Starting phenix.real_space_refine on Thu Jan 18 10:22:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebm_9026/01_2024/6ebm_9026_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebm_9026/01_2024/6ebm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebm_9026/01_2024/6ebm_9026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebm_9026/01_2024/6ebm_9026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebm_9026/01_2024/6ebm_9026_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebm_9026/01_2024/6ebm_9026_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5636 2.51 5 N 1392 2.21 5 O 1468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8532 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2133 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 189 Chain: "D" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2133 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 189 Chain: "F" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2133 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 189 Chain: "H" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2133 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 189 Time building chain proxies: 5.87, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 3.60 Conformation dependent library (CDL) restraints added in 1.8 seconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.821A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.577A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 184 removed outlier: 3.814A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 4.160A pdb=" N GLN B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 removed outlier: 3.661A pdb=" N CYS B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.713A pdb=" N PHE B 250 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 253 through 276 removed outlier: 3.536A pdb=" N ILE B 257 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Proline residue: B 265 - end of helix removed outlier: 3.713A pdb=" N ASN B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.659A pdb=" N ILE B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.959A pdb=" N GLN B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 346 removed outlier: 3.684A pdb=" N LEU B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 369 removed outlier: 3.772A pdb=" N TRP B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.514A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 414 removed outlier: 3.503A pdb=" N ILE B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'D' and resid 121 through 131 removed outlier: 3.585A pdb=" N MET D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.559A pdb=" N LEU D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 184 removed outlier: 3.789A pdb=" N ALA D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 174 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 removed outlier: 4.221A pdb=" N GLN D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 243 removed outlier: 3.644A pdb=" N CYS D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.669A pdb=" N PHE D 250 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE D 251 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 276 removed outlier: 3.588A pdb=" N ILE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP D 259 " --> pdb=" O MET D 255 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Proline residue: D 265 - end of helix removed outlier: 3.710A pdb=" N ASN D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.676A pdb=" N ILE D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.930A pdb=" N GLN D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 346 removed outlier: 3.703A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 336 " --> pdb=" O PHE D 332 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 369 removed outlier: 3.764A pdb=" N TRP D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 369 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 removed outlier: 3.503A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 392 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 414 removed outlier: 3.506A pdb=" N ILE D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'F' and resid 121 through 131 removed outlier: 3.581A pdb=" N MET F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.532A pdb=" N TRP F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 184 removed outlier: 3.822A pdb=" N ALA F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 210 removed outlier: 4.082A pdb=" N GLN F 207 " --> pdb=" O HIS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 243 removed outlier: 3.774A pdb=" N CYS F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 239 " --> pdb=" O PHE F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 252 removed outlier: 3.651A pdb=" N PHE F 250 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR F 252 " --> pdb=" O GLY F 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 247 through 252' Processing helix chain 'F' and resid 253 through 275 removed outlier: 3.548A pdb=" N ILE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP F 259 " --> pdb=" O MET F 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.628A pdb=" N ILE F 294 " --> pdb=" O GLN F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 306 Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.924A