Starting phenix.real_space_refine on Fri Jul 3 22:17:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z7h_14532/07_2026/7z7h_14532.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7h_14532/07_2026/7z7h_14532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z7h_14532/07_2026/7z7h_14532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7h_14532/07_2026/7z7h_14532.map" model { file = "/net/cci-nas-00/data/ceres_data/7z7h_14532/07_2026/7z7h_14532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7h_14532/07_2026/7z7h_14532.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z7h_14532/07_2026/7z7h_14532.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z7h_14532/07_2026/7z7h_14532.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 5 5.21 5 S 109 5.16 5 C 10165 2.51 5 N 2720 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16111 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1427 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 12, 'TRANS': 168} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.74, per 1000 atoms: 0.23 Number of scatterers: 16111 At special positions: 0 Unit cell: (124.2, 88.2, 197.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 109 16.00 P 12 15.00 Mg 5 11.99 O 3100 8.00 N 2720 7.00 C 10165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 749.5 milliseconds 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3774 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 31 sheets defined 51.2% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'D' and resid 55 through 61 removed outlier: 4.087A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.550A pdb=" N TRP D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 113 through 126 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.522A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.503A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.618A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.533A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.675A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Proline residue: D 258 - end of helix removed outlier: 4.306A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 288 through 296 removed outlier: 4.592A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.802A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 349 removed outlier: 4.368A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 349 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 356 removed outlier: 3.699A pdb=" N MET D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 373 removed outlier: 4.074A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 137 through 148 removed outlier: 3.954A pdb=" N PHE F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 172 through 184 removed outlier: 4.488A pdb=" N ASP F 176 " --> pdb=" O PRO F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.935A pdb=" N THR F 250 " --> pdb=" O GLN F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 275 No H-bonds generated for 'chain 'F' and resid 273 through 275' Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.563A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 128 removed outlier: 4.297A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.727A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.703A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.664A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.582A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix removed outlier: 4.461A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 288 through 296 removed outlier: 4.288A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.757A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.550A pdb=" N SER B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.680A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 113 through 128 Processing helix chain 'E' and resid 137 through 144 removed outlier: 3.549A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.517A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 201 through 217 removed outlier: 4.205A pdb=" N GLU E 205 " --> pdb=" O VAL E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.648A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 252 through 260 removed outlier: 3.785A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 268 Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.478A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 349 removed outlier: 4.339A pdb=" N VAL E 339 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 349 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 removed outlier: 3.795A pdb=" N MET E 355 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.600A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 113 through 128 Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.516A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.504A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.700A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.512A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.142A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.375A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.626A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.536A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.637A pdb=" N MET C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.601A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.560A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.745A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.611A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.620A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.706A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 268 Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.770A pdb=" N LYS A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.590A pdb=" N ASN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.512A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.628A pdb=" N LEU A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.823A pdb=" N MET A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.623A pdb=" N LYS A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.520A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.578A pdb=" N VAL D 35 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.530A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'F' and resid 226 through 228 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 226 through 228 current: chain 'F' and resid 192 through 195 removed outlier: 3.611A pdb=" N SER F 265 " --> pdb=" O HIS F 258 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU F 209 " --> pdb=" O HIS F 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.888A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 19 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 17 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.537A pdb=" N THR B 66 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.560A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.601A pdb=" N ALA E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 19 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 170 removed outlier: 7.504A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.882A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.723A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 66 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.342A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.045A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.593A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 66 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AD2, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.790A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 238 through 241 731 hydrogen bonds defined for protein. 1938 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: 2.82 Time building geometry restraints manager: 1.80 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: 5200 1.34 - 1.46: 3174 1.46 - 1.58: 7876 1.58 - 1.69: 20 1.69 - 1.81: 196 Bond restraints: 16466 Sorted by residual: bond pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.393 1.639 -0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C4' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.430 1.632 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C2 APR D 403 " pdb=" N1 APR D 403 " ideal model delta sigma weight residual 1.331 1.531 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C6 APR D 403 " pdb=" N1 APR D 403 " ideal model delta sigma weight residual 1.338 1.527 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C7 NCA F 300 " pdb=" N7 NCA F 300 " ideal model delta sigma weight residual 1.340 1.525 -0.185 2.00e-02 2.50e+03 8.57e+01 ... (remaining 16461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 21788 3.40 - 6.81: 508 6.81 - 10.21: 44 10.21 - 13.61: 6 13.61 - 17.02: 2 Bond angle restraints: 22348 Sorted by residual: angle pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " pdb=" C4' APR D 403 " ideal model delta sigma weight residual 111.27 94.25 17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" O1A APR D 403 " pdb=" PA APR D 403 " pdb=" O2A APR D 403 " ideal model delta sigma weight residual 121.71 107.08 14.63 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C MET A 283 " pdb=" N LYS A 284 " pdb=" CA LYS A 284 " ideal model delta sigma weight residual 121.94 112.61 9.33 2.00e+00 2.50e-01 2.18e+01 angle pdb=" O1B APR D 403 " pdb=" PB APR D 403 " pdb=" O2B APR D 403 " ideal model delta sigma weight residual 122.24 108.72 13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" N MET A 283 " pdb=" CA MET A 283 " pdb=" C MET A 283 " ideal model delta sigma weight residual 111.71 116.48 -4.77 1.15e+00 7.56e-01 1.72e+01 ... (remaining 22343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 9337 22.61 - 45.21: 478 45.21 - 67.82: 65 67.82 - 90.43: 12 90.43 - 113.03: 5 Dihedral angle restraints: 9897 sinusoidal: 4009 harmonic: 5888 Sorted by residual: dihedral pdb=" CA PHE F 126 " pdb=" C