bond restraints: 8740 Sorted by residual: bond pdb=" C LEU F 400 " pdb=" N PRO F 401 " ideal model delta sigma weight residual 1.333 1.365 -0.032 7.80e-03 1.64e+04 1.69e+01 bond pdb=" C LEU H 400 " pdb=" N PRO H 401 " ideal model delta sigma weight residual 1.333 1.362 -0.029 7.80e-03 1.64e+04 1.41e+01 bond pdb=" C LEU D 400 " pdb=" N PRO D 401 " ideal model delta sigma weight residual 1.333 1.361 -0.028 7.80e-03 1.64e+04 1.29e+01 bond pdb=" C LEU B 400 " pdb=" N PRO B 401 " ideal model delta sigma weight residual 1.333 1.361 -0.028 7.80e-03 1.64e+04 1.27e+01 bond pdb=" CB VAL H 371 " pdb=" CG1 VAL H 371 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.37e+00 ... (remaining 8735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 10615 1.60 - 3.21: 1077 3.21 - 4.81: 171 4.81 - 6.41: 44 6.41 - 8.01: 21 Bond angle restraints: 11928 Sorted by residual: angle pdb=" N ILE F 210 " pdb=" CA ILE F 210 " pdb=" C ILE F 210 " ideal model delta sigma weight residual 113.53 107.94 5.59 9.80e-01 1.04e+00 3.25e+01 angle pdb=" N ASP F 129 " pdb=" CA ASP F 129 " pdb=" C ASP F 129 " ideal model delta sigma weight residual 111.36 105.54 5.82 1.09e+00 8.42e-01 2.85e+01 angle pdb=" N ASP H 129 " pdb=" CA ASP H 129 " pdb=" C ASP H 129 " ideal model delta sigma weight residual 111.36 105.68 5.68 1.09e+00 8.42e-01 2.72e+01 angle pdb=" N ILE D 210 " pdb=" CA ILE D 210 " pdb=" C ILE D 210 " ideal model delta sigma weight residual 113.43 107.78 5.65 1.09e+00 8.42e-01 2.69e+01 angle pdb=" N ASP D 129 " pdb=" CA ASP D 129 " pdb=" C ASP D 129 " ideal model delta sigma weight residual 111.36 105.73 5.63 1.09e+00 8.42e-01 2.67e+01 ... (remaining 11923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.06: 4303 10.06 - 20.12: 561 20.12 - 30.17: 88 30.17 - 40.23: 16 40.23 - 50.29: 4 Dihedral angle restraints: 4972 sinusoidal: 1596 harmonic: 3376 Sorted by residual: dihedral pdb=" CA PHE B 235 " pdb=" C PHE B 235 " pdb=" N GLU B 236 " pdb=" CA GLU B 236 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA PHE D 235 " pdb=" C PHE D 235 " pdb=" N GLU D 236 " pdb=" CA GLU D 236 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA PRO F 186 " pdb=" C PRO F 186 " pdb=" N ILE F 187 " pdb=" CA ILE F 187 " ideal model delta harmonic sigma weight residual 180.00 155.84 24.16 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 593 0.037 - 0.074: 536 0.074 - 0.111: 202 0.111 - 0.148: 41 0.148 - 0.185: 40 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA VAL H 377 " pdb=" N VAL H 377 " pdb=" C VAL H 377 " pdb=" CB VAL H 377 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA VAL F 377 " pdb=" N VAL F 377 " pdb=" C VAL F 377 " pdb=" CB VAL F 377 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA VAL D 377 " pdb=" N VAL D 377 " pdb=" C VAL D 377 " pdb=" CB VAL D 377 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 1409 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 294 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C ILE D 294 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE D 294 " -0.018 2.00e-02 2.50e+03 pdb=" N MET D 295 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 294 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ILE B 294 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE B 294 " -0.017 2.00e-02 2.50e+03 pdb=" N MET B 295 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 294 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C ILE F 294 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE F 294 " 0.017 2.00e-02 2.50e+03 pdb=" N MET F 295 " 0.015 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 104 2.62 - 3.19: 8120 3.19 - 3.76: 13288 3.76 - 4.33: 18219 4.33 - 4.90: 27980 Nonbonded interactions: 67711 Sorted by model distance: nonbonded pdb=" OD1 ASP B 375 " pdb=" N MET B 376 " model vdw 2.049 3.120 nonbonded