pdb=" N GLN F 311 " --> pdb=" O SER F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 346 removed outlier: 3.640A pdb=" N LEU F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 336 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 369 removed outlier: 3.769A pdb=" N TRP F 363 " --> pdb=" O ASP F 359 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 365 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 399 removed outlier: 3.566A pdb=" N LEU F 389 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 414 removed outlier: 3.514A pdb=" N ILE F 405 " --> pdb=" O PRO F 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' Processing helix chain 'H' and resid 121 through 131 removed outlier: 3.583A pdb=" N MET H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.512A pdb=" N TRP H 150 " --> pdb=" O GLN H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 184 removed outlier: 3.814A pdb=" N ALA H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU H 174 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR H 184 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 210 removed outlier: 3.987A pdb=" N GLN H 207 " --> pdb=" O HIS H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 243 removed outlier: 3.723A pdb=" N CYS H 229 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL H 239 " --> pdb=" O PHE H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.614A pdb=" N PHE H 250 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE H 251 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 252 " --> pdb=" O GLY H 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 247 through 252' Processing helix chain 'H' and resid 253 through 276 removed outlier: 4.456A pdb=" N ASP H 259 " --> pdb=" O MET H 255 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE H 263 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) Proline residue: H 265 - end of helix removed outlier: 3.753A pdb=" N ASN H 276 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 296 removed outlier: 3.654A pdb=" N ILE H 294 " --> pdb=" O GLN H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 306 Processing helix chain 'H' and resid 307 through 319 removed outlier: 3.955A pdb=" N GLN H 311 " --> pdb=" O SER H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 346 removed outlier: 3.699A pdb=" N LEU H 327 " --> pdb=" O GLU H 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA H 345 " --> pdb=" O ALA H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 369 removed outlier: 3.774A pdb=" N TRP H 363 " --> pdb=" O ASP H 359 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 365 " --> pdb=" O PHE H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 399 removed outlier: 3.575A pdb=" N LEU H 389 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS H 390 " --> pdb=" O VAL H 386 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 391 " --> pdb=" O GLY H 387 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE H 392 " --> pdb=" O SER H 388 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 414 removed outlier: 3.651A pdb=" N ASN H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS H 414 " --> pdb=" O ASN H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 417 No H-bonds generated for 'chain 'H' and resid 415 through 417' 482 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 3.88 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: 100.03 - 106.85: 262 106.85 - 113.67: 4801 113.67 - 120.49: 3739 120.49 - 127.31: 3055 127.31 - 134.13: 71 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 2.520 nonbonded pdb=" OD1 ASP D 375 " pdb=" N MET D 376 " model vdw 2.050 2.520 nonbonded pdb=" OD1 ASP F 375 " pdb=" N MET F 376 " model vdw 2.052 2.520 nonbonded pdb=" OD1 ASP H 375 " pdb=" N MET H 376 " model vdw 2.054 2.520 nonbonded pdb=" O VAL D 365 " pdb=" OG1 THR D 369 " model vdw 2.249 2.440 ... (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 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: 4.840 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: 11.750 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.300 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.105 8740 Z= 0.748 Angle : 1.096 8.013 11928 Z= 0.655 Chirality : 0.060 0.185 1412 Planarity : 0.008 0.062 1508 Dihedral : 9.309 50.289 2812 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.18), residues: 1184 helix: -3.06 (0.12), residues: 832 sheet: None (None), residues: 0 loop : -3.08 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 232 HIS 0.012 0.007 HIS F 306 PHE 0.024 0.004 PHE D 329 TYR 0.011 0.003 TYR D 373 ARG 0.007 0.001 ARG H 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 0.994 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: 0.2719 time to fit residues: 104.7328 Evaluate side-chains 213 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN B 410 ASN D 408 ASN F 408 ASN F 410 ASN H 408 ASN H 410 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8740 Z= 0.208 Angle : 0.669 10.186 11928 Z= 0.359 Chirality : 0.042 0.126 1412 Planarity : 0.005 0.038 1508 Dihedral : 5.538 23.161 1256 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.11 % Allowed : 12.56 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.23), residues: 1184 helix: -1.11 (0.15), residues: 876 sheet: None (None), residues: 0 loop : -2.43 