PHE F 126 " pdb=" N PRO F 127 " pdb=" CA PRO F 127 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 53.04 -113.03 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 50.80 -110.79 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 9894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2035 0.082 - 0.164: 412 0.164 - 0.245: 33 0.245 - 0.327: 1 0.327 - 0.409: 3 Chirality restraints: 2484 Sorted by residual: chirality pdb=" C4' APR D 403 " pdb=" C3' APR D 403 " pdb=" C5' APR D 403 " pdb=" O4' APR D 403 " both_signs ideal model delta sigma weight residual False -2.54 -2.95 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C1' APR D 403 " pdb=" C2' APR D 403 " pdb=" N9 APR D 403 " pdb=" O4' APR D 403 " both_signs ideal model delta sigma weight residual False 2.40 2.78 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C4D APR D 403 " pdb=" C3D APR D 403 " pdb=" C5D APR D 403 " pdb=" O4D APR D 403 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2481 not shown) Planarity restraints: 2849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 117 " 0.160 9.50e-02 1.11e+02 8.76e-02 3.46e+01 pdb=" NE ARG F 117 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 117 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG F 117 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG F 117 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 89 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C THR B 89 " -0.061 2.00e-02 2.50e+03 pdb=" O THR B 89 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE B 90 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 89 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR A 89 " -0.059 2.00e-02 2.50e+03 pdb=" O THR A 89 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE A 90 " 0.020 2.00e-02 2.50e+03 ... (remaining 2846 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 88 2.40 - 3.03: 10541 3.03 - 3.65: 23992 3.65 - 4.28: 33818 4.28 - 4.90: 56215 Nonbonded interactions: 124654 Sorted by model distance: nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.777 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.829 2.170 nonbonded pdb=" O1A ADP D 401 " pdb="MG MG D 402 " model vdw 1.853 2.170 nonbonded pdb=" O3A ADP B 401 " pdb="MG MG B 402 " model vdw 1.873 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.964 2.170 ... (remaining 124649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 5 through 402) selection = chain 'E' } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.380 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.013 0.868 16468 Z= 0.843 Angle : 1.248 17.017 22348 Z= 0.687 Chirality : 0.064 0.409 2484 Planarity : 0.007 0.088 2849 Dihedral : 13.964 113.033 6123 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2009 helix: -0.49 (0.17), residues: 617 sheet: 0.72 (0.24), residues: 440 loop : -0.14 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.011 ARG F 117 TYR 0.033 0.006 TYR A 294 PHE 0.032 0.004 PHE D 31 TRP 0.052 0.004 TRP E 356 HIS 0.019 0.003 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.01063 / 0.50 (16466) covalent geometry : angle 1.24834 / 0.69 (22348) hydrogen bonds : bond 0.22843 / 14.80 ( 721) hydrogen bonds : angle 8.47394 / 5.90 ( 1938) Misc. bond : bond 0.61451 / 29.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.630 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 123 MET cc_start: 0.8850 (mmp) cc_final: 0.8555 (tpp) REVERT: F 183 TYR cc_start: 0.8305 (m-80) cc_final: 0.7876 (m-80) REVERT: F 212 ILE cc_start: 0.8540 (mt) cc_final: 0.8326 (pt) REVERT: F 282 ARG cc_start: 0.7291 (ptt-90) cc_final: 0.7077 (mpp-170) REVERT: B 34 ILE cc_start: 0.9248 (mt) cc_final: 0.8900 (tp) REVERT: B 153 LEU cc_start: 0.8834 (tp) cc_final: 0.8492 (tt) REVERT: E 65 LEU cc_start: 0.7066 (mt) cc_final: 0.6708 (mt) REVERT: E 78 ASN cc_start: 0.7159 (t0) cc_final: 0.6898 (t0) REVERT: E 356 TRP cc_start: 0.7091 (m100) cc_final: 0.6534 (m100) REVERT: C 9 VAL cc_start: 0.9438 (t) cc_final: 0.9232 (m) REVERT: C 155 SER cc_start: 0.8645 (t) cc_final: 0.8379 (m) REVERT: A 123 MET cc_start: 0.8228 (mmp) cc_final: 0.7963 (mmt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1176 time to fit residues: 46.3483 Evaluate side-chains 152 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 111 ASN D 115 ASN D 252 ASN B 111 ASN B 115 ASN B 162 ASN B 252 ASN E 59 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN C 59 GLN C 111 ASN C 162 ASN A 12 ASN A 59 GLN A 111 ASN A 162 ASN A 252 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.070915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.061147 restraints weight = 85960.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.062795 restraints weight = 48874.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.063955 restraints weight = 32264.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.064758 restraints weight = 23465.