Starting phenix.real_space_refine on Thu Feb 13 01:43:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ebm_9026/02_2025/6ebm_9026_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ebm_9026/02_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_9026/02_2025/6ebm_9026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ebm_9026/02_2025/6ebm_9026.map" model { file = "/net/cci-nas-00/data/ceres_data/6ebm_9026/02_2025/6ebm_9026_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ebm_9026/02_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-5592/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: 5.80, per 1000 atoms: 0.68 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.82 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: 2.01 Time building geometry restraints manager: 2.58 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.090 Find NCS groups from input model: 0.310 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- 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= 0.748 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 *********************** 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 : 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: 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: 0.2741 time to fit residues: 105.6987 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 : 1.337 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.098531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073453 restraints weight = 27348.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075432 restraints weight = 14646.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076785 restraints weight = 10374.232| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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= 0.229 Angle : 0.681 9.336 11928 Z= 0.367 Chirality : 0.042 0.130 1412 Planarity : 0.006 0.037 1508 Dihedral : 5.533 23.629 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 *********************** 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 : 0.988 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: 0.8913 (ptp-170) cc_final: 0.8255 (ptp90) REVERT: B 312 ILE cc_start: 0.9125 (mt) cc_final: 0.8921 (mm) REVERT: D 226 GLU cc_start: 0.9073 (tp30) cc_final: 0.8756 (tp30) REVERT: D 232 TRP cc_start: 0.8558 (t-100) cc_final: 0.8280 (t-100) REVERT: D 236 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7948 (mt-10) REVERT: D 266 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7420 (t80) REVERT: D 291 ILE cc_start: 0.9323 (mt) cc_final: 0.9052 (tt) REVERT: F 299 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8533 (ptp-170) REVERT: F 321 MET cc_start: 0.6724 (mmm) cc_final: 0.6505 (mmt) REVERT: F 329 PHE cc_start: 0.8707 (t80) cc_final: 0.8502 (t80) REVERT: H 263 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9190 (tp) REVERT: H 308 LYS cc_start: 0.8818 (mptt) cc_final: 0.8487 (mmtm) REVERT: H 321 MET cc_start: 0.6794 (mmm) cc_final: 0.6554 (mmt) outliers start: 15 outliers final: 6 residues processed: 289 average time/residue: 0.2517 time to fit residues: 94.1405 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 : 0.910 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 0.0670 chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 0.0060 chunk 37 optimal weight: 0.9990 overall best weight: 0.4934 ------------------------------------------------------------------------------- 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 = 0.098907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073549 restraints weight = 28437.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075628 restraints weight = 14844.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076656 restraints weight = 10361.059| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 0.044 8740 Z= 0.188 Angle : 0.639 10.863 11928 Z= 0.332 Chirality : 0.042 0.130 1412 Planarity : 0.005 0.033 1508 Dihedral : 4.945 20.176 1256 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.11 % Allowed : 17.49 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1184 helix: -0.26 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -2.02 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 232 HIS 0.003 0.001 HIS D 414 PHE 0.039 0.001 PHE D 292 TYR 0.024 0.002 TYR B 266 ARG 0.005 0.001 ARG H 350 *********************** 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 296 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.927 