pdb=" OD1 ASP D 375 " pdb=" N MET D 376 " model vdw 2.050 3.120 nonbonded pdb=" OD1 ASP F 375 " pdb=" N MET F 376 " model vdw 2.052 3.120 nonbonded pdb=" OD1 ASP H 375 " pdb=" N MET H 376 " model vdw 2.054 3.120 nonbonded pdb=" O VAL D 365 " pdb=" OG1 THR D 369 " model vdw 2.249 3.040 ... (remaining 67706 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: 0.06 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.520 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.012 0.105 8740 Z= 0.528 Angle : 1.096 8.013 11928 Z= 0.655 Chirality : 0.060 0.185 1412 Planarity : 0.008 0.062 1508 Dihedral : 9.309 50.289 2812 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: -4.86 (0.18), residues: 1184 helix: -3.06 (0.12), residues: 832 sheet: None (None), residues: 0 loop : -3.08 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 232 HIS 0.012 0.007 HIS F 306 PHE 0.024 0.004 PHE D 329 TYR 0.011 0.003 TYR D 373 ARG 0.007 0.001 ARG H 299 Details of bonding type rmsd hydrogen bonds : bond 0.33277 ( 482) hydrogen bonds : angle 10.38633 ( 1359) covalent geometry : bond 0.01154 ( 8740) covalent geometry : angle 1.09645 (11928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 CYS cc_start: 0.8561 (m) cc_final: 0.8341 (p) REVERT: B 291 ILE cc_start: 0.9479 (mt) cc_final: 0.9180 (mt) REVERT: B 299 ARG cc_start: 0.8712 (ptp-170) cc_final: 0.8437 (ptp-170) REVERT: B 312 ILE cc_start: 0.9058 (mt) cc_final: 0.8806 (mm) REVERT: B 329 PHE cc_start: 0.8749 (t80) cc_final: 0.8535 (t80) REVERT: D 293 ARG cc_start: 0.8541 (ttt180) cc_final: 0.8322 (ttt-90) REVERT: D 312 ILE cc_start: 0.9089 (mt) cc_final: 0.8859 (mm) REVERT: F 180 PHE cc_start: 0.8861 (t80) cc_final: 0.8654 (t80) REVERT: F 229 CYS cc_start: 0.8739 (m) cc_final: 0.8426 (p) REVERT: F 259 ASP cc_start: 0.8812 (m-30) cc_final: 0.8573 (m-30) REVERT: F 263 ILE cc_start: 0.9201 (pt) cc_final: 0.8653 (pt) REVERT: F 291 ILE cc_start: 0.9213 (mt) cc_final: 0.8931 (mt) REVERT: F 296 ARG cc_start: 0.8982 (mtp180) cc_final: 0.8612 (mtp85) REVERT: F 312 ILE cc_start: 0.9064 (mt) cc_final: 0.8709 (mm) REVERT: H 229 CYS cc_start: 0.8624 (m) cc_final: 0.8364 (p) REVERT: H 258 ILE cc_start: 0.9511 (mt) cc_final: 0.9084 (mm) REVERT: H 291 ILE cc_start: 0.9251 (mt) cc_final: 0.9019 (mt) REVERT: H 296 ARG cc_start: 0.8959 (mtp180) cc_final: 0.8689 (mtp85) REVERT: H 415 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7950 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2628 time to fit residues: 101.5825 Evaluate side-chains 213 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 ASN F 410 ASN H 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.098284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074082 restraints weight = 27301.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076017 restraints weight = 14413.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077467 restraints weight = 10188.109| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8740 Z= 0.162 Angle : 0.681 9.336 11928 Z= 0.367 Chirality : 0.042 0.130 1412 Planarity : 0.006 0.037 1508 Dihedral : 5.533 23.628 1256 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.94 % Allowed : 12.95 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.31 (0.23), residues: 1184 helix: -1.08 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -2.46 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 150 HIS 0.003 0.001 HIS F 306 PHE 0.030 0.002 PHE B 292 TYR 0.016 0.002 TYR F 267 ARG 0.007 0.001 ARG F 305 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 482) hydrogen bonds : angle 5.39620 ( 1359) covalent geometry : bond 0.00348 ( 8740) covalent geometry : angle 0.68127 (11928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 285 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 299 ARG cc_start: 0.8918 (ptp-170) cc_final: 