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.065323 restraints weight = 18376.287| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16468 Z= 0.207 Angle : 0.795 9.036 22348 Z= 0.410 Chirality : 0.048 0.264 2484 Planarity : 0.005 0.052 2849 Dihedral : 7.613 87.755 2278 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.74 % Allowed : 8.11 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 2009 helix: 0.24 (0.18), residues: 738 sheet: 0.91 (0.25), residues: 385 loop : 0.64 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 117 TYR 0.018 0.002 TYR E 306 PHE 0.026 0.002 PHE E 90 TRP 0.015 0.002 TRP C 79 HIS 0.009 0.002 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (16466) covalent geometry : angle 0.79517 / 0.41 (22348) hydrogen bonds : bond 0.05284 / 3.49 ( 721) hydrogen bonds : angle 6.10461 / 4.22 ( 1938) Misc. bond : bond 0.00622 / 0.30 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.666 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: F 183 TYR cc_start: 0.8268 (m-80) cc_final: 0.8010 (m-80) REVERT: F 215 ASP cc_start: 0.8674 (p0) cc_final: 0.8281 (t70) REVERT: B 34 ILE cc_start: 0.9421 (mt) cc_final: 0.9152 (tp) REVERT: B 325 MET cc_start: 0.8158 (tpp) cc_final: 0.7502 (mmp) REVERT: E 65 LEU cc_start: 0.7036 (mt) cc_final: 0.6634 (mt) REVERT: E 78 ASN cc_start: 0.6396 (t0) cc_final: 0.6089 (t0) REVERT: E 325 MET cc_start: 0.6153 (ttm) cc_final: 0.5834 (ptm) REVERT: C 65 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7516 (mt) REVERT: C 269 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8043 (mtt) REVERT: C 283 MET cc_start: 0.7689 (mmp) cc_final: 0.7360 (mmm) REVERT: A 313 MET cc_start: 0.7508 (mmm) cc_final: 0.6972 (mmm) outliers start: 30 outliers final: 14 residues processed: 193 average time/residue: 0.1037 time to fit residues: 31.1259 Evaluate side-chains 151 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 63 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 122 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.070737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061024 restraints weight = 86795.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.062646 restraints weight = 49477.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063775 restraints weight = 32744.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064577 restraints weight = 23909.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.065135 restraints weight = 18771.534| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16468 Z= 0.133 Angle : 0.670 8.784 22348 Z= 0.337 Chirality : 0.044 0.237 2484 Planarity : 0.004 0.048 2849 Dihedral : 6.783 70.147 2278 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.33 % Allowed : 10.02 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2009 helix: 0.42 (0.19), residues: 743 sheet: 1.06 (0.24), residues: 405 loop : 0.99 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 196 TYR 0.014 0.001 TYR E 306 PHE 0.019 0.002 PHE E 90 TRP 0.024 0.002 TRP E 356 HIS 0.007 0.001 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16466) covalent geometry : angle 0.67007 / 0.34 (22348) hydrogen bonds : bond 0.04107 / 2.72 ( 721) hydrogen bonds : angle 5.50865 / 3.80 ( 1938) Misc. bond : bond 0.00157 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 MET cc_start: 0.7724 (ttt) cc_final: 0.7452 (tmm) REVERT: D 123 MET cc_start: 0.8812 (tpp) cc_final: 0.8505 (tpp) REVERT: F 183 TYR cc_start: 0.8165 (m-80) cc_final: 0.7805 (m-80) REVERT: F 215 ASP cc_start: 0.8674 (p0) cc_final: 0.8316 (t70) REVERT: B 34 ILE cc_start: 0.9408 (mt) cc_final: 0.9091 (tp) REVERT: B 325 MET cc_start: 0.8088 (tpp) cc_final: 0.7432 (mmp) REVERT: B 355 MET cc_start: 0.7218 (mmp) cc_final: 0.6916 (mmm) REVERT: E 44 MET cc_start: -0.0098 (mmt) cc_final: -0.0517 (mpp) REVERT: E 78 ASN cc_start: 0.6337 (t0) cc_final: 0.5940 (t0) REVERT: E 294 TYR cc_start: 0.7293 (m-10) cc_final: 0.7016 (m-10) REVERT: E 325 MET cc_start: 0.6265 (ttm) cc_final: 0.5919 (ptm) REVERT: C 269 MET cc_start: 0.8401 (tpp) cc_final: 0.8047 (mtt) REVERT: A 124 PHE cc_start: 0.7499 (m-80) cc_final: 0.7218 (m-10) outliers start: 23 outliers final: 12 residues processed: 176 average time/residue: 0.1087 time to fit residues: 30.2393 Evaluate side-chains 147 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain A residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.0770 chunk 166 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 111 ASN C 12 ASN A 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.070934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.061272 restraints weight = 86711.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.062886 restraints weight = 49351.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.064010 restraints weight = 32580.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.064797 restraints weight = 23791.