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 229 CYS cc_start: 0.8752 (m) cc_final: 0.8342 (p) REVERT: B 232 TRP cc_start: 0.8627 (t-100) cc_final: 0.8250 (t-100) REVERT: B 299 ARG cc_start: 0.8958 (ptp-170) cc_final: 0.8338 (ptp90) REVERT: B 312 ILE cc_start: 0.9117 (mt) cc_final: 0.8638 (mm) REVERT: B 315 GLN cc_start: 0.8665 (mt0) cc_final: 0.8336 (mp10) REVERT: B 414 HIS cc_start: 0.8210 (m-70) cc_final: 0.8009 (m-70) REVERT: D 226 GLU cc_start: 0.8940 (tp30) cc_final: 0.8736 (tp30) REVERT: D 232 TRP cc_start: 0.8785 (t-100) cc_final: 0.8460 (t-100) REVERT: D 236 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7471 (mt-10) REVERT: D 266 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7402 (t80) REVERT: D 291 ILE cc_start: 0.9099 (mt) cc_final: 0.8666 (tt) REVERT: D 346 GLU cc_start: 0.7824 (tp30) cc_final: 0.7541 (tp30) REVERT: F 232 TRP cc_start: 0.9023 (t-100) cc_final: 0.8800 (t-100) REVERT: F 236 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8580 (mt-10) REVERT: F 293 ARG cc_start: 0.8425 (ttt180) cc_final: 0.7995 (ttt-90) REVERT: F 299 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8580 (ptt-90) REVERT: H 308 LYS cc_start: 0.8688 (mptt) cc_final: 0.8467 (mmtp) outliers start: 24 outliers final: 13 residues processed: 279 average time/residue: 0.2335 time to fit residues: 85.9077 Evaluate side-chains 246 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 315 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: 10.0000 chunk 25 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.099365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074709 restraints weight = 27883.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.077356 restraints weight = 15409.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.077097 restraints weight = 9774.071| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8740 Z= 0.200 Angle : 0.678 12.940 11928 Z= 0.346 Chirality : 0.043 0.142 1412 Planarity : 0.004 0.036 1508 Dihedral : 4.683 18.742 1256 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.15 % Allowed : 20.21 % Favored : 75.65 % 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: -0.44 (0.25), residues: 1184 helix: 0.32 (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 0.039 0.001 PHE D 292 TYR 0.020 0.002 TYR B 266 ARG 0.005 0.001 ARG D 350 *********************** 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 278 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.926 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 232 TRP cc_start: 0.8776 (t-100) cc_final: 0.8437 (t-100) REVERT: B 236 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 288 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8817 (t) REVERT: B 299 ARG cc_start: 0.9018 (ptp-170) cc_final: 0.8269 (ptp90) REVERT: B 312 ILE cc_start: 0.9038 (mt) cc_final: 0.8531 (mm) REVERT: B 315 GLN cc_start: 0.8588 (mt0) cc_final: 0.8219 (mp10) REVERT: D 175 ILE cc_start: 0.9433 (pt) cc_final: 0.9209 (tp) REVERT: D 229 CYS cc_start: 0.8754 (m) cc_final: 0.8305 (p) REVERT: D 232 TRP cc_start: 0.8828 (t-100) cc_final: 0.8481 (t-100) REVERT: D 236 GLU cc_start: 0.8621 (mt-10) cc_final: 0.7876 (mt-10) REVERT: F 232 TRP cc_start: 0.9081 (t-100) cc_final: 0.8805 (t-100) REVERT: F 236 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8503 (mt-10) REVERT: H 153 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8304 (t80) REVERT: H 291 ILE cc_start: 0.9472 (tt) cc_final: 0.9188 (tt) REVERT: H 308 LYS cc_start: 0.8713 (mptt) cc_final: 0.8513 (mmtp) REVERT: H 321 MET cc_start: 0.7001 (mmt) cc_final: 0.6792 (mmt) REVERT: H 346 GLU cc_start: 0.8184 (tt0) cc_final: 0.7922 (tt0) REVERT: H 413 TYR cc_start: 0.8160 (t80) cc_final: 0.7916 (t80) outliers start: 32 outliers final: 17 residues processed: 259 average time/residue: 0.2378 time to fit residues: 80.4806 Evaluate side-chains 242 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 D residue 153 PHE Chi-restraints excluded: chain D residue 315 GLN 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 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 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: 0.9980 chunk 110 optimal weight: 0.0000 chunk 112 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 0.0270 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 30.0000 overall best weight: 0.4042 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.098947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.073991 restraints weight = 28086.