0.8251 (ptp90) REVERT: B 312 ILE cc_start: 0.9138 (mt) cc_final: 0.8936 (mm) REVERT: D 226 GLU cc_start: 0.9090 (tp30) cc_final: 0.8774 (tp30) REVERT: D 232 TRP cc_start: 0.8578 (t-100) cc_final: 0.8284 (t-100) REVERT: D 236 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7968 (mt-10) REVERT: D 266 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7420 (t80) REVERT: D 291 ILE cc_start: 0.9326 (mt) cc_final: 0.9056 (tt) REVERT: F 299 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8528 (ptp-170) REVERT: F 321 MET cc_start: 0.6729 (mmm) cc_final: 0.6515 (mmt) REVERT: F 329 PHE cc_start: 0.8728 (t80) cc_final: 0.8513 (t80) REVERT: H 263 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9189 (tp) REVERT: H 308 LYS cc_start: 0.8853 (mptt) cc_final: 0.8524 (mmtm) REVERT: H 321 MET cc_start: 0.6805 (mmm) cc_final: 0.6564 (mmt) outliers start: 15 outliers final: 6 residues processed: 289 average time/residue: 0.2419 time to fit residues: 90.3216 Evaluate side-chains 229 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 220 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 266 TYR Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 351 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 0.0470 chunk 26 optimal weight: 0.0030 chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 overall best weight: 0.3688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.098966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074625 restraints weight = 28389.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076754 restraints weight = 14551.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078160 restraints weight = 10068.771| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8740 Z= 0.127 Angle : 0.642 11.211 11928 Z= 0.334 Chirality : 0.042 0.151 1412 Planarity : 0.005 0.034 1508 Dihedral : 4.971 20.243 1256 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.11 % Allowed : 17.23 % Favored : 79.66 % 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: -1.20 (0.24), residues: 1184 helix: -0.29 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -2.00 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 232 HIS 0.004 0.001 HIS D 414 PHE 0.041 0.001 PHE D 292 TYR 0.025 0.002 TYR B 266 ARG 0.005 0.001 ARG H 350 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 482) hydrogen bonds : angle 4.91024 ( 1359) covalent geometry : bond 0.00271 ( 8740) covalent geometry : angle 0.64230 (11928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 277 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 CYS cc_start: 0.8698 (m) cc_final: 0.8299 (p) REVERT: B 232 TRP cc_start: 0.8557 (t-100) cc_final: 0.8316 (t-100) REVERT: B 299 ARG cc_start: 0.8947 (ptp-170) cc_final: 0.8487 (ptp-170) REVERT: B 312 ILE cc_start: 0.9071 (mt) cc_final: 0.8599 (mm) REVERT: B 315 GLN cc_start: 0.8644 (mt0) cc_final: 0.8304 (mp10) REVERT: D 226 GLU cc_start: 0.8894 (tp30) cc_final: 0.8690 (tp30) REVERT: D 232 TRP cc_start: 0.8731 (t-100) cc_final: 0.8415 (t-100) REVERT: D 236 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7768 (mt-10) REVERT: D 266 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.7305 (t80) REVERT: D 291 ILE cc_start: 0.9135 (mt) cc_final: 0.8694 (tt) REVERT: D 346 GLU cc_start: 0.7768 (tp30) cc_final: 0.7498 (tp30) REVERT: F 236 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8615 (mt-10) REVERT: F 293 ARG cc_start: 0.8418 (ttt180) cc_final: 0.8006 (ttt-90) REVERT: F 299 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8553 (ptt-90) REVERT: H 308 LYS cc_start: 0.8651 (mptt) cc_final: 0.8432 (mmtp) outliers start: 24 outliers final: 12 residues processed: 284 average time/residue: 0.2435 time to fit residues: 91.8245 Evaluate side-chains 245 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 266 TYR Chi-restraints excluded: chain H residue 290 GLN Chi-restraints excluded: chain H residue 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 61 optimal weight: 0.0270 chunk 1 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.098010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.074566 restraints weight = 27829.