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.065351 restraints weight = 18710.395| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16468 Z= 0.113 Angle : 0.637 10.044 22348 Z= 0.314 Chirality : 0.043 0.182 2484 Planarity : 0.004 0.049 2849 Dihedral : 6.427 60.889 2278 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.22 % Allowed : 10.66 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2009 helix: 0.53 (0.19), residues: 743 sheet: 0.90 (0.24), residues: 420 loop : 1.06 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 177 TYR 0.015 0.001 TYR A 294 PHE 0.033 0.001 PHE A 352 TRP 0.008 0.001 TRP B 340 HIS 0.007 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (16466) covalent geometry : angle 0.63745 / 0.31 (22348) hydrogen bonds : bond 0.03659 / 2.43 ( 721) hydrogen bonds : angle 5.26553 / 3.62 ( 1938) Misc. bond : bond 0.00115 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8797 (tpp) cc_final: 0.8524 (tpp) REVERT: F 183 TYR cc_start: 0.8104 (m-80) cc_final: 0.7776 (m-80) REVERT: F 215 ASP cc_start: 0.8622 (p0) cc_final: 0.8068 (t70) REVERT: B 34 ILE cc_start: 0.9376 (mt) cc_final: 0.9102 (tp) REVERT: B 227 MET cc_start: 0.8384 (tpp) cc_final: 0.7980 (mpp) REVERT: B 325 MET cc_start: 0.7935 (tpp) cc_final: 0.7463 (mmp) REVERT: B 355 MET cc_start: 0.7188 (mmp) cc_final: 0.6942 (mmm) REVERT: E 44 MET cc_start: -0.0158 (mmt) cc_final: -0.0468 (mpp) REVERT: E 78 ASN cc_start: 0.6176 (t0) cc_final: 0.5770 (t0) REVERT: E 241 GLU cc_start: 0.7806 (tp30) cc_final: 0.7483 (tp30) REVERT: E 283 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8043 (mmp) REVERT: E 294 TYR cc_start: 0.7414 (m-10) cc_final: 0.7123 (m-10) REVERT: E 325 MET cc_start: 0.6297 (ttm) cc_final: 0.5976 (ptm) REVERT: C 269 MET cc_start: 0.8397 (tpp) cc_final: 0.8018 (mtt) REVERT: C 283 MET cc_start: 0.7799 (mmp) cc_final: 0.7428 (mmm) REVERT: C 313 MET cc_start: 0.8831 (tpp) cc_final: 0.8543 (ttt) REVERT: A 313 MET cc_start: 0.7390 (mmm) cc_final: 0.6967 (mmm) outliers start: 21 outliers final: 10 residues processed: 158 average time/residue: 0.1056 time to fit residues: 26.7375 Evaluate side-chains 143 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 192 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN B 87 HIS ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.067067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.057433 restraints weight = 87845.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.058947 restraints weight = 50537.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.060016 restraints weight = 33794.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.060758 restraints weight = 24947.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.061290 restraints weight = 19838.648| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16468 Z= 0.220 Angle : 0.737 8.714 22348 Z= 0.370 Chirality : 0.047 0.164 2484 Planarity : 0.005 0.053 2849 Dihedral : 6.537 59.545 2278 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.38 % Allowed : 12.05 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 2009 helix: 0.31 (0.19), residues: 743 sheet: 0.57 (0.24), residues: 410 loop : 0.58 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 183 TYR 0.014 0.002 TYR F 183 PHE 0.021 0.002 PHE A 352 TRP 0.016 0.002 TRP B 356 HIS 0.009 0.002 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (16466) covalent geometry : angle 0.73672 / 0.37 (22348) hydrogen bonds : bond 0.05054 / 3.35 ( 721) hydrogen bonds : angle 5.55779 / 3.85 ( 1938) Misc. bond : bond 0.00144 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8917 (tpp) cc_final: 0.8493 (tpp) REVERT: D 227 MET cc_start: 0.7008 (tpp) cc_final: 0.6705 (tpp) REVERT: F 163 LYS cc_start: 0.7467 (tmtt) cc_final: 0.6630 (pttp) REVERT: F 183 TYR cc_start: 0.8348 (m-80) cc_final: 0.8019 (m-80) REVERT: F 215 ASP cc_start: 0.8608 (p0) cc_final: 0.8160 (t70) REVERT: B 227 MET cc_start: 0.8382 (tpp) cc_final: 0.7970 (mpp) REVERT: B 325 MET cc_start: 0.8013 (tpp) cc_final: 0.7598 (mmp) REVERT: B 355 MET cc_start: 0.7477 (mmp) cc_final: 0.7088 (mmm) REVERT: E 44 MET cc_start: -0.0420 (mmt) cc_final: -0.0642 (mpp) REVERT: E 65 LEU cc_start: 0.6865 (mt) cc_final: 0.6531 (mt) REVERT: E 78 ASN cc_start: 0.6378 (t0) cc_final: 0.6083 (t0) REVERT: E 176 MET cc_start: 0.6769 (tpt) cc_final: 0.6397 (tpt) REVERT: E 283 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8192 (mmp) REVERT: E 325 MET cc_start: 0.6666 (ttm) cc_final: 0.6462 (ptm) REVERT: C 269 MET cc_start: 0.8560 (tpp) cc_final: 0.8243 (mtt) REVERT: C 313 MET cc_start: 0.8809 (tpp) cc_final: 0.8605 (ttt) REVERT: A 190 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7827 (mmp) outliers start: 41 outliers final: 23 residues processed: 164 average time/residue: 0.1031 time to fit residues: 27.2414 Evaluate side-chains 156 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 317 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.066643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.057092 restraints weight = 88487.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.058586 restraints weight = 50879.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.059637 restraints weight = 34098.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.060368 restraints weight = 25232.