Starting phenix.real_space_refine on Mon Nov 17 21:04:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ebm_9026/11_2025/6ebm_9026_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ebm_9026/11_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_9026/11_2025/6ebm_9026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ebm_9026/11_2025/6ebm_9026.map" model { file = "/net/cci-nas-00/data/ceres_data/6ebm_9026/11_2025/6ebm_9026_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ebm_9026/11_2025/6ebm_9026_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'GLU:plan': 14, 'PHE:plan': 4, 'ARG:plan': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 7, 'HIS:plan': 2} 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: {'GLU:plan': 14, 'PHE:plan': 4, 'ARG:plan': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 7, 'HIS:plan': 2} 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: {'GLU:plan': 14, 'PHE:plan': 4, 'ARG:plan': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 7, 'HIS:plan': 2} 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: {'GLU:plan': 14, 'PHE:plan': 4, 'ARG:plan': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 189 Time building chain proxies: 2.16, per 1000 atoms: 0.25 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: 0.70 Conformation dependent library (CDL) restraints added in 423.0 milliseconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 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: 0.97 Time building geometry restraints manager: 0.95 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 4.210 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.100 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.105 8740 Z= 0.528 Angle : 1.096 8.013 11928 Z= 0.655 Chirality : 0.060 0.185 1412 Planarity : 0.008 0.062 1508 Dihedral : 9.309 50.289 2812 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.007 0.001 ARG H 299 TYR 0.011 0.003 TYR D 373 PHE 0.024 0.004 PHE D 329 TRP 0.013 0.003 TRP D 232 HIS 0.012 0.007 HIS F 306 Details of bonding type rmsd covalent geometry : bond 0.01154 ( 8740) covalent geometry : angle 1.09645 (11928) hydrogen bonds : bond 0.33277 ( 482) hydrogen bonds : angle 10.38633 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.346 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: 0.1337 time to fit residues: 51.8746 Evaluate side-chains 213 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.098107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073718 restraints weight = 27671.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.075801 restraints weight = 14543.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076864 restraints weight = 10234.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077895 restraints weight = 8567.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.078134 restraints weight = 7633.622| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8740 Z= 0.162 Angle : 0.681 9.379 11928 Z= 0.369 Chirality : 0.043 0.132 1412 Planarity : 0.006 0.039 1508 Dihedral : 5.576 23.587 1256 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.20 % Allowed : 12.82 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.23), residues: 1184 helix: -1.09 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -2.44 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 305 TYR 0.013 0.002 TYR F 267 PHE 0.029 0.002 PHE B 292 TRP 0.015 0.002 TRP H 232 HIS 0.003 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8740) covalent geometry : angle 0.68083 (11928) hydrogen bonds : bond 0.05825 ( 482) hydrogen bonds : angle 5.42786 ( 1359) *********************** 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: 17 poor density : 283 time to evaluate : 0.329 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 299 ARG cc_start: 0.8914 (ptp-170) cc_final: 0.8259 (ptp90) REVERT: B 312 ILE cc_start: 0.9140 (mt) cc_final: 0.8925 (mm) REVERT: D 226 GLU cc_start: 0.9085 (tp30) cc_final: 0.8767 (tp30) REVERT: D 232 TRP cc_start: 0.8575 (t-100) cc_final: 0.8334 (t-100) REVERT: D 236 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8042 (mt-10) REVERT: D 266 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.7312 (t80) REVERT: D 291 ILE cc_start: 0.9326 (mt) cc_final: 0.9073 (tt) REVERT: F 299 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8534 (ptp-170) REVERT: F 321 MET cc_start: 0.6673 (mmm) cc_final: 0.6460 (mmt) REVERT: F 329 PHE cc_start: 0.8727 (t80) cc_final: 0.8520 (t80) REVERT: H 263 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9178 (tp) REVERT: H 308 LYS cc_start: 0.8840 (mptt) cc_final: 0.8534 (mmtm) outliers start: 17 outliers final: 7 residues processed: 288 average time/residue: 0.1183 time to fit residues: 44.2532 Evaluate side-chains 232 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 222 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 266 TYR Chi-restraints excluded: chain H residue 290 GLN 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 30 optimal weight: 0.0670 chunk 74 optimal weight: 0.1980 chunk 14 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.098996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074671 restraints weight = 27938.