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 232 HIS 0.003 0.001 HIS D 306 PHE 0.029 0.002 PHE D 292 TYR 0.012 0.002 TYR H 155 ARG 0.006 0.001 ARG F 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 285 time to evaluate : 1.037 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: D 226 GLU cc_start: 0.9010 (tp30) cc_final: 0.8543 (mm-30) REVERT: D 229 CYS cc_start: 0.8826 (p) cc_final: 0.8600 (m) REVERT: D 230 ILE cc_start: 0.9323 (mm) cc_final: 0.9113 (tp) REVERT: D 232 TRP cc_start: 0.8506 (t-100) cc_final: 0.8270 (t-100) REVERT: D 236 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 266 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.7167 (t80) REVERT: D 291 ILE cc_start: 0.9323 (mt) cc_final: 0.9030 (tt) REVERT: F 321 MET cc_start: 0.6462 (mmm) cc_final: 0.6225 (mmt) REVERT: H 263 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9093 (tp) REVERT: H 308 LYS cc_start: 0.8520 (mptt) cc_final: 0.8227 (mmtm) REVERT: H 415 ARG cc_start: 0.8239 (ttp80) cc_final: 0.8019 (tmm-80) outliers start: 24 outliers final: 13 residues processed: 295 average time/residue: 0.2484 time to fit residues: 94.6131 Evaluate side-chains 233 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 218 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain H residue 165 ILE 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 351 ASP Chi-restraints excluded: chain H residue 388 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 84 optimal weight: 0.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8740 Z= 0.237 Angle : 0.650 10.327 11928 Z= 0.345 Chirality : 0.043 0.156 1412 Planarity : 0.005 0.032 1508 Dihedral : 5.085 21.226 1256 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.57 % Allowed : 15.80 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1184 helix: -0.27 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -1.95 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 232 HIS 0.003 0.001 HIS B 306 PHE 0.040 0.002 PHE B 292 TYR 0.025 0.002 TYR B 266 ARG 0.006 0.001 ARG F 305 *********************** 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 287 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 244 time to evaluate : 1.145 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: 0.8638 (m) cc_final: 0.8300 (p) REVERT: B 299 ARG cc_start: 0.9033 (ptp-170) cc_final: 0.8817 (ptt180) REVERT: D 175 ILE cc_start: 0.9414 (pt) cc_final: 0.9135 (tp) REVERT: D 226 GLU cc_start: 0.8979 (tp30) cc_final: 0.8539 (mm-30) REVERT: D 229 CYS cc_start: 0.8868 (p) cc_final: 0.8575 (m) REVERT: D 230 ILE cc_start: 0.9409 (mm) cc_final: 0.9199 (tp) REVERT: D 232 TRP cc_start: 0.8676 (t-100) cc_final: 0.8429 (t-100) REVERT: D 236 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 266 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7234 (t80) REVERT: D 413 TYR cc_start: 0.7577 (t80) cc_final: 0.7309 (t80) REVERT: F 236 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8397 (mt-10) REVERT: F 240 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7949 (mmm160) REVERT: F 299 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8530 (ptp-170) REVERT: F 321 MET cc_start: 0.6564 (mmm) cc_final: 0.6255 (mmt) REVERT: H 236 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8667 (mt-10) outliers start: 43 outliers final: 24 residues processed: 263 average time/residue: 0.2373 time to fit residues: 82.2725 Evaluate side-chains 249 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 259 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 234 SER 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 388 SER Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 266 TYR Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 351 ASP Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain H residue 397 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.0030 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 105 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8740 Z= 0.188 Angle : 0.649 11.670 11928 Z= 0.337 Chirality : 0.043 0.141 1412 Planarity : 0.004 0.036 1508 Dihedral : 4.816 19.904 1256 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.18 % Allowed : 19.17 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1184 helix: 0.33 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.44 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 232 HIS 0.006 0.001 HIS D 414 PHE 0.044 0.001 PHE D 292 TYR 0.020 0.001 TYR B 266 ARG 0.005 0.001 ARG D 240 *********************** 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 297 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 1.068 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 229 CYS cc_start: 0.8616 (m) cc_final: 0.8203 (p) REVERT: B 288 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8874 (p) REVERT: B 291 ILE cc_start: 0.9314 (mt) cc_final: 0.8577 (tt) REVERT: B 299 ARG cc_start: 0.9070 (ptp-170) cc_final: 0.8762 (ptt180) REVERT: D 175 ILE cc_start: 0.9386 (pt) cc_final: 0.9133 (tp) REVERT: D 226 GLU cc_start: 0.8929 (tp30) cc_final: 0.8658 (mm-30) REVERT: D 229 CYS cc_start: 0.8767 (p) cc_final: 0.8550 (m) REVERT: D 230 ILE cc_start: 0.9399 (mm) cc_final: 0.9146 (tp) REVERT: D 232 TRP cc_start: 0.8625 (t-100) cc_final: 0.8402 (t-100) REVERT: D 236 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7552 (mt-10) REVERT: D 346 GLU cc_start: 0.7829 (tp30) cc_final: 0.7473 (tp30) REVERT: F 240 ARG cc_start: 0.8224 (mtp180) cc_final: 0.8023 (mmm160) REVERT: F 299 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8256 (ptp-170) REVERT: F 346 GLU cc_start: 0.8367 (tt0) cc_final: 0.8069 (tt0) REVERT: H 153 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7900 (t80) REVERT: H 413 TYR cc_start: 0.7809 (t80) cc_final: 0.7605 (t80) outliers start: 40 outliers final: 29 residues processed: 272 average time/residue: 0.2207 time to fit residues: 79.3922 Evaluate side-chains 255 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 234 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 315 GLN 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 315 GLN Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 266 TYR Chi-restraints excluded: chain F residue 299 ARG Chi-restraints excluded: chain F residue 315 GLN Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 229 CYS Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 259 ASP 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 315 GLN Chi-restraints excluded: chain H residue 351 ASP Chi-restraints excluded: chain H residue 392 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 77 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5131 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= 0.191 Angle : 0.655 11.185 11928 Z= 0.341 Chirality : 0.043 0.151 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.632 18.392 1256 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.66 % Allowed : 21.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1184 helix: 0.64 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -1.10 (0.36), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 232 HIS 0.005 0.001 HIS B 414 PHE 0.053 0.002 PHE H 292 TYR 0.019 0.001 TYR B 266 ARG 0.005 0.001 ARG H 350 *********************** 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 264 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 228 time to evaluate : 1.029 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 291 ILE cc_start: 0.9128 (mt) cc_final: 0.8594 (mt) REVERT: B 318 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8747 (ttpt) REVERT: D 175 ILE cc_start: 0.9381 (pt) cc_final: 0.9143 (tp) REVERT: D 226 GLU cc_start: 0.9072 (tp30) cc_final: 0.8701 (mm-30) REVERT: D 230 ILE cc_start: 0.9411 (mm) cc_final: 0.9168 (tp) REVERT: D 232 TRP cc_start: 0.8628 (t-100) cc_final: 0.8390 (t-100) REVERT: D 236 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7413 (mt-10) REVERT: D 299 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7666 (ptp-170) REVERT: D 346 GLU cc_start: 0.7768 (tp30) cc_final: 0.7485 (tp30) REVERT: F 183 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7688 (pt0) REVERT: F 232 TRP cc_start: 0.8707 (t-100) cc_final: 0.8346 (t-100) REVERT: F 240 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7982 (mmm160) REVERT: F 346 GLU cc_start: 0.8464 (tt0) cc_final: 0.8261 (tt0) REVERT: H 153 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7919 (t80) outliers start: 36 outliers final: 23 residues processed: 242 average time/residue: 0.2438 time to fit residues: 76.5431 Evaluate side-chains 241 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 315 GLN 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 259 ASP Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 351 ASP 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 388 SER Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 397 THR 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 300 ILE Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 346 GLU 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 37 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 0.0050 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5280 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= 0.251 Angle : 0.690 12.015 11928 Z= 0.363 Chirality : 0.045 0.192 1412 Planarity : 0.004 0.036 1508 Dihedral : 4.644 18.431 1256 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 6.09 % Allowed : 20.47 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1184 helix: 0.66 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 232 HIS 0.004 0.002 HIS B 414 PHE 0.052 0.002 PHE D 292 TYR 0.020 0.002 TYR B 266 ARG 0.004 0.001 ARG H 350 *********************** 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 269 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 0.930 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: 0.8782 (p) cc_final: 0.8561 (p) REVERT: B 291 ILE cc_start: 0.9163 (mt) cc_final: 0.8605 (mt) REVERT: B 299 ARG cc_start: 0.9146 (ptp-170) cc_final: 0.8795 (ptt180) REVERT: D 175 ILE cc_start: 0.9422 (pt) cc_final: 0.9184 (tp) REVERT: D 230 ILE cc_start: 0.9378 (mm) cc_final: 0.9159 (tp) REVERT: D 232 TRP cc_start: 0.8655 (t-100) cc_final: 0.8387 (t-100) REVERT: D 236 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7370 (mt-10) REVERT: D 299 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7955 (ptp-170) REVERT: D 346 GLU cc_start: 0.7953 (tp30) cc_final: 0.7606 (tp30) REVERT: D 409 PHE cc_start: 0.8919 (t80) cc_final: 0.8357 (t80) REVERT: F 183 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7655 (pt0) REVERT: H 153 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7946 (t80) REVERT: H 232 TRP cc_start: 0.8805 (t-100) cc_final: 0.8469 (t-100) outliers start: 47 outliers final: 38 residues processed: 246 average time/residue: 0.2426 time to fit residues: 77.2744 Evaluate side-chains 250 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 234 SER 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 337 LEU Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain F residue 234 SER 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 388 SER Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 290 GLN Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 346 GLU Chi-restraints excluded: chain H residue 351 ASP Chi-restraints excluded: chain H residue 388 SER 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 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.0020 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 44 optimal weight: 0.1980 chunk 66 optimal weight: 20.0000 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5555 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= 0.199 Angle : 0.737 14.588 11928 Z= 0.376 Chirality : 0.044 0.244 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.503 18.976 1256 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.15 % Allowed : 23.32 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1184 helix: 0.65 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -0.64 (0.38), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 232 HIS 0.005 0.001 HIS B 414 PHE 0.054 0.001 PHE D 292 TYR 0.030 0.002 TYR H 266 ARG 0.004 0.001 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 0.987 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 240 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: D 175 ILE cc_start: 0.9374 (pt) cc_final: 0.9144 (tp) REVERT: D 230 ILE cc_start: 0.9348 (mm) cc_final: 0.9108 (tp) REVERT: D 232 TRP cc_start: 0.8620 (t-100) cc_final: 0.8323 (t-100) REVERT: D 236 GLU cc_start: 0.8482 (mt-10) cc_final: 0.6791 (mt-10) REVERT: D 240 ARG cc_start: 0.8999 (ttm110) cc_final: 0.7880 (mmt90) REVERT: D 299 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8280 (ptp-170) REVERT: D 346 GLU cc_start: 0.7934 (tp30) cc_final: 0.7563 (tp30) REVERT: D 415 ARG cc_start: 0.8077 (tmm-80) cc_final: 0.7731 (ttp80) REVERT: F 183 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7571 (pt0) REVERT: F 346 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: H 153 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7913 (t80) REVERT: H 232 TRP cc_start: 0.8812 (t-100) cc_final: 0.8596 (t-100) outliers start: 32 outliers final: 25 residues processed: 245 average time/residue: 0.2456 time to fit residues: 77.9491 Evaluate side-chains 246 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 218 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 315 GLN 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 259 ASP Chi-restraints excluded: chain D residue 299 ARG 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 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 346 GLU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 238 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 0.2980 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8740 Z= 0.199 Angle : 0.745 14.721 11928 Z= 0.375 Chirality : 0.044 0.331 1412 Planarity : 0.004 0.044 1508 Dihedral : 4.373 19.875 1256 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.02 % Allowed : 26.42 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1184 helix: 0.73 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 363 HIS 0.005 0.001 HIS B 414 PHE 0.063 0.002 PHE F 292 TYR 0.027 0.001 TYR H 266 ARG 0.012 0.001 ARG H 189 *********************** 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 261 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 230 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7517 (ptp) REVERT: B 175 ILE cc_start: 0.9381 (pt) cc_final: 0.9122 (tp) REVERT: D 163 ARG cc_start: 0.8547 (ttt180) cc_final: 0.8285 (ttm-80) REVERT: D 175 ILE cc_start: 0.9347 (pt) cc_final: 0.9130 (tp) REVERT: D 230 ILE cc_start: 0.9362 (mm) cc_final: 0.9118 (tp) REVERT: D 232 TRP cc_start: 0.8595 (t-100) cc_final: 0.8308 (t-100) REVERT: D 236 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7299 (mt-10) REVERT: D 299 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8310 (ptp-170) REVERT: D 346 GLU cc_start: 0.7916 (tp30) cc_final: 0.7580 (tp30) REVERT: D 415 ARG cc_start: 0.8043 (tmm-80) cc_final: 0.7719 (ttp80) REVERT: F 299 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8585 (ptt-90) REVERT: F 346 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: H 153 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7868 (t80) REVERT: H 232 TRP cc_start: 0.8812 (t-100) cc_final: 0.8461 (t-100) outliers start: 31 outliers final: 21 residues processed: 242 average time/residue: 0.2613 time to fit residues: 82.0224 Evaluate side-chains 248 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 315 GLN 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 259 ASP Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 351 ASP 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 346 GLU Chi-restraints excluded: chain F residue 351 ASP 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 234 SER Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 351 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.0010 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8740 