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.060887 restraints weight = 20089.665| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 16468 Z= 0.208 Angle : 0.704 11.269 22348 Z= 0.353 Chirality : 0.046 0.183 2484 Planarity : 0.004 0.053 2849 Dihedral : 6.481 57.353 2278 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.03 % Allowed : 14.14 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 2009 helix: 0.31 (0.19), residues: 743 sheet: 0.29 (0.24), residues: 410 loop : 0.37 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 196 TYR 0.014 0.002 TYR F 183 PHE 0.015 0.002 PHE A 352 TRP 0.015 0.002 TRP B 356 HIS 0.007 0.002 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (16466) covalent geometry : angle 0.70411 / 0.35 (22348) hydrogen bonds : bond 0.04490 / 2.98 ( 721) hydrogen bonds : angle 5.49797 / 3.81 ( 1938) Misc. bond : bond 0.00111 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8945 (tpp) cc_final: 0.8481 (tpp) REVERT: F 122 MET cc_start: 0.5494 (mtp) cc_final: 0.5051 (mtp) REVERT: F 163 LYS cc_start: 0.7499 (tmtt) cc_final: 0.6705 (pttp) REVERT: F 183 TYR cc_start: 0.8395 (m-80) cc_final: 0.8039 (m-80) REVERT: F 215 ASP cc_start: 0.8694 (p0) cc_final: 0.8230 (t70) REVERT: F 231 GLU cc_start: 0.8122 (pt0) cc_final: 0.7788 (pm20) REVERT: B 75 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8515 (pt) REVERT: B 227 MET cc_start: 0.8400 (tpp) cc_final: 0.8183 (mpp) REVERT: B 279 TYR cc_start: 0.8364 (t80) cc_final: 0.8131 (t80) REVERT: B 325 MET cc_start: 0.7954 (tpp) cc_final: 0.7604 (mmp) REVERT: B 355 MET cc_start: 0.7521 (mmp) cc_final: 0.7088 (mmm) REVERT: E 65 LEU cc_start: 0.6891 (mt) cc_final: 0.6557 (mt) REVERT: E 107 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.4957 (mt-10) REVERT: E 325 MET cc_start: 0.7022 (ttm) cc_final: 0.6708 (ptt) REVERT: C 269 MET cc_start: 0.8607 (tpp) cc_final: 0.8183 (mtt) REVERT: A 123 MET cc_start: 0.8710 (tpp) cc_final: 0.8397 (mmt) REVERT: A 227 MET cc_start: 0.7884 (ttm) cc_final: 0.7631 (ttm) REVERT: A 317 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7215 (tp) outliers start: 35 outliers final: 19 residues processed: 159 average time/residue: 0.1067 time to fit residues: 26.6241 Evaluate side-chains 152 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 317 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 67 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 200 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 107 optimal weight: 0.0060 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.067201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.057702 restraints weight = 87593.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.059197 restraints weight = 50183.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.060251 restraints weight = 33573.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060968 restraints weight = 24782.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.061493 restraints weight = 19786.935| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16468 Z= 0.151 Angle : 0.658 11.019 22348 Z= 0.325 Chirality : 0.044 0.181 2484 Planarity : 0.004 0.051 2849 Dihedral : 6.274 56.906 2278 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.85 % Allowed : 14.89 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 2009 helix: 0.45 (0.19), residues: 738 sheet: 0.27 (0.24), residues: 410 loop : 0.40 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.012 0.001 TYR A 362 PHE 0.019 0.002 PHE A 352 TRP 0.011 0.001 TRP B 79 HIS 0.007 0.001 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16466) covalent geometry : angle 0.65757 / 0.32 (22348) hydrogen bonds : bond 0.04090 / 2.72 ( 721) hydrogen bonds : angle 5.31987 / 3.69 ( 1938) Misc. bond : bond 0.00087 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8932 (tpp) cc_final: 0.8471 (tpp) REVERT: F 122 MET cc_start: 0.5562 (mtp) cc_final: 0.5298 (mtp) REVERT: F 163 LYS cc_start: 0.7449 (tmtt) cc_final: 0.6654 (pttp) REVERT: F 183 TYR cc_start: 0.8338 (m-80) cc_final: 0.7959 (m-80) REVERT: F 215 ASP cc_start: 0.8663 (p0) cc_final: 0.8222 (t70) REVERT: F 231 GLU cc_start: 0.8081 (pt0) cc_final: 0.7746 (pm20) REVERT: B 227 MET cc_start: 0.8356 (tpp) cc_final: 0.8126 (mpp) REVERT: B 325 MET cc_start: 0.7922 (tpp) cc_final: 0.7487 (mmp) REVERT: B 355 MET cc_start: 0.7549 (mmp) cc_final: 0.7218 (mmm) REVERT: E 8 LEU cc_start: 0.8521 (mt) cc_final: 0.7967 (tp) REVERT: E 78 ASN cc_start: 0.6673 (t0) cc_final: 0.6406 (t0) REVERT: E 107 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.4939 (mt-10) REVERT: E 325 MET cc_start: 0.6995 (ttm) cc_final: 0.6638 (ptm) REVERT: C 269 MET cc_start: 0.8606 (tpp) cc_final: 0.8156 (mtt) REVERT: A 123 MET cc_start: 0.8705 (tpp) cc_final: 0.8391 (mmt) REVERT: A 227 MET cc_start: 0.7814 (ttm) cc_final: 0.7540 (ttm) REVERT: A 317 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7365 (tp) outliers start: 32 outliers final: 19 residues processed: 152 average time/residue: 0.1054 time to fit residues: 26.0877 Evaluate side-chains 150 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 317 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 132 optimal weight: 0.0670 chunk 148 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.066716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.057256 restraints weight = 88086.