Starting phenix.real_space_refine on Wed Mar 4 21:32:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z7h_14532/03_2026/7z7h_14532.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7h_14532/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z7h_14532/03_2026/7z7h_14532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7h_14532/03_2026/7z7h_14532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z7h_14532/03_2026/7z7h_14532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7h_14532/03_2026/7z7h_14532.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 3 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: 3.72, 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: 1.31 Conformation dependent library (CDL) restraints added in 702.1 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: 0.71 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: 2.53 Time building geometry restraints manager: 1.72 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: 9354 22.61 - 45.21: 491 45.21 - 67.82: 75 67.82 - 90.43: 15 90.43 - 113.03: 5 Dihedral angle restraints: 9940 sinusoidal: 4052 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 9937 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 14.273 113.033 6166 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 covalent geometry : bond 0.01063 (16466) covalent geometry : angle 1.24834 (22348) hydrogen bonds : bond 0.22843 ( 721) hydrogen bonds : angle 8.47394 ( 1938) Misc. bond : bond 0.61451 ( 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 : 0.594 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: 0.1249 time to fit residues: 48.9217 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 : 0.524 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 111 ASN D 115 ASN D 246 GLN 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 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 = 0.070886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.061141 restraints weight = 86177.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.062793 restraints weight = 49052.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.063944 restraints weight = 32332.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.064737 restraints weight = 23540.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.065311 restraints weight = 18445.592| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16468 Z= 0.212 Angle : 0.803 8.699 22348 Z= 0.415 Chirality : 0.048 0.283 2484 Planarity : 0.005 0.047 2849 Dihedral : 8.667 89.725 2321 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.68 % Allowed : 8.23 % Favored : 90.09 % 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: 0.66 (0.18), residues: 2009 helix: 0.24 (0.18), residues: 738 sheet: 0.95 (0.25), residues: 385 loop : 0.61 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 117 TYR 0.018 0.002 TYR E 306 PHE 0.025 0.002 PHE E 90 TRP 0.015 0.002 TRP E 79 HIS 0.009 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00471 (16466) covalent geometry : angle 0.80262 (22348) hydrogen bonds : bond 0.05671 ( 721) hydrogen bonds : angle 6.20714 ( 1938) Misc. bond : bond 0.00647 ( 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 201 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.443 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: F 183 TYR cc_start: 0.8276 (m-80) cc_final: 0.8000 (m-80) REVERT: F 215 ASP cc_start: 0.8716 (p0) cc_final: 0.8268 (t70) REVERT: B 34 ILE cc_start: 0.9412 (mt) cc_final: 0.9137 (tp) REVERT: B 325 MET cc_start: 0.8166 (tpp) cc_final: 0.7479 (mmp) REVERT: E 65 LEU cc_start: 0.7082 (mt) cc_final: 0.6679 (mt) REVERT: E 78 ASN cc_start: 0.6355 (t0) cc_final: 0.6046 (t0) REVERT: C 269 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7994 (mtt) REVERT: A 313 MET cc_start: 0.7512 (mmm) cc_final: 0.6977 (mmm) outliers start: 29 outliers final: 15 residues processed: 189 average time/residue: 0.1178 time to fit residues: 34.4698 Evaluate side-chains 147 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 269 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 129 VAL 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: 1.9990 chunk 187 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 98 optimal weight: 0.0980 chunk 158 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 HIS A 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.071409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.061718 restraints weight = 86683.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.063350 restraints weight = 49372.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.064491 restraints weight = 32607.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.065285 restraints weight = 23800.