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076172 restraints weight = 14776.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077668 restraints weight = 10343.241| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8740 Z= 0.190 Angle : 0.648 10.745 11928 Z= 0.338 Chirality : 0.042 0.123 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.504 17.929 1256 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.11 % Allowed : 22.41 % Favored : 74.48 % 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: 0.37 (0.26), residues: 1184 helix: 0.92 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.06 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 232 HIS 0.001 0.000 HIS H 306 PHE 0.057 0.001 PHE F 292 TYR 0.020 0.001 TYR B 266 ARG 0.006 0.001 ARG D 240 *********************** 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 269 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 1.042 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: 0.8651 (t-100) cc_final: 0.8400 (t-100) REVERT: B 236 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7980 (mt-10) REVERT: B 288 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.9026 (t) REVERT: B 299 ARG cc_start: 0.9015 (ptp-170) cc_final: 0.8373 (ptp90) REVERT: B 312 ILE cc_start: 0.9024 (mt) cc_final: 0.8451 (mm) REVERT: B 315 GLN cc_start: 0.8533 (mt0) cc_final: 0.8167 (mp10) REVERT: B 318 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8910 (ttpt) REVERT: D 175 ILE cc_start: 0.9388 (pt) cc_final: 0.9155 (tp) REVERT: D 183 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: D 232 TRP cc_start: 0.8688 (t-100) cc_final: 0.8448 (t-100) REVERT: D 236 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7278 (mt-10) REVERT: D 240 ARG cc_start: 0.9126 (ttm110) cc_final: 0.8803 (mtt-85) REVERT: D 293 ARG cc_start: 0.8357 (mtp180) cc_final: 0.8124 (mtp180) REVERT: D 346 GLU cc_start: 0.7802 (tp30) cc_final: 0.7415 (tp30) REVERT: F 232 TRP cc_start: 0.8874 (t-100) cc_final: 0.8638 (t-100) REVERT: F 236 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8181 (mt-10) REVERT: F 346 GLU cc_start: 0.8361 (tt0) cc_final: 0.8125 (tm-30) REVERT: H 153 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8183 (t80) REVERT: H 232 TRP cc_start: 0.8857 (t-100) cc_final: 0.8608 (t-100) REVERT: H 299 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8054 (ptp-170) REVERT: H 413 TYR cc_start: 0.8115 (t80) cc_final: 0.7882 (t80) outliers start: 24 outliers final: 15 residues processed: 255 average time/residue: 0.2497 time to fit residues: 82.4712 Evaluate side-chains 246 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 326 LEU 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 238 LEU Chi-restraints excluded: chain H residue 299 ARG Chi-restraints excluded: chain H residue 315 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.096757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072449 restraints weight = 28167.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073672 restraints weight = 16952.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073865 restraints weight = 11553.230| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8740 Z= 0.280 Angle : 0.697 13.393 11928 Z= 0.368 Chirality : 0.044 0.136 1412 Planarity : 0.004 0.036 1508 Dihedral : 4.547 17.338 1256 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.18 % Allowed : 22.41 % 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: 0.69 (0.19), residues: 828 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 232 HIS 0.004 0.002 HIS B 306 PHE 0.044 0.002 PHE D 292 TYR 0.020 0.002 TYR B 266 ARG 0.006 0.001 ARG F 189 *********************** 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 268 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 0.903 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: B 232 TRP cc_start: 0.8759 (t-100) cc_final: 0.8464 (t-100) REVERT: B 236 GLU cc_start: 0.8837 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 299 ARG cc_start: 0.9043 (ptp-170) cc_final: 0.8148 (ptp-170) REVERT: B 346 GLU cc_start: 0.8393 (tp30) cc_final: 0.8050 (tp30) REVERT: D 232 TRP cc_start: 0.8791 (t-100) cc_final: 0.8487 (t-100) REVERT: D 236 GLU cc_start: 0.8700 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 240 ARG cc_start: 0.9246 (ttm110) cc_final: 0.8758 (mmt90) REVERT: D 409 PHE cc_start: 0.9042 (t80) cc_final: 0.8374 (t80) REVERT: F 183 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7716 (pt0) REVERT: F 232 TRP cc_start: 0.9103 (t-100) cc_final: 0.8762 (t-100) REVERT: F 236 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8305 (mt-10) REVERT: F 295 MET cc_start: 0.7937 (mmp) cc_final: 0.7643 (mmt) REVERT: H 153 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8324 (t80) REVERT: H 183 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: H 240 ARG cc_start: 0.8772 (mtp180) cc_final: 0.8429 (mtp180) REVERT: H 293 ARG cc_start: 0.8567 (ttt-90) cc_final: 0.8159 (mtp85) REVERT: H 321 MET cc_start: 0.7009 (mmm) cc_final: 0.6715 (mmt) outliers start: 40 outliers final: 27 residues processed: 245 average time/residue: 0.2368 time to fit residues: 75.9194 Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 351 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 315 GLN 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 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 259 ASP 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 337 LEU 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 183 GLU Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 290 GLN Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 351 ASP Chi-restraints excluded: chain H residue 359 ASP Chi-restraints excluded: chain H residue 392 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 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 = 0.3719 r_free = 0.3719 target = 0.097930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072565 restraints weight = 28011.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074631 restraints weight = 15089.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075654 restraints weight = 10670.980| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5533 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= 0.218 Angle : 0.721 14.885 11928 Z= 0.370 Chirality : 0.043 0.236 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.382 16.891 1256 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.37 % Allowed : 23.70 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.26), residues: 1184 helix: 0.91 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 232 HIS 0.005 0.001 HIS D 414 PHE 0.063 0.002 PHE F 292 TYR 0.021 0.002 TYR B 266 ARG 0.004 0.001 ARG D 305 *********************** 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: 26 poor density : 229 time to evaluate : 0.933 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 232 TRP cc_start: 0.8690 (t-100) cc_final: 0.8443 (t-100) REVERT: B 236 GLU cc_start: 0.8776 (mt-10) cc_final: 0.7756 (mt-10) REVERT: B 299 ARG cc_start: 0.8994 (ptp-170) cc_final: 0.8290 (ptp90) REVERT: B 346 GLU cc_start: 0.8388 (tp30) cc_final: 0.8071 (tp30) REVERT: D 232 TRP cc_start: 0.8707 (t-100) cc_final: 0.8388 (t-100) REVERT: D 236 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7483 (mt-10) REVERT: D 409 PHE cc_start: 0.9018 (t80) cc_final: 0.8409 (t80) REVERT: D 415 ARG cc_start: 0.8541 (tmm-80) cc_final: 0.7875 (ttp80) REVERT: F 232 TRP cc_start: 0.8986 (t-100) cc_final: 0.8725 (t-100) REVERT: F 236 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8267 (mt-10) REVERT: F 295 MET cc_start: 0.8027 (mmp) cc_final: 0.7656 (mmt) REVERT: F 299 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8607 (ptt-90) REVERT: H 153 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8206 (t80) REVERT: H 240 ARG cc_start: 0.8625 (mtp180) cc_final: 0.8288 (mtp180) REVERT: H 299 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8553 (ptt-90) outliers start: 26 outliers final: 17 residues processed: 240 average time/residue: 0.2520 time to fit residues: 78.5613 Evaluate side-chains 239 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 315 GLN 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 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 299 ARG Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 392 ILE 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: 4.9990 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN H 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071965 restraints weight = 28574.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073270 restraints weight = 15931.