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.058741 restraints weight = 50606.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.059773 restraints weight = 33869.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.060502 restraints weight = 25078.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.061016 restraints weight = 19973.371| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16468 Z= 0.171 Angle : 0.668 9.360 22348 Z= 0.331 Chirality : 0.045 0.236 2484 Planarity : 0.004 0.050 2849 Dihedral : 6.308 57.055 2278 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.38 % Allowed : 14.66 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 2009 helix: 0.48 (0.20), residues: 738 sheet: 0.23 (0.25), residues: 410 loop : 0.30 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 312 TYR 0.017 0.001 TYR F 183 PHE 0.016 0.002 PHE D 352 TRP 0.013 0.002 TRP B 356 HIS 0.008 0.001 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (16466) covalent geometry : angle 0.66845 / 0.33 (22348) hydrogen bonds : bond 0.04208 / 2.83 ( 721) hydrogen bonds : angle 5.33938 / 3.70 ( 1938) Misc. bond : bond 0.00092 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8928 (tpp) cc_final: 0.8500 (tpp) REVERT: D 227 MET cc_start: 0.7007 (tpp) cc_final: 0.6769 (tpp) REVERT: F 122 MET cc_start: 0.5766 (mtp) cc_final: 0.5470 (mtp) REVERT: F 163 LYS cc_start: 0.7529 (tmtt) cc_final: 0.6734 (pttp) REVERT: F 183 TYR cc_start: 0.8324 (m-80) cc_final: 0.7998 (m-80) REVERT: F 214 MET cc_start: 0.7841 (tpp) cc_final: 0.7612 (tpp) REVERT: F 215 ASP cc_start: 0.8654 (p0) cc_final: 0.8288 (t70) REVERT: F 231 GLU cc_start: 0.8009 (pt0) cc_final: 0.7685 (pm20) REVERT: B 325 MET cc_start: 0.7889 (tpp) cc_final: 0.7485 (mmp) REVERT: B 355 MET cc_start: 0.7586 (mmp) cc_final: 0.7310 (mmm) REVERT: E 8 LEU cc_start: 0.8522 (mt) cc_final: 0.7986 (tp) REVERT: E 65 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6282 (mt) REVERT: E 107 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.4999 (mt-10) REVERT: E 283 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8216 (mmp) REVERT: E 325 MET cc_start: 0.7043 (ttm) cc_final: 0.6791 (ptm) REVERT: A 119 MET cc_start: 0.8936 (ttm) cc_final: 0.8522 (ttt) REVERT: A 123 MET cc_start: 0.8610 (tpp) cc_final: 0.8298 (mmt) REVERT: A 227 MET cc_start: 0.7825 (ttm) cc_final: 0.7564 (ttm) REVERT: A 317 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7407 (tp) outliers start: 41 outliers final: 24 residues processed: 157 average time/residue: 0.1075 time to fit residues: 27.4079 Evaluate side-chains 154 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 317 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 194 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.067016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.057510 restraints weight = 88583.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.059028 restraints weight = 50686.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.060084 restraints weight = 33860.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.060817 restraints weight = 24979.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.061342 restraints weight = 19849.788| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16468 Z= 0.135 Angle : 0.647 10.555 22348 Z= 0.317 Chirality : 0.044 0.186 2484 Planarity : 0.004 0.049 2849 Dihedral : 6.197 56.169 2278 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.74 % Allowed : 15.35 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 2009 helix: 0.56 (0.20), residues: 738 sheet: 0.26 (0.25), residues: 410 loop : 0.37 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 312 TYR 0.012 0.001 TYR B 133 PHE 0.022 0.002 PHE E 262 TRP 0.011 0.001 TRP B 356 HIS 0.007 0.001 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (16466) covalent geometry : angle 0.64734 / 0.32 (22348) hydrogen bonds : bond 0.03838 / 2.58 ( 721) hydrogen bonds : angle 5.20026 / 3.61 ( 1938) Misc. bond : bond 0.00071 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 MET cc_start: 0.7733 (ttt) cc_final: 0.7461 (tmm) REVERT: D 123 MET cc_start: 0.8939 (tpp) cc_final: 0.8476 (tpp) REVERT: D 227 MET cc_start: 0.6951 (tpp) cc_final: 0.6712 (tpp) REVERT: F 122 MET cc_start: 0.5666 (mtp) cc_final: 0.5383 (mtp) REVERT: F 163 LYS cc_start: 0.7490 (tmtt) cc_final: 0.6683 (pttp) REVERT: F 183 TYR cc_start: 0.8292 (m-80) cc_final: 0.7943 (m-80) REVERT: F 214 MET cc_start: 0.7892 (tpp) cc_final: 0.7654 (tpp) REVERT: F 215 ASP cc_start: 0.8632 (p0) cc_final: 0.8304 (t70) REVERT: F 231 GLU cc_start: 0.8003 (pt0) cc_final: 0.7674 (pm20) REVERT: B 227 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: B 325 MET cc_start: 0.7856 (tpp) cc_final: 