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076804 restraints weight = 14364.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078233 restraints weight = 9931.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078667 restraints weight = 8171.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.079421 restraints weight = 7580.937| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8740 Z= 0.127 Angle : 0.642 10.802 11928 Z= 0.333 Chirality : 0.042 0.136 1412 Planarity : 0.005 0.034 1508 Dihedral : 4.973 20.887 1256 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.85 % Allowed : 16.97 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.25), residues: 1184 helix: -0.27 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -1.97 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 350 TYR 0.026 0.002 TYR B 266 PHE 0.041 0.002 PHE D 292 TRP 0.021 0.002 TRP H 232 HIS 0.004 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8740) covalent geometry : angle 0.64166 (11928) hydrogen bonds : bond 0.04653 ( 482) hydrogen bonds : angle 4.96976 ( 1359) *********************** 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 300 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 CYS cc_start: 0.8674 (m) cc_final: 0.8285 (p) REVERT: B 232 TRP cc_start: 0.8514 (t-100) cc_final: 0.8212 (t-100) REVERT: B 299 ARG cc_start: 0.8928 (ptp-170) cc_final: 0.8477 (ptp-170) REVERT: B 312 ILE cc_start: 0.9101 (mt) cc_final: 0.8631 (mm) REVERT: B 315 GLN cc_start: 0.8600 (mt0) cc_final: 0.8283 (mp10) REVERT: D 226 GLU cc_start: 0.8892 (tp30) cc_final: 0.8681 (mm-30) REVERT: D 232 TRP cc_start: 0.8652 (t-100) cc_final: 0.8389 (t-100) REVERT: D 236 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7917 (mt-10) REVERT: D 266 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.7255 (t80) REVERT: D 291 ILE cc_start: 0.9141 (mt) cc_final: 0.8707 (tt) REVERT: D 346 GLU cc_start: 0.7744 (tp30) cc_final: 0.7529 (tp30) REVERT: D 413 TYR cc_start: 0.7796 (t80) cc_final: 0.7485 (t80) REVERT: F 299 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8412 (ptp-170) REVERT: H 308 LYS cc_start: 0.8647 (mptt) cc_final: 0.8425 (mmtp) outliers start: 22 outliers final: 11 residues processed: 283 average time/residue: 0.1095 time to fit residues: 40.9078 Evaluate side-chains 241 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 228 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE 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 238 LEU Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain 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 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.096806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072835 restraints weight = 28712.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074908 restraints weight = 14717.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075797 restraints weight = 10158.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077012 restraints weight = 8590.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077279 restraints weight = 7572.023| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8740 Z= 0.146 Angle : 0.662 11.558 11928 Z= 0.346 Chirality : 0.043 0.147 1412 Planarity : 0.004 0.036 1508 Dihedral : 4.761 19.136 1256 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.66 % Allowed : 19.82 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.25), residues: 1184 helix: 0.28 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -1.81 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 240 TYR 0.019 0.002 TYR B 266 PHE 0.053 0.002 PHE H 292 TRP 0.026 0.002 TRP H 232 HIS 0.006 0.002 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8740) covalent geometry : angle 0.66188 (11928) hydrogen bonds : bond 0.04316 ( 482) hydrogen bonds : angle 4.83112 ( 1359) *********************** 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 281 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 CYS cc_start: 0.8703 (m) cc_final: 0.8387 (p) REVERT: B 232 TRP cc_start: 0.8633 (t-100) cc_final: 0.8415 (t-100) REVERT: B 236 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 288 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8884 (p) REVERT: B 299 ARG cc_start: 0.9010 (ptp-170) cc_final: 0.8106 (ptp90) REVERT: B 312 ILE cc_start: 0.9035 (mt) cc_final: 0.8539 (mm) REVERT: B 315 GLN cc_start: 0.8638 (mt0) cc_final: 0.8294 (mp10) REVERT: D 229 CYS cc_start: 0.8656 (m) cc_final: 0.8325 (p) REVERT: D 232 TRP cc_start: 0.8681 (t-100) cc_final: 0.8454 (t-100) REVERT: D 236 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7218 (mt-10) REVERT: D 266 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7268 (t80) REVERT: F 232 TRP cc_start: 0.8839 (t-100) cc_final: 0.8563 (t-100) REVERT: F 240 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7908 (mmm160) REVERT: F 299 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8310 (ptp-170) REVERT: H 153 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8099 (t80) REVERT: H 308 LYS cc_start: 0.8707 (mptt) cc_final: 0.8506 (mmtp) REVERT: H 346 GLU cc_start: 0.8137 (tt0) cc_final: 0.7908 (tt0) REVERT: H 413 TYR cc_start: 0.8181 (t80) cc_final: 0.7934 (t80) outliers start: 36 outliers final: 21 residues processed: 257 average time/residue: 0.1130 time to fit residues: 38.2442 Evaluate side-chains 251 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 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 Chi-restraints excluded: chain H residue 351 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 27 optimal weight: 0.5980 chunk 85 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 chunk 102 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.097412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072176 restraints weight = 28374.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074110 restraints weight = 15116.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075336 restraints weight = 10555.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075797 restraints weight = 8795.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076159 restraints weight = 8131.319| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5004 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= 0.151 Angle : 0.670 10.850 11928 Z= 0.353 Chirality : 0.043 0.132 1412 Planarity : 0.004 0.036 1508 Dihedral : 4.612 17.843 1256 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.89 % Allowed : 22.41 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1184 helix: 0.59 (0.19), residues: 828 sheet: None (None), residues: 0 loop : -1.36 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 189 TYR 0.019 0.002 TYR B 266 PHE 0.050 0.002 PHE D 292 TRP 0.027 0.002 TRP H 232 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8740) covalent geometry : angle 0.67014 (11928) hydrogen bonds : bond 0.04166 ( 482) hydrogen bonds : angle 4.69682 ( 1359) *********************** 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: 30 poor density : 239 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 PHE cc_start: 0.8782 (t80) cc_final: 0.8147 (t80) REVERT: B 232 TRP cc_start: 0.8749 (t-100) cc_final: 0.8422 (t-100) REVERT: B 236 GLU cc_start: 0.8767 (mt-10) cc_final: 0.7944 (mt-10) REVERT: B 299 ARG cc_start: 0.9030 (ptp-170) cc_final: 0.8353 (ptp90) REVERT: D 232 TRP cc_start: 0.8742 (t-100) cc_final: 0.8417 (t-100) REVERT: D 236 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7604 (mt-10) REVERT: D 266 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7236 (t80) REVERT: D 293 ARG cc_start: 0.8339 (ttt-90) cc_final: 0.8112 (mtp180) REVERT: F 180 PHE cc_start: 0.8818 (t80) cc_final: 0.8597 (t80) REVERT: F 240 ARG cc_start: 0.8318 (mtp180) cc_final: 0.7983 (mmm160) REVERT: F 293 ARG cc_start: 0.8322 (mtp180) cc_final: 0.8074 (mtp180) REVERT: H 153 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8231 (t80) REVERT: H 232 TRP cc_start: 0.8908 (t-100) cc_final: 0.8605 (t-100) REVERT: H 299 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8057 (ptp-170) REVERT: H 321 MET cc_start: 0.6864 (mmt) cc_final: 0.6463 (mmt) REVERT: H 413 TYR cc_start: 0.8200 (t80) cc_final: 0.7968 (t80) outliers start: 30 outliers final: 20 residues processed: 251 average time/residue: 0.1175 time to fit residues: 38.4825 Evaluate side-chains 243 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 266 TYR 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 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 351 ASP Chi-restraints excluded: chain H residue 392 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 103 optimal weight: 0.0000 chunk 96 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.098039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074833 restraints weight = 28047.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075773 restraints weight = 15392.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076263 restraints weight = 11007.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.076410 restraints weight = 10742.