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073210 restraints weight = 11570.201| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.005 0.048 8740 Z= 0.322 Angle : 0.760 13.460 11928 Z= 0.399 Chirality : 0.046 0.279 1412 Planarity : 0.004 0.036 1508 Dihedral : 4.476 16.837 1256 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.02 % Allowed : 24.09 % Favored : 71.89 % 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: 0.61 (0.26), residues: 1184 helix: 0.86 (0.19), residues: 824 sheet: None (None), residues: 0 loop : -0.47 (0.38), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 232 HIS 0.005 0.002 HIS B 306 PHE 0.054 0.002 PHE D 292 TYR 0.022 0.002 TYR B 266 ARG 0.008 0.001 ARG D 240 *********************** 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 246 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.021 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 171 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7664 (ptp) REVERT: B 232 TRP cc_start: 0.8769 (t-100) cc_final: 0.8502 (t-100) REVERT: B 236 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8296 (mt-10) REVERT: D 163 ARG cc_start: 0.8869 (ttt180) cc_final: 0.8632 (ttm-80) REVERT: D 232 TRP cc_start: 0.8762 (t-100) cc_final: 0.8411 (t-100) REVERT: D 236 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8160 (mt-10) REVERT: D 240 ARG cc_start: 0.9178 (ttm110) cc_final: 0.8594 (mpp80) REVERT: D 409 PHE cc_start: 0.9079 (t80) cc_final: 0.8378 (t80) REVERT: F 299 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8488 (ptt-90) REVERT: H 153 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8328 (t80) REVERT: H 183 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: H 240 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8467 (mtp180) REVERT: H 293 ARG cc_start: 0.8524 (mtp180) cc_final: 0.8049 (mtp85) REVERT: H 299 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8505 (ptt-90) outliers start: 31 outliers final: 26 residues processed: 230 average time/residue: 0.2540 time to fit residues: 75.9886 Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 171 MET 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 259 ASP Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 337 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 337 LEU 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 183 GLU Chi-restraints excluded: chain H residue 230 ILE Chi-restraints excluded: chain H residue 238 LEU 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 Chi-restraints excluded: chain H residue 359 ASP Chi-restraints excluded: chain H residue 392 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.0040 chunk 61 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 112 optimal weight: 0.4980 chunk 88 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.097703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074301 restraints weight = 28131.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076458 restraints weight = 14511.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077660 restraints weight = 9865.449| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8740 Z= 0.203 Angle : 0.767 15.729 11928 Z= 0.384 Chirality : 0.044 0.250 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.265 18.462 1256 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.11 % Allowed : 25.26 % Favored : 71.63 % 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: 1.05 (0.27), residues: 1184 helix: 1.08 (0.19), residues: 800 sheet: None (None), residues: 0 loop : 0.09 (0.39), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 232 HIS 0.005 0.001 HIS D 414 PHE 0.053 0.001 PHE D 292 TYR 0.023 0.001 TYR B 266 ARG 0.007 0.001 ARG D 240 *********************** 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 258 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.931 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 171 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7699 (ptp) REVERT: B 232 TRP cc_start: 0.8632 (t-100) cc_final: 0.8381 (t-100) REVERT: B 236 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8108 (mt-10) REVERT: B 299 ARG cc_start: 0.9107 (ptp-170) cc_final: 0.8886 (ptt180) REVERT: B 346 GLU cc_start: 0.8472 (tp30) cc_final: 0.8195 (tp30) REVERT: D 232 TRP cc_start: 0.8674 (t-100) cc_final: 0.8364 (t-100) REVERT: D 236 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7988 (mt-10) REVERT: D 240 ARG cc_start: 0.9018 (ttm110) cc_final: 0.8604 (mpp80) REVERT: D 409 PHE cc_start: 0.8981 (t80) cc_final: 0.8398 (t80) REVERT: D 415 ARG cc_start: 0.8487 (tmm-80) cc_final: 0.7845 (ttp80) REVERT: F 295 MET cc_start: 0.8030 (mmp) cc_final: 0.7717 (mmt) REVERT: F 346 GLU cc_start: 0.8464 (tt0) cc_final: 0.8124 (tm-30) REVERT: H 153 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8159 (t80) REVERT: H 240 ARG cc_start: 0.8558 (mtp180) cc_final: 0.8291 (mtp180) REVERT: H 293 ARG cc_start: 0.8502 (mtp180) cc_final: 0.8042 (mtp85) REVERT: H 299 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8768 (ptt-90) outliers start: 24 outliers final: 20 residues processed: 245 average time/residue: 0.2471 time to fit residues: 78.4262 Evaluate side-chains 248 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 171 MET 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 315 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 402 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 299 ARG Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.097480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073925 restraints weight = 27970.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075958 restraints weight = 14885.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.077199 restraints weight = 10261.639| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8740 Z= 0.226 Angle : 0.791 15.873 11928 Z= 0.398 Chirality : 0.046 0.297 1412 Planarity : 0.004 0.039 1508 Dihedral : 4.239 18.041 1256 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.24 % Allowed : 26.04 % 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: 0.99 (0.27), residues: 1184 helix: 1.02 (0.19), residues: 812 sheet: None (None), residues: 0 loop : 0.06 (0.39), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 232 HIS 0.005 0.001 HIS D 414 PHE 0.055 0.002 PHE D 292 TYR 0.023 0.001 TYR B 266 ARG 0.007 0.001 ARG D 240 ********************** 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 252 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.988 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 171 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7702 (ptp) REVERT: B 185 LEU cc_start: 0.9380 (tp) cc_final: 0.9048 (tp) REVERT: B 232 TRP cc_start: 0.8688 (t-100) cc_final: 0.8479 (t-100) REVERT: B 236 GLU cc_start: 0.8651 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 346 GLU cc_start: 0.8421 (tp30) cc_final: 0.8147 (tp30) REVERT: D 232 TRP cc_start: 0.8675 (t-100) cc_final: 0.8401 (t-100) REVERT: D 236 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7247 (mt-10) REVERT: D 299 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8395 (ptp-170) REVERT: D 409 PHE cc_start: 0.9023 (t80) cc_final: 0.8454 (t80) REVERT: D 415 ARG cc_start: 0.8430 (tmm-80) cc_final: 0.7823 (ttp80) REVERT: F 295 MET cc_start: 0.8056 (mmp) cc_final: 0.7800 (mmt) REVERT: F 299 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8391 (ptt-90) REVERT: H 153 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8152 (t80) REVERT: H 240 ARG cc_start: 0.8562 (mtp180) cc_final: 0.8325 (mtp180) REVERT: H 293 ARG cc_start: 0.8552 (mtp180) cc_final: 0.8057 (mtp85) REVERT: H 299 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8488 (ptt-90) REVERT: H 321 MET cc_start: 0.6658 (mmt) cc_final: 0.6400 (ttm) outliers start: 25 outliers final: 19 residues processed: 238 average time/residue: 0.2560 time to fit residues: 78.4854 Evaluate side-chains 246 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 171 MET 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 299 ARG Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 402 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 299 ARG Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain H residue 408 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 73 optimal weight: 0.0970 chunk 106 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.096256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074150 restraints weight = 27920.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075134 restraints weight = 16227.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075585 restraints weight = 11762.039| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8740 Z= 0.339 Angle : 0.842 15.409 11928 Z= 0.432 Chirality : 0.048 0.299 1412 Planarity : 0.005 0.039 1508 Dihedral : 4.455 18.682 1256 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.50 % Allowed : 26.04 % Favored : 70.47 % 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: 0.97 (0.27), residues: 1184 helix: 1.05 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 232 HIS 0.005 0.002 HIS B 306 PHE 0.055 0.002 PHE D 292 TYR 0.023 0.002 TYR B 266 ARG 0.007 0.001 ARG D 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.00 seconds wall clock time: 55 minutes 33.01 seconds (3333.01 seconds total)