0.7468 (mmp) REVERT: B 355 MET cc_start: 0.7537 (mmp) cc_final: 0.7285 (mmm) REVERT: E 8 LEU cc_start: 0.8499 (mt) cc_final: 0.7953 (tp) REVERT: E 78 ASN cc_start: 0.6651 (t0) cc_final: 0.6321 (t0) REVERT: E 107 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.4912 (mt-10) REVERT: E 325 MET cc_start: 0.6989 (ttm) cc_final: 0.6741 (ptt) REVERT: A 119 MET cc_start: 0.8854 (ttm) cc_final: 0.8515 (ttt) REVERT: A 123 MET cc_start: 0.8634 (tpp) cc_final: 0.8392 (mmt) REVERT: A 317 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7600 (tp) outliers start: 30 outliers final: 21 residues processed: 147 average time/residue: 0.1019 time to fit residues: 24.3541 Evaluate side-chains 154 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 179 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 0.4980 chunk 168 optimal weight: 0.0870 chunk 174 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.068490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.059104 restraints weight = 88007.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.060648 restraints weight = 49950.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.061726 restraints weight = 33133.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062471 restraints weight = 24229.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.062990 restraints weight = 19168.763| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 16468 Z= 0.105 Angle : 0.622 11.436 22348 Z= 0.301 Chirality : 0.043 0.197 2484 Planarity : 0.004 0.048 2849 Dihedral : 5.910 56.517 2278 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.81 % Allowed : 16.45 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 2009 helix: 0.96 (0.20), residues: 698 sheet: 0.45 (0.25), residues: 385 loop : 0.46 (0.22), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 196 TYR 0.013 0.001 TYR E 306 PHE 0.013 0.001 PHE C 352 TRP 0.015 0.001 TRP D 356 HIS 0.005 0.001 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (16466) covalent geometry : angle 0.62173 / 0.30 (22348) hydrogen bonds : bond 0.03216 / 2.17 ( 721) hydrogen bonds : angle 4.97617 / 3.45 ( 1938) Misc. bond : bond 0.00044 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4018 Ramachandran restraints generated. 2009 Oldfield, 0 Emsley, 2009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8897 (tpp) cc_final: 0.8456 (tpp) REVERT: D 227 MET cc_start: 0.6997 (tpp) cc_final: 0.6792 (tpp) REVERT: F 122 MET cc_start: 0.5731 (mtp) cc_final: 0.5040 (mmm) REVERT: F 163 LYS cc_start: 0.7343 (tmtt) cc_final: 0.6557 (pttt) REVERT: F 183 TYR cc_start: 0.8234 (m-80) cc_final: 0.7908 (m-80) REVERT: F 214 MET cc_start: 0.7906 (tpp) cc_final: 0.7706 (tpp) REVERT: F 215 ASP cc_start: 0.8586 (p0) cc_final: 0.8274 (t70) REVERT: F 231 GLU cc_start: 0.7946 (pt0) cc_final: 0.7630 (pm20) REVERT: B 227 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7979 (mpp) REVERT: B 325 MET cc_start: 0.7719 (tpp) cc_final: 0.7375 (mmp) REVERT: E 78 ASN cc_start: 0.6596 (t0) cc_final: 0.6277 (t0) REVERT: E 107 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.4637 (mt-10) REVERT: E 294 TYR cc_start: 0.7826 (m-10) cc_final: 0.7501 (m-10) REVERT: A 123 MET cc_start: 0.8693 (tpp) cc_final: 0.8493 (mmt) REVERT: A 129 VAL cc_start: 0.8335 (m) cc_final: 0.8013 (p) outliers start: 14 outliers final: 7 residues processed: 150 average time/residue: 0.1076 time to fit residues: 25.9682 Evaluate side-chains 144 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain A residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 161 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 169 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.068258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.058905 restraints weight = 88032.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.060412 restraints weight = 50123.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.061452 restraints weight = 33397.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062183 restraints weight = 24585.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.062699 restraints weight = 19524.375| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 16468 Z= 0.109 Angle : 0.640 12.278 22348 Z= 0.306 Chirality : 0.042 0.163 2484 Planarity : 0.004 0.048 2849 Dihedral : 5.853 57.084 2278 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.93 % Allowed : 16.57 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 2009 helix: 1.03 (0.20), residues: 698 sheet: 0.44 (0.25), residues: 410 loop : 0.45 (0.22), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 206 TYR 0.015 0.001 TYR A 279 PHE 0.020 0.001 PHE C 352 TRP 0.024 0.001 TRP C 86 HIS 0.006 0.001 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16466) covalent geometry : angle 0.64014 / 0.31 (22348) hydrogen bonds : bond 0.03288 / 2.21 ( 721) hydrogen bonds : angle 4.93903 / 3.42 ( 1938) Misc. bond : bond 0.00049 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.88 seconds wall clock time: 39 minutes 57.60 seconds (2397.60 seconds total)