Z= 0.266 Angle : 0.792 15.087 11928 Z= 0.401 Chirality : 0.046 0.372 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.419 18.401 1256 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.31 % Allowed : 25.13 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1184 helix: 0.80 (0.19), residues: 820 sheet: None (None), residues: 0 loop : -0.45 (0.40), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 232 HIS 0.004 0.002 HIS B 414 PHE 0.063 0.002 PHE F 292 TYR 0.023 0.002 TYR H 266 ARG 0.006 0.001 ARG H 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 0.911 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: D 163 ARG cc_start: 0.8530 (ttt180) cc_final: 0.8279 (ttm-80) REVERT: D 175 ILE cc_start: 0.9378 (pt) cc_final: 0.9177 (tp) REVERT: D 230 ILE cc_start: 0.9384 (mm) cc_final: 0.9157 (tp) REVERT: D 232 TRP cc_start: 0.8584 (t-100) cc_final: 0.8308 (t-100) REVERT: D 236 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 240 ARG cc_start: 0.8964 (ttm110) cc_final: 0.8420 (mpp80) REVERT: D 299 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8148 (ptp-170) REVERT: D 346 GLU cc_start: 0.8063 (tp30) cc_final: 0.7672 (tp30) REVERT: D 409 PHE cc_start: 0.8875 (t80) cc_final: 0.8328 (t80) REVERT: F 346 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: H 153 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7944 (t80) REVERT: H 229 CYS cc_start: 0.8551 (p) cc_final: 0.8350 (m) outliers start: 41 outliers final: 34 residues processed: 237 average time/residue: 0.2425 time to fit residues: 74.6831 Evaluate side-chains 248 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 388 SER 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 326 LEU Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 397 THR 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 346 GLU Chi-restraints excluded: chain F residue 351 ASP Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain H residue 153 PHE Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 351 ASP Chi-restraints excluded: chain H residue 353 GLN Chi-restraints excluded: chain H residue 388 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8740 Z= 0.210 Angle : 0.806 15.812 11928 Z= 0.401 Chirality : 0.046 0.396 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.372 18.673 1256 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.89 % Allowed : 26.42 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1184 helix: 0.80 (0.19), residues: 820 sheet: None (None), residues: 0 loop : -0.33 (0.41), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 232 HIS 0.005 0.001 HIS B 414 PHE 0.054 0.002 PHE D 292 TYR 0.023 0.002 TYR H 266 ARG 0.006 0.001 ARG H 350 ********************** 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 262 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 1.060 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 240 ARG cc_start: 0.8995 (mmm-85) cc_final: 0.8322 (mmm-85) REVERT: B 414 HIS cc_start: 0.7431 (m-70) cc_final: 0.7190 (m90) REVERT: D 230 ILE cc_start: 0.9366 (mm) cc_final: 0.9132 (tp) REVERT: D 232 TRP cc_start: 0.8552 (t-100) cc_final: 0.8284 (t-100) REVERT: D 236 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7138 (mt-10) REVERT: D 299 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8094 (ptp-170) REVERT: D 346 GLU cc_start: 0.8018 (tp30) cc_final: 0.7646 (tp30) REVERT: F 185 LEU cc_start: 0.9311 (mt) cc_final: 0.9094 (mm) REVERT: F 293 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7864 (mtm180) REVERT: F 346 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: H 153 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7981 (t80) REVERT: H 232 TRP cc_start: 0.8829 (t-100) cc_final: 0.8407 (t-100) outliers start: 30 outliers final: 25 residues processed: 244 average time/residue: 0.2372 time to fit residues: 75.4293 Evaluate side-chains 252 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 224 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 259 ASP 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 402 VAL 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 346 GLU Chi-restraints excluded: chain F residue 351 ASP 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 234 SER Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 351 ASP Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.098260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074396 restraints weight = 28185.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076259 restraints weight = 15955.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077075 restraints weight = 11417.733| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6149 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= 0.202 Angle : 0.817 17.295 11928 Z= 0.402 Chirality : 0.046 0.400 1412 Planarity : 0.004 0.037 1508 Dihedral : 4.262 19.035 1256 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.50 % Allowed : 27.46 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 1184 helix: 0.86 (0.19), residues: 820 sheet: None (None), residues: 0 loop : -0.26 (0.41), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 232 HIS 0.005 0.001 HIS B 414 PHE 0.052 0.001 PHE D 292 TYR 0.023 0.002 TYR H 266 ARG 0.005 0.001 ARG F 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.88 seconds wall clock time: 41 minutes 7.54 seconds (2467.54 seconds total)