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.065845 restraints weight = 18689.180| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16468 Z= 0.123 Angle : 0.670 7.939 22348 Z= 0.338 Chirality : 0.044 0.241 2484 Planarity : 0.004 0.075 2849 Dihedral : 7.640 83.327 2321 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.27 % Allowed : 10.14 % Favored : 88.59 % 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: 1.06 (0.19), residues: 2009 helix: 0.42 (0.19), residues: 748 sheet: 1.06 (0.24), residues: 410 loop : 1.05 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 196 TYR 0.015 0.001 TYR E 306 PHE 0.019 0.002 PHE E 90 TRP 0.022 0.001 TRP E 356 HIS 0.007 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00260 (16466) covalent geometry : angle 0.67040 (22348) hydrogen bonds : bond 0.04103 ( 721) hydrogen bonds : angle 5.53074 ( 1938) Misc. bond : bond 0.00202 ( 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 184 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 283 MET cc_start: 0.8304 (mmp) cc_final: 0.8096 (mmp) REVERT: F 183 TYR cc_start: 0.8121 (m-80) cc_final: 0.7755 (m-80) REVERT: F 215 ASP cc_start: 0.8641 (p0) cc_final: 0.8301 (t70) REVERT: B 34 ILE cc_start: 0.9383 (mt) cc_final: 0.9104 (tp) REVERT: B 325 MET cc_start: 0.8110 (tpp) cc_final: 0.7433 (mmp) REVERT: B 355 MET cc_start: 0.7182 (mmp) cc_final: 0.6865 (mmm) REVERT: E 44 MET cc_start: -0.0323 (mmt) cc_final: -0.0663 (mpp) REVERT: E 78 ASN cc_start: 0.6190 (t0) cc_final: 0.5985 (t0) REVERT: E 325 MET cc_start: 0.6244 (tpp) cc_final: 0.5359 (ptm) REVERT: C 269 MET cc_start: 0.8344 (tpp) cc_final: 0.7970 (mtt) REVERT: C 283 MET cc_start: 0.7804 (mmp) cc_final: 0.7456 (mmm) REVERT: A 123 MET cc_start: 0.8368 (mmt) cc_final: 0.8084 (mmt) REVERT: A 313 MET cc_start: 0.7625 (mmm) cc_final: 0.7056 (mmm) outliers start: 22 outliers final: 9 residues processed: 178 average time/residue: 0.1067 time to fit residues: 30.3509 Evaluate side-chains 146 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 149 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain E residue 129 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 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: 20.0000 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 0.0000 chunk 166 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN A 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.069782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.060064 restraints weight = 87849.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061631 restraints weight = 50599.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.062736 restraints weight = 33688.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.063512 restraints weight = 24699.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.064069 restraints weight = 19524.339| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16468 Z= 0.147 Angle : 0.668 9.908 22348 Z= 0.331 Chirality : 0.044 0.194 2484 Planarity : 0.004 0.050 2849 Dihedral : 7.115 79.872 2321 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 10.66 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.19), residues: 2009 helix: 0.47 (0.19), residues: 744 sheet: 0.99 (0.24), residues: 410 loop : 0.90 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 196 TYR 0.014 0.001 TYR A 279 PHE 0.018 0.002 PHE A 352 TRP 0.012 0.001 TRP C 79 HIS 0.010 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00324 (16466) covalent geometry : angle 0.66825 (22348) hydrogen bonds : bond 0.04110 ( 721) hydrogen bonds : angle 5.39152 ( 1938) Misc. bond : bond 0.00145 ( 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 176 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8783 (tpp) cc_final: 0.8536 (tpp) REVERT: F 183 TYR cc_start: 0.8221 (m-80) cc_final: 0.7648 (m-80) REVERT: F 215 ASP cc_start: 0.8645 (p0) cc_final: 0.8056 (t70) REVERT: B 325 MET cc_start: 0.8002 (tpp) cc_final: 0.7536 (mmp) REVERT: B 355 MET cc_start: 0.7307 (mmp) cc_final: 0.6851 (mmm) REVERT: E 44 MET cc_start: -0.0048 (mmt) cc_final: -0.0509 (mpp) REVERT: E 78 ASN cc_start: 0.6314 (t0) cc_final: 0.6032 (t0) REVERT: E 241 GLU cc_start: 0.7770 (tp30) cc_final: 0.7523 (tp30) REVERT: C 269 MET cc_start: 0.8457 (tpp) cc_final: 0.8100 (mtt) REVERT: C 313 MET cc_start: 0.8847 (tpp) cc_final: 0.8527 (ttt) outliers start: 29 outliers final: 18 residues processed: 166 average time/residue: 0.1113 time to fit residues: 29.4141 Evaluate side-chains 148 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 349 LEU 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 C residue 30 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 65 LEU 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: 7.9990 chunk 177 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.065342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.055736 restraints weight = 88992.