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076627 restraints weight = 9688.366| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8740 Z= 0.135 Angle : 0.679 10.960 11928 Z= 0.357 Chirality : 0.043 0.159 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.571 17.953 1256 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.79 % Allowed : 21.50 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1184 helix: 0.56 (0.19), residues: 828 sheet: None (None), residues: 0 loop : -1.05 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 240 TYR 0.019 0.001 TYR B 266 PHE 0.056 0.002 PHE H 292 TRP 0.016 0.001 TRP H 232 HIS 0.006 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8740) covalent geometry : angle 0.67888 (11928) hydrogen bonds : bond 0.04042 ( 482) hydrogen bonds : angle 4.62584 ( 1359) *********************** 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 267 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.334 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: 0.8736 (t-100) cc_final: 0.8448 (t-100) REVERT: B 236 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 299 ARG cc_start: 0.9022 (ptp-170) cc_final: 0.7817 (ptp90) REVERT: D 175 ILE cc_start: 0.9374 (pt) cc_final: 0.9152 (tp) REVERT: D 232 TRP cc_start: 0.8759 (t-100) cc_final: 0.8447 (t-100) REVERT: D 236 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7500 (mt-10) REVERT: D 299 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7659 (ptp-170) REVERT: F 240 ARG cc_start: 0.8440 (mtp180) cc_final: 0.8046 (mmm160) REVERT: F 295 MET cc_start: 0.7835 (mmp) cc_final: 0.7524 (mmt) REVERT: F 299 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8627 (ptt-90) REVERT: H 153 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8326 (t80) REVERT: H 232 TRP cc_start: 0.8972 (t-100) cc_final: 0.8734 (t-100) REVERT: H 240 ARG cc_start: 0.8744 (mtp180) cc_final: 0.8415 (mtp180) REVERT: H 321 MET cc_start: 0.6841 (mmt) cc_final: 0.6503 (mmp) outliers start: 37 outliers final: 23 residues processed: 246 average time/residue: 0.1123 time to fit residues: 36.1799 Evaluate side-chains 246 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 351 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 299 ARG 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 D residue 402 VAL Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 351 ASP 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 86 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.097383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074621 restraints weight = 28368.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075368 restraints weight = 15873.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075643 restraints weight = 12115.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076006 restraints weight = 11064.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075988 restraints weight = 10809.943| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8740 Z= 0.152 Angle : 0.717 15.338 11928 Z= 0.374 Chirality : 0.044 0.221 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.456 18.005 1256 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.89 % Allowed : 23.32 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 1184 helix: 0.60 (0.19), residues: 832 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 240 TYR 0.017 0.001 TYR B 266 PHE 0.055 0.002 PHE D 292 TRP 0.011 0.001 TRP H 232 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8740) covalent geometry : angle 0.71689 (11928) hydrogen bonds : bond 0.04029 ( 482) hydrogen bonds : angle 4.67914 ( 1359) *********************** 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 253 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.408 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: 0.8696 (t-100) cc_final: 0.8462 (t-100) REVERT: B 236 GLU cc_start: 0.8814 (mt-10) cc_final: 0.7870 (mt-10) REVERT: B 299 ARG cc_start: 0.8984 (ptp-170) cc_final: 0.8343 (ptp90) REVERT: B 346 GLU cc_start: 0.8414 (tp30) cc_final: 0.8082 (tp30) REVERT: D 232 TRP cc_start: 0.8738 (t-100) cc_final: 0.8448 (t-100) REVERT: D 236 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7481 (mt-10) REVERT: D 293 ARG cc_start: 0.8447 (mtp180) cc_final: 0.8209 (mtp180) REVERT: D 299 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8274 (ptp-170) REVERT: D 409 PHE cc_start: 0.8992 (t80) cc_final: 0.8404 (t80) REVERT: F 240 ARG cc_start: 0.8442 (mtp180) cc_final: 0.8011 (mmm160) REVERT: F 295 MET cc_start: 0.7850 (mmp) cc_final: 0.7580 (mmt) REVERT: H 153 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8288 (t80) REVERT: H 240 ARG cc_start: 0.8716 (mtp180) cc_final: 0.8406 (mtp180) REVERT: H 299 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8077 (ptp-170) REVERT: H 321 MET cc_start: 0.6912 (mmt) cc_final: 0.6590 (mmt) outliers start: 30 outliers final: 21 residues processed: 235 average time/residue: 0.1214 time to fit residues: 37.0724 Evaluate side-chains 232 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 392 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 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 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 229 CYS 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 351 ASP 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 26 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.099042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.074682 restraints weight = 27853.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076181 restraints weight = 15501.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076675 restraints weight = 11117.