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.076816 restraints weight = 14170.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078269 restraints weight = 9686.213| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8740 Z= 0.132 Angle : 0.670 12.556 11928 Z= 0.345 Chirality : 0.043 0.142 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.709 18.845 1256 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.15 % Allowed : 20.34 % Favored : 75.52 % 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: -0.47 (0.25), residues: 1184 helix: 0.30 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -1.75 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 232 HIS 0.007 0.001 HIS D 414 PHE 0.041 0.001 PHE D 292 TYR 0.020 0.002 TYR B 266 ARG 0.007 0.001 ARG D 350 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 482) hydrogen bonds : angle 4.70207 ( 1359) covalent geometry : bond 0.00297 ( 8740) covalent geometry : angle 0.67018 (11928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 TRP cc_start: 0.8604 (t-100) cc_final: 0.8373 (t-100) REVERT: B 288 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8824 (t) REVERT: B 299 ARG cc_start: 0.8978 (ptp-170) cc_final: 0.8351 (ptp-170) REVERT: B 312 ILE cc_start: 0.9017 (mt) cc_final: 0.8495 (mm) REVERT: B 315 GLN cc_start: 0.8581 (mt0) cc_final: 0.8219 (mp10) REVERT: D 175 ILE cc_start: 0.9404 (pt) cc_final: 0.9184 (tp) REVERT: D 229 CYS cc_start: 0.8594 (m) cc_final: 0.8216 (p) REVERT: D 232 TRP cc_start: 0.8644 (t-100) cc_final: 0.8430 (t-100) REVERT: D 236 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7565 (mt-10) REVERT: F 299 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8553 (ptt-90) REVERT: H 153 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8102 (t80) REVERT: H 291 ILE cc_start: 0.9465 (tt) cc_final: 0.9215 (tt) REVERT: H 346 GLU cc_start: 0.8061 (tt0) cc_final: 0.7822 (tt0) REVERT: H 413 TYR cc_start: 0.8145 (t80) cc_final: 0.7878 (t80) outliers start: 32 outliers final: 17 residues processed: 265 average time/residue: 0.2314 time to fit residues: 80.4865 Evaluate side-chains 247 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 266 TYR Chi-restraints excluded: chain H residue 290 GLN Chi-restraints excluded: chain H residue 315 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 101 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.098347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073368 restraints weight = 27976.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075468 restraints weight = 14835.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076661 restraints weight = 10453.537| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8740 Z= 0.135 Angle : 0.660 10.753 11928 Z= 0.343 Chirality : 0.042 0.180 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.512 17.871 1256 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.89 % Allowed : 22.93 % Favored : 73.19 % 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: 0.39 (0.26), residues: 1184 helix: 0.92 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.01 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 232 HIS 0.005 0.001 HIS D 414 PHE 0.055 0.001 PHE F 292 TYR 0.019 0.002 TYR B 266 ARG 0.006 0.001 ARG D 240 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 482) hydrogen bonds : angle 4.63492 ( 1359) covalent geometry : bond 0.00312 ( 8740) covalent geometry : angle 0.65950 (11928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 TRP cc_start: 0.8717 (t-100) cc_final: 0.8393 (t-100) REVERT: B 299 ARG cc_start: 0.9034 (ptp-170) cc_final: 0.7715 (ptp90) REVERT: D 175 ILE cc_start: 0.9406 (pt) cc_final: 0.9177 (tp) REVERT: D 232 TRP cc_start: 0.8732 (t-100) cc_final: 0.8469 (t-100) REVERT: D 236 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7596 (mt-10) REVERT: D 288 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8683 (t) REVERT: D 293 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8090 (mtp180) REVERT: D 321 MET cc_start: 0.6295 (mmm) cc_final: 0.6093 (mmm) REVERT: D 346 GLU cc_start: 0.7886 (tp30) cc_final: 0.7494 (tp30) REVERT: F 232 TRP cc_start: 0.8869 (t-100) cc_final: 0.8323 (t-100) REVERT: F 299 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8635 (ptt-90) REVERT: F 346 GLU cc_start: 0.8396 (tt0) cc_final: 0.8116 (tm-30) REVERT: H 153 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8234 (t80) REVERT: H 232 TRP cc_start: 0.8911 (t-100) cc_final: 0.8571 (t-100) REVERT: H 299 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8058 (ptp-170) REVERT: H 321 MET cc_start: 0.6846 (mmt) cc_final: 0.6434 (mmt) REVERT: H 413 TYR cc_start: 0.8138 (t80) cc_final: 0.7919 (t80) outliers start: 30 outliers final: 21 residues processed: 253 average time/residue: 0.2593 time to fit residues: 85.5756 Evaluate side-chains 254 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 290 GLN Chi-restraints excluded: chain H residue 299 ARG Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 351 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 112 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.098118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.074260 restraints weight = 28062.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076049 restraints weight = 15370.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076061 restraints weight = 10078.200| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8740 Z= 0.143 Angle : 0.670 10.447 11928 Z= 0.353 Chirality : 0.043 0.156 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.491 16.907 1256 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.76 % Allowed : 23.83 % Favored : 72.41 % 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: 0.15 (0.26), residues: 1184 helix: 0.68 (0.19), residues: 828 sheet: None (None), residues: 0 loop : -1.16 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 232 HIS 0.006 0.001 HIS D 414 PHE 0.056 0.002 PHE F 292 TYR 0.020 0.002 TYR B 266 ARG 0.005 0.001 ARG D 240 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 482) hydrogen bonds : angle 4.61124 ( 1359) covalent geometry : bond 0.00331 ( 8740) covalent geometry : angle 0.67042 (11928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 TRP cc_start: 0.8719 (t-100) cc_final: 0.8401 (t-100) REVERT: D 175 ILE cc_start: 0.9377 (pt) cc_final: 0.9150 (tp) REVERT: D 232 TRP cc_start: 0.8791 (t-100) cc_final: 0.8470 (t-100) REVERT: D 236 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7508 (mt-10) REVERT: D 321 MET cc_start: 0.6317 (mmm) cc_final: 0.6090 (mmm) REVERT: D 409 PHE cc_start: 0.9000 (t80) cc_final: 0.8454 (t80) REVERT: D 415 ARG cc_start: 0.8555 (tmm-80) cc_final: 0.7853 (ttp80) REVERT: F 293 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7706 (ttt-90) REVERT: F 295 MET cc_start: 0.7868 (mmp) cc_final: 0.7559 (mmt) REVERT: F 346 GLU cc_start: 0.8510 (tt0) cc_final: 0.8204 (tm-30) REVERT: H 153 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8317 (t80) REVERT: H 232 TRP cc_start: 0.8972 (t-100) cc_final: 0.8749 (t-100) REVERT: H 240 ARG cc_start: 0.8706 (mtp180) cc_final: 0.8373 (mtp180) REVERT: H 293 ARG cc_start: 0.8546 (ttt-90) cc_final: 0.8123 (mtp85) REVERT: H 321 MET cc_start: 0.6851 (mmt) cc_final: 0.6497 (mmt) REVERT: H 413 TYR cc_start: 0.8182 (t80) cc_final: 0.7963 (t80) outliers start: 29 outliers final: 20 residues processed: 248 average time/residue: 0.2384 time to fit residues: 76.8191 Evaluate side-chains 242 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 351 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.098509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074692 restraints weight = 28114.