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.057202 restraints weight = 51377.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058237 restraints weight = 34565.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.058954 restraints weight = 25690.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.059454 restraints weight = 20561.569| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 16468 Z= 0.339 Angle : 0.859 8.745 22348 Z= 0.441 Chirality : 0.050 0.191 2484 Planarity : 0.006 0.062 2849 Dihedral : 7.693 77.061 2321 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.32 % Allowed : 12.75 % Favored : 84.94 % 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: -0.02 (0.18), residues: 2009 helix: -0.05 (0.19), residues: 744 sheet: 0.18 (0.24), residues: 410 loop : 0.15 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 312 TYR 0.016 0.002 TYR A 169 PHE 0.028 0.003 PHE A 31 TRP 0.023 0.002 TRP B 356 HIS 0.012 0.002 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00752 (16466) covalent geometry : angle 0.85914 (22348) hydrogen bonds : bond 0.06040 ( 721) hydrogen bonds : angle 6.07858 ( 1938) Misc. bond : bond 0.00122 ( 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 169 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8965 (tpp) cc_final: 0.8546 (tpp) REVERT: F 122 MET cc_start: 0.5725 (ttt) cc_final: 0.5310 (mtp) REVERT: F 215 ASP cc_start: 0.8692 (p0) cc_final: 0.8216 (t70) REVERT: F 231 GLU cc_start: 0.8195 (pt0) cc_final: 0.7809 (pm20) REVERT: B 299 MET cc_start: 0.8473 (mmm) cc_final: 0.7838 (mmm) REVERT: B 325 MET cc_start: 0.8079 (tpp) cc_final: 0.7591 (mmp) REVERT: B 355 MET cc_start: 0.7559 (mmp) cc_final: 0.6917 (mmm) REVERT: E 44 MET cc_start: -0.0131 (mmt) cc_final: -0.0439 (mpp) REVERT: E 65 LEU cc_start: 0.6900 (mt) cc_final: 0.6523 (mt) REVERT: E 78 ASN cc_start: 0.6915 (t0) cc_final: 0.6633 (t0) REVERT: E 82 MET cc_start: 0.7066 (tpt) cc_final: 0.6718 (mmp) REVERT: E 176 MET cc_start: 0.6892 (tpt) cc_final: 0.6496 (tpt) REVERT: E 254 ARG cc_start: 0.7168 (mtm180) cc_final: 0.6884 (ptm160) REVERT: E 325 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6476 (ptm) REVERT: C 47 MET cc_start: 0.4992 (OUTLIER) cc_final: 0.4699 (tpt) REVERT: C 269 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8377 (mtt) REVERT: C 313 MET cc_start: 0.8842 (tpp) cc_final: 0.8581 (ttt) REVERT: A 123 MET cc_start: 0.8672 (tpp) cc_final: 0.8305 (mmt) outliers start: 40 outliers final: 27 residues processed: 159 average time/residue: 0.1036 time to fit residues: 26.6636 Evaluate side-chains 154 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 352 PHE 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 F residue 196 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 349 LEU 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 289 ILE Chi-restraints excluded: chain E residue 325 MET 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 194 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 364 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.067384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.057816 restraints weight = 88013.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.059333 restraints weight = 50298.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.060383 restraints weight = 33597.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.061122 restraints weight = 24862.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061622 restraints weight = 19766.329| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16468 Z= 0.132 Angle : 0.654 9.320 22348 Z= 0.326 Chirality : 0.044 0.187 2484 Planarity : 0.004 0.051 2849 Dihedral : 7.059 75.380 2321 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.91 % Allowed : 14.66 % Favored : 83.43 % 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: 0.39 (0.19), residues: 2009 helix: 0.37 (0.19), residues: 739 sheet: 0.25 (0.24), residues: 410 loop : 0.39 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 196 TYR 0.012 0.001 TYR F 183 PHE 0.017 0.002 PHE B 223 TRP 0.011 0.001 TRP B 340 HIS 0.005 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00288 (16466) covalent geometry : angle 0.65439 (22348) hydrogen bonds : bond 0.04048 ( 721) hydrogen bonds : angle 5.38835 ( 1938) Misc. bond : bond 0.00088 ( 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: 33 poor density : 137 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8926 (tpp) cc_final: 0.8451 (tpp) REVERT: F 122 MET cc_start: 0.5652 (ttt) cc_final: 0.5344 (mtp) REVERT: F 163 LYS cc_start: 0.7504 (tmtt) cc_final: 0.6672 (pttp) REVERT: F 215 ASP cc_start: 0.8611 (p0) cc_final: 0.8213 (t70) REVERT: F 231 GLU cc_start: 0.8161 (pt0) cc_final: 0.7779 (pm20) REVERT: B 325 MET cc_start: 0.7958 (tpp) cc_final: 0.7609 (mmp) REVERT: B 