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077293 restraints weight = 10128.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077282 restraints weight = 9550.368| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8740 Z= 0.148 Angle : 0.757 16.108 11928 Z= 0.389 Chirality : 0.045 0.289 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.392 17.769 1256 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.89 % Allowed : 24.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.27), residues: 1184 helix: 0.90 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.14 (0.38), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 189 TYR 0.017 0.001 TYR H 266 PHE 0.062 0.002 PHE F 292 TRP 0.014 0.001 TRP H 232 HIS 0.005 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8740) covalent geometry : angle 0.75691 (11928) hydrogen bonds : bond 0.04021 ( 482) hydrogen bonds : angle 4.73849 ( 1359) *********************** 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 248 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.332 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: 0.8745 (t-100) cc_final: 0.8463 (t-100) REVERT: B 236 GLU cc_start: 0.8824 (mt-10) cc_final: 0.7764 (mt-10) REVERT: B 299 ARG cc_start: 0.8994 (ptp-170) cc_final: 0.8418 (ptp90) REVERT: B 346 GLU cc_start: 0.8438 (tp30) cc_final: 0.8080 (tp30) REVERT: D 163 ARG cc_start: 0.8846 (ttt180) cc_final: 0.8604 (ttm-80) REVERT: D 171 MET cc_start: 0.8064 (ptp) cc_final: 0.7837 (ptp) REVERT: D 175 ILE cc_start: 0.9357 (pt) cc_final: 0.9145 (tp) REVERT: D 232 TRP cc_start: 0.8811 (t-100) cc_final: 0.8450 (t-100) REVERT: D 236 GLU cc_start: 0.8707 (mt-10) cc_final: 0.7552 (mt-10) REVERT: D 293 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8234 (mtp180) REVERT: D 299 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8536 (ptp-170) REVERT: D 409 PHE cc_start: 0.8988 (t80) cc_final: 0.8375 (t80) REVERT: F 240 ARG cc_start: 0.8481 (mtp180) cc_final: 0.7963 (mmm160) REVERT: F 295 MET cc_start: 0.7969 (mmp) cc_final: 0.7644 (mmt) REVERT: H 153 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (t80) REVERT: H 240 ARG cc_start: 0.8718 (mtp180) cc_final: 0.8428 (mtp180) REVERT: H 299 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8751 (ptt-90) REVERT: H 321 MET cc_start: 0.6906 (mmt) cc_final: 0.6589 (mmt) outliers start: 30 outliers final: 23 residues processed: 231 average time/residue: 0.1225 time to fit residues: 36.7280 Evaluate side-chains 237 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 299 ARG Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 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 229 CYS Chi-restraints excluded: chain H residue 238 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 351 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 20 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.098122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074703 restraints weight = 28272.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076594 restraints weight = 15700.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077976 restraints weight = 11089.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078636 restraints weight = 9215.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.078826 restraints weight = 8299.246| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8740 Z= 0.139 Angle : 0.758 16.730 11928 Z= 0.382 Chirality : 0.045 0.357 1412 Planarity : 0.004 0.045 1508 Dihedral : 4.306 17.726 1256 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.24 % Allowed : 25.52 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1184 helix: 0.93 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -0.08 (0.39), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 189 TYR 0.018 0.001 TYR H 266 PHE 0.056 0.001 PHE D 292 TRP 0.012 0.001 TRP H 232 HIS 0.006 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8740) covalent geometry : angle 0.75752 (11928) hydrogen bonds : bond 0.03995 ( 482) hydrogen bonds : angle 4.67714 ( 1359) *********************** 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 251 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.319 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 236 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 299 ARG cc_start: 0.8975 (ptp-170) cc_final: 0.8342 (ptp90) REVERT: B 346 GLU cc_start: 0.8230 (tp30) cc_final: 0.7957 (tp30) REVERT: D 175 ILE cc_start: 0.9326 (pt) cc_final: 0.9118 (tp) REVERT: D 232 TRP cc_start: 0.8559 (t-100) cc_final: 0.8336 (t-100) REVERT: D 236 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7076 (mt-10) REVERT: D 299 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8531 (ptp-170) REVERT: D 409 PHE cc_start: 0.8944 (t80) cc_final: 0.8356 (t80) REVERT: F 153 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7641 (t80) REVERT: F 240 ARG cc_start: 0.8299 (mtp180) cc_final: 0.7360 (mtp180) REVERT: F 295 MET cc_start: 0.7836 (mmp) cc_final: 0.7567 (mmt) REVERT: F 299 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7745 (ptp-170) REVERT: H 240 ARG cc_start: 0.8434 (mtp180) cc_final: 0.8192 (mtp180) REVERT: H 299 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8731 (ptt-90) REVERT: H 321 MET cc_start: 0.6805 (mmt) cc_final: 0.6502 (mmt) outliers start: 25 outliers final: 17 residues processed: 235 average time/residue: 0.1189 time to fit residues: 36.2852 Evaluate side-chains 242 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 392 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 392 ILE Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 229 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 112 optimal weight: 0.0770 chunk 79 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.098214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075588 restraints weight = 28119.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077159 restraints weight = 19838.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077546 restraints weight = 12278.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077659 restraints weight = 12177.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078182 restraints weight = 10791.006| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8740 Z= 0.140 Angle : 0.803 16.721 11928 Z= 0.400 Chirality : 0.047 0.394 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.253 18.337 1256 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.98 % Allowed : 26.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1184 helix: 0.95 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -0.06 (0.39), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 189 TYR 0.016 0.001 TYR H 266 PHE 0.057 0.002 PHE D 292 TRP 0.035 0.002 TRP B 232 HIS 0.006 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8740) covalent geometry : angle 0.80255 (11928) hydrogen bonds : bond 0.03938 ( 482) hydrogen bonds : angle 4.69170 ( 1359) ********************** 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 253 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.339 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 299 ARG cc_start: 0.9006 (ptp-170) cc_final: 0.8417 (ptp90) REVERT: B 346 GLU cc_start: 0.8371 (tp30) cc_final: 0.8047 (tp30) REVERT: D 232 TRP cc_start: 0.8757 (t-100) cc_final: 0.8436 (t-100) REVERT: D 236 GLU cc_start: 0.8657 (mt-10) cc_final: 0.7876 (mt-10) REVERT: D 240 ARG cc_start: 0.9066 (ttm110) cc_final: 0.8532 (mtm-85) REVERT: D 299 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8499 (ptp-170) REVERT: D 409 PHE cc_start: 0.8980 (t80) cc_final: 0.8369 (t80) REVERT: D 415 ARG cc_start: 0.8425 (tmm-80) cc_final: 0.7973 (ttp80) REVERT: F 153 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7900 (t80) REVERT: F 240 ARG cc_start: 0.8545 (mtp180) cc_final: 0.7638 (mtp180) REVERT: F 295 MET cc_start: 0.7936 (mmp) cc_final: 0.7696 (mmt) REVERT: F 299 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7862 (ptp-170) REVERT: H 240 ARG cc_start: 0.8724 (mtp180) cc_final: 0.8423 (mtp180) REVERT: H 299 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8014 (ptp-170) REVERT: H 321 MET cc_start: 0.6914 (mmt) cc_final: 0.6597 (mmp) outliers start: 23 outliers final: 18 residues processed: 240 average time/residue: 0.1193 time to fit residues: 37.2556 Evaluate side-chains 241 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 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 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 402 VAL Chi-restraints excluded: chain H residue 229 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.097341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075069 restraints weight = 28213.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076064 restraints weight = 18189.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076785 restraints weight = 12688.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077217 restraints weight = 11639.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077243 restraints weight = 10623.612| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8740 Z= 0.162 Angle : 0.817 17.318 11928 Z= 0.409 Chirality : 0.048 0.421 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.257 18.234 1256 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.37 % Allowed : 26.81 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 1184 helix: 1.03 (0.19), residues: 804 sheet: None (None), residues: 0 loop : 0.16 (0.39), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 189 TYR 0.016 0.001 TYR D 413 PHE 0.057 0.002 PHE D 292 TRP 0.044 0.002 TRP B 232 HIS 0.004 0.002 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8740) covalent geometry : angle 0.81663 (11928) hydrogen bonds : bond 0.04044 ( 482) hydrogen bonds : angle 4.74270 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.10 seconds wall clock time: 30 minutes 30.58 seconds (1830.58 seconds total)