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076546 restraints weight = 16607.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077026 restraints weight = 10443.327| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8740 Z= 0.139 Angle : 0.692 15.050 11928 Z= 0.356 Chirality : 0.043 0.212 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.331 19.845 1256 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.24 % Allowed : 25.00 % Favored : 71.76 % 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: 0.33 (0.26), residues: 1184 helix: 0.69 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 232 HIS 0.005 0.002 HIS D 414 PHE 0.057 0.002 PHE D 292 TYR 0.021 0.001 TYR B 266 ARG 0.007 0.001 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 482) hydrogen bonds : angle 4.58809 ( 1359) covalent geometry : bond 0.00326 ( 8740) covalent geometry : angle 0.69208 (11928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 TRP cc_start: 0.8681 (t-100) cc_final: 0.8390 (t-100) REVERT: B 346 GLU cc_start: 0.8368 (tp30) cc_final: 0.8044 (tp30) REVERT: D 175 ILE cc_start: 0.9348 (pt) cc_final: 0.9113 (tp) REVERT: D 232 TRP cc_start: 0.8699 (t-100) cc_final: 0.8434 (t-100) REVERT: D 236 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8012 (mt-10) REVERT: D 240 ARG cc_start: 0.9121 (ttm110) cc_final: 0.8521 (mpp80) REVERT: D 346 GLU cc_start: 0.8093 (tp30) cc_final: 0.7884 (tp30) REVERT: D 409 PHE cc_start: 0.8982 (t80) cc_final: 0.8457 (t80) REVERT: D 415 ARG cc_start: 0.8493 (tmm-80) cc_final: 0.7808 (ttp80) REVERT: F 295 MET cc_start: 0.7900 (mmp) cc_final: 0.7581 (mmt) REVERT: H 153 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (t80) REVERT: H 240 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8296 (mtp180) REVERT: H 413 TYR cc_start: 0.8132 (t80) cc_final: 0.7931 (t80) outliers start: 25 outliers final: 19 residues processed: 241 average time/residue: 0.2399 time to fit residues: 75.2541 Evaluate side-chains 240 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 315 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 29 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.098075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075680 restraints weight = 28547.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077452 restraints weight = 16452.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077768 restraints weight = 11235.666| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8740 Z= 0.141 Angle : 0.760 15.701 11928 Z= 0.384 Chirality : 0.044 0.284 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.324 19.863 1256 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.98 % Allowed : 26.30 % Favored : 70.73 % 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: 0.78 (0.26), residues: 1184 helix: 0.91 (0.19), residues: 796 sheet: None (None), residues: 0 loop : -0.10 (0.37), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 232 HIS 0.006 0.001 HIS D 414 PHE 0.057 0.001 PHE D 292 TYR 0.022 0.001 TYR B 266 ARG 0.007 0.001 ARG F 189 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 482) hydrogen bonds : angle 4.66787 ( 1359) covalent geometry : bond 0.00326 ( 8740) covalent geometry : angle 0.75999 (11928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 TRP cc_start: 0.8646 (t-100) cc_final: 0.8377 (t-100) REVERT: B 346 GLU cc_start: 0.8268 (tp30) cc_final: 0.7956 (tp30) REVERT: D 175 ILE cc_start: 0.9326 (pt) cc_final: 0.9098 (tp) REVERT: D 232 TRP cc_start: 0.8660 (t-100) cc_final: 0.8409 (t-100) REVERT: D 236 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7059 (mt-10) REVERT: D 240 ARG cc_start: 0.9018 (ttm110) cc_final: 0.8620 (mmt90) REVERT: D 305 ARG cc_start: 0.8706 (tpp80) cc_final: 0.8477 (tpp80) REVERT: D 346 GLU cc_start: 0.7964 (tp30) cc_final: 0.7748 (tp30) REVERT: D 409 PHE cc_start: 0.9003 (t80) cc_final: 0.8516 (t80) REVERT: D 415 ARG cc_start: 0.8286 (tmm-80) cc_final: 0.7896 (ttp80) REVERT: F 295 MET cc_start: 0.7880 (mmp) cc_final: 0.7611 (mmt) REVERT: F 299 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8558 (ptp90) REVERT: F 346 GLU cc_start: 0.8407 (tt0) cc_final: 0.8029 (tm-30) REVERT: H 153 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8170 (t80) REVERT: H 240 ARG cc_start: 0.8560 (mtp180) cc_final: 0.8255 (mtp180) REVERT: H 293 ARG cc_start: 0.8364 (mtp180) cc_final: 0.7973 (mtp85) outliers start: 23 outliers final: 18 residues processed: 239 average time/residue: 0.2377 time to fit residues: 74.5996 Evaluate side-chains 241 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 315 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 88 optimal weight: 40.0000 chunk 40 optimal weight: 0.0020 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.099001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075996 restraints weight = 28753.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078206 restraints weight = 17151.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.079315 restraints weight = 11143.191| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8740 Z= 0.137 Angle : 0.786 16.226 11928 Z= 0.391 Chirality : 0.045 0.359 1412 Planarity : 0.004 0.038 1508 Dihedral : 4.228 20.103 1256 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.33 % Allowed : 26.94 % Favored : 70.73 % 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: 0.88 (0.27), residues: 1184 helix: 0.94 (0.19), residues: 800 sheet: None (None), residues: 0 loop : 0.03 (0.38), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 232 HIS 0.007 0.001 HIS D 414 PHE 0.057 0.002 PHE D 292 TYR 0.022 0.001 TYR B 266 ARG 0.006 0.001 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 482) hydrogen bonds : angle 4.65422 ( 1359) covalent geometry : bond 0.00313 ( 8740) covalent geometry : angle 0.78610 (11928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 TRP cc_start: 0.8771 (t-100) cc_final: 0.8471 (t-100) REVERT: B 240 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.7857 (mmm-85) REVERT: B 346 GLU cc_start: 0.8308 (tp30) cc_final: 0.8016 (tp30) REVERT: D 175 ILE cc_start: 0.9320 (pt) cc_final: 0.9110 (tp) REVERT: D 232 TRP cc_start: 0.8705 (t-100) cc_final: 0.8436 (t-100) REVERT: D 236 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7140 (mt-10) REVERT: D 240 ARG cc_start: 0.9022 (ttm110) cc_final: 0.8620 (mmt90) REVERT: D 346 GLU cc_start: 0.7936 (tp30) cc_final: 0.7730 (tp30) REVERT: D 409 PHE cc_start: 0.8994 (t80) cc_final: 0.8507 (t80) REVERT: D 415 ARG cc_start: 0.8280 (tmm-80) cc_final: 0.7879 (ttp80) REVERT: F 295 MET cc_start: 0.7964 (mmp) cc_final: 0.7666 (mmt) REVERT: F 299 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8648 (ptp90) REVERT: F 346 GLU cc_start: 0.8402 (tt0) cc_final: 0.8063 (tm-30) REVERT: H 153 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8219 (t80) REVERT: H 175 ILE cc_start: 0.9379 (pt) cc_final: 0.9127 (tp) REVERT: H 240 ARG cc_start: 0.8602 (mtp180) cc_final: 0.8319 (mtp180) REVERT: H 293 ARG cc_start: 0.8421 (mtp180) cc_final: 0.7997 (mtp85) outliers start: 18 outliers final: 15 residues processed: 235 average time/residue: 0.2276 time to fit residues: 70.3230 Evaluate side-chains 237 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 315 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.0020 chunk 70 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 overall best weight: 0.4506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.099299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077350 restraints weight = 28561.