355 MET cc_start: 0.7516 (mmp) cc_final: 0.7143 (mmm) REVERT: E 8 LEU cc_start: 0.8418 (mt) cc_final: 0.8037 (tp) REVERT: E 44 MET cc_start: -0.0441 (mmt) cc_final: -0.1191 (pmm) REVERT: E 65 LEU cc_start: 0.6822 (mt) cc_final: 0.6497 (mt) REVERT: E 78 ASN cc_start: 0.6789 (t0) cc_final: 0.6392 (t0) REVERT: E 82 MET cc_start: 0.6853 (tpt) cc_final: 0.6510 (mmp) REVERT: E 107 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.4975 (mt-10) REVERT: C 47 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.4744 (tpt) REVERT: C 269 MET cc_start: 0.8615 (tpp) cc_final: 0.8283 (mtt) REVERT: C 355 MET cc_start: 0.8351 (mpp) cc_final: 0.8111 (ptp) REVERT: A 123 MET cc_start: 0.8691 (tpp) cc_final: 0.8376 (mmt) REVERT: A 313 MET cc_start: 0.7450 (mmm) cc_final: 0.7020 (mmm) outliers start: 33 outliers final: 19 residues processed: 159 average time/residue: 0.1100 time to fit residues: 28.2574 Evaluate side-chains 149 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE 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 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 185 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 325 MET 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 100 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 219 VAL 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: 8.9990 chunk 119 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.066205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.056722 restraints weight = 88054.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.058215 restraints weight = 50590.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.059248 restraints weight = 33834.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.059963 restraints weight = 25021.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.060466 restraints weight = 19939.647| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16468 Z= 0.205 Angle : 0.696 8.154 22348 Z= 0.349 Chirality : 0.045 0.170 2484 Planarity : 0.004 0.051 2849 Dihedral : 7.094 72.896 2321 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.20 % Allowed : 14.83 % 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: 0.21 (0.19), residues: 2009 helix: 0.37 (0.19), residues: 744 sheet: 0.12 (0.24), residues: 410 loop : 0.17 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 206 TYR 0.011 0.001 TYR A 362 PHE 0.018 0.002 PHE A 352 TRP 0.015 0.002 TRP B 356 HIS 0.008 0.002 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00460 (16466) covalent geometry : angle 0.69639 (22348) hydrogen bonds : bond 0.04567 ( 721) hydrogen bonds : angle 5.54883 ( 1938) Misc. bond : bond 0.00095 ( 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 165 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8937 (tpp) cc_final: 0.8504 (tpp) REVERT: D 355 MET cc_start: 0.8090 (mmm) cc_final: 0.7883 (tpt) REVERT: F 122 MET cc_start: 0.5915 (ttt) cc_final: 0.5590 (mtp) REVERT: F 163 LYS cc_start: 0.7556 (tmtt) cc_final: 0.6749 (pttp) REVERT: F 215 ASP cc_start: 0.8727 (p0) cc_final: 0.8292 (t70) REVERT: F 231 GLU cc_start: 0.8080 (pt0) cc_final: 0.7710 (pm20) REVERT: B 227 MET cc_start: 0.8448 (tpp) cc_final: 0.8146 (mpp) REVERT: B 325 MET cc_start: 0.7955 (tpp) cc_final: 0.7634 (mmp) REVERT: B 355 MET cc_start: 0.7559 (mmp) cc_final: 0.7113 (mmm) REVERT: E 8 LEU cc_start: 0.8403 (mt) cc_final: 0.8060 (tp) REVERT: E 65 LEU cc_start: 0.6898 (mt) cc_final: 0.6588 (mt) REVERT: E 78 ASN cc_start: 0.6824 (t0) cc_final: 0.6544 (t0) REVERT: E 82 MET cc_start: 0.6880 (tpt) cc_final: 0.6558 (mmp) REVERT: E 107 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5061 (mt-10) REVERT: E 283 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8299 (mmp) REVERT: E 325 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6391 (ptm) REVERT: C 269 MET cc_start: 0.8597 (tpp) cc_final: 0.8161 (mtt) REVERT: A 123 MET cc_start: 0.8686 (tpp) cc_final: 0.8378 (mmt) REVERT: A 317 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7232 (tp) outliers start: 38 outliers final: 23 residues processed: 154 average time/residue: 0.1029 time to fit residues: 25.9902 Evaluate side-chains 152 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE 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 B residue 75 ILE Chi-restraints excluded: chain B residue 165 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 349 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 325 MET 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 C residue 289 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 219 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: 5.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 132 optimal weight: 0.0030 chunk 148 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.067000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.057492 restraints weight = 88122.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059002 restraints weight = 50548.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.060047 restraints weight = 33698.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.060779 restraints weight = 24849.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061288 restraints weight = 19748.271| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16468 Z= 0.138 Angle : 0.642 7.941 22348 Z= 0.317 Chirality : 0.044 0.179 2484 Planarity : 0.004 0.049 2849 Dihedral : 6.894 74.768 2321 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.09 % Allowed : 15.30 % Favored : 82.62 % 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: 0.54 (0.20), residues: 739 sheet: 0.16 (0.24), residues: 410 loop : 0.29 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 206 TYR 0.013 0.001 TYR E 306 PHE 0.014 0.001 PHE E 90 TRP 0.010 0.001 TRP C 79 HIS 0.007 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00308 (16466) covalent geometry : angle 0.64175 (22348) hydrogen bonds : bond 0.03911 ( 721) hydrogen bonds : angle 5.30615 ( 1938) Misc. bond : bond 0.00075 ( 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 168 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8912 (tpp) cc_final: 0.8487 (tpp) REVERT: F 122 MET cc_start: 0.5987 (ttt) cc_final: 0.5663 (mtp) REVERT: F 163 LYS cc_start: 0.7516 (tmtt) cc_final: 0.6721 (pttp) REVERT: F 214 MET cc_start: 0.7820 (tpp) cc_final: 0.7614 (tpp) REVERT: F 215 ASP cc_start: 0.8680 (p0) cc_final: 0.8225 (t70) REVERT: F 231 GLU cc_start: 0.8036 (pt0) cc_final: 0.7688 (pm20) REVERT: B 227 MET cc_start: 0.8402 (tpp) cc_final: 0.8169 (mpp) REVERT: B 325 MET cc_start: 0.7896 (tpp) cc_final: 0.7481 (mmp) REVERT: B 355 MET cc_start: 0.7550 (mmp) cc_final: 0.7279 (mmm) REVERT: E 8 LEU cc_start: 0.8405 (mt) cc_final: 0.8056 (tp) REVERT: E 65 LEU cc_start: 0.6870 (mt) cc_final: 0.6608 (mt) REVERT: E 78 ASN cc_start: 0.6835 (t0) cc_final: 0.6508 (t0) REVERT: E 82 MET cc_start: 0.6860 (tpt) cc_final: 0.6544 (mmp) REVERT: E 107 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.4895 (mt-10) REVERT: E 325 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6501 (ptm) REVERT: C 269 MET cc_start: 0.8547 (tpp) cc_final: 0.8162 (mtt) REVERT: C 355 MET cc_start: 0.8318 (mpp) cc_final: 0.7904 (ptp) REVERT: A 123 MET cc_start: 0.8626 (tpp) cc_final: 0.8333 (mmt) REVERT: A 317 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7468 (tp) outliers start: 36 outliers final: 22 residues processed: 157 average time/residue: 0.0971 time to fit residues: 25.0572 Evaluate side-chains 152 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE 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 B residue 165 ILE 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 185 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 325 MET 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 153 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 219 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: 6.9990 chunk 116 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 124 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.065505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055996 restraints weight = 89928.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.057472 restraints weight = 52020.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.058495 restraints weight = 35008.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.059221 restraints weight = 25972.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.059729 restraints weight = 20719.794| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16468 Z= 0.217 Angle : 0.710 8.239 22348 Z= 0.355 Chirality : 0.046 0.187 2484 Planarity : 0.004 0.050 2849 Dihedral : 7.146 71.885 2321 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.97 % Allowed : 15.59 % Favored : 82.44 % 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: 0.14 (0.19), residues: 2009 helix: 0.36 (0.19), residues: 749 sheet: 0.04 (0.25), residues: 408 loop : 0.08 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 256 TYR 0.012 0.001 TYR A 362 PHE 0.022 0.002 PHE C 352 TRP 0.017 0.002 TRP B 356 HIS 0.009 0.002 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00487 (16466) covalent geometry : angle 0.71035 (22348) hydrogen bonds : bond 0.04623 ( 721) hydrogen bonds : angle 5.52894 ( 1938) Misc. bond : bond 0.00087 ( 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 160 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: D 123 MET cc_start: 0.8952 (tpp) cc_final: 0.8549 (tpp) REVERT: F 122 MET cc_start: 0.5876 (ttt) cc_final: 0.5637 (mtp) REVERT: F 163 LYS cc_start: 0.7594 (tmtt) cc_final: 0.6760 (pttp) REVERT: F 214 MET cc_start: 0.7926 (tpp) cc_final: 0.7