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.078772 restraints weight = 19338.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.079230 restraints weight = 12684.630| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8740 Z= 0.140 Angle : 0.815 16.367 11928 Z= 0.404 Chirality : 0.046 0.360 1412 Planarity : 0.004 0.038 1508 Dihedral : 4.162 19.433 1256 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.46 % Allowed : 27.59 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1184 helix: 0.87 (0.19), residues: 828 sheet: None (None), residues: 0 loop : -0.15 (0.40), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 363 HIS 0.006 0.001 HIS D 414 PHE 0.059 0.001 PHE D 292 TYR 0.023 0.001 TYR B 266 ARG 0.006 0.001 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 482) hydrogen bonds : angle 4.65930 ( 1359) covalent geometry : bond 0.00322 ( 8740) covalent geometry : angle 0.81466 (11928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 TRP cc_start: 0.8797 (t-100) cc_final: 0.8494 (t-100) REVERT: D 175 ILE cc_start: 0.9312 (pt) cc_final: 0.9098 (tp) REVERT: D 232 TRP cc_start: 0.8755 (t-100) cc_final: 0.8456 (t-100) REVERT: D 236 GLU cc_start: 0.8700 (mt-10) cc_final: 0.7011 (mt-10) REVERT: D 240 ARG cc_start: 0.9055 (ttm110) cc_final: 0.7811 (mmt90) REVERT: D 409 PHE cc_start: 0.9007 (t80) cc_final: 0.8512 (t80) REVERT: D 415 ARG cc_start: 0.8371 (tmm-80) cc_final: 0.7911 (ttp80) REVERT: F 291 ILE cc_start: 0.9361 (tt) cc_final: 0.8356 (tt) REVERT: F 295 MET cc_start: 0.7975 (mmp) cc_final: 0.7711 (mmt) REVERT: F 346 GLU cc_start: 0.8416 (tt0) cc_final: 0.8070 (tm-30) REVERT: H 153 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8278 (t80) REVERT: H 175 ILE cc_start: 0.9366 (pt) cc_final: 0.9114 (tp) REVERT: H 240 ARG cc_start: 0.8655 (mtp180) cc_final: 0.8454 (mtp180) REVERT: H 293 ARG cc_start: 0.8460 (mtp180) cc_final: 0.8090 (mtp85) REVERT: H 299 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8685 (ptt-90) outliers start: 19 outliers final: 15 residues processed: 233 average time/residue: 0.2702 time to fit residues: 83.2626 Evaluate side-chains 235 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 299 ARG Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 315 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 101 optimal weight: 0.3980 chunk 113 optimal weight: 0.0000 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN D 256 ASN F 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.098869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075095 restraints weight = 28840.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077150 restraints weight = 16009.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078103 restraints weight = 11273.498| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8740 Z= 0.147 Angle : 0.830 15.849 11928 Z= 0.415 Chirality : 0.047 0.368 1412 Planarity : 0.004 0.038 1508 Dihedral : 4.163 19.095 1256 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.59 % Allowed : 28.24 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1184 helix: 0.86 (0.19), residues: 828 sheet: None (None), residues: 0 loop : -0.08 (0.40), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 363 HIS 0.006 0.001 HIS D 414 PHE 0.059 0.002 PHE D 292 TYR 0.022 0.001 TYR B 266 ARG 0.006 0.001 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 482) hydrogen bonds : angle 4.80230 ( 1359) covalent geometry : bond 0.00343 ( 8740) covalent geometry : angle 0.83044 (11928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.30 seconds wall clock time: 58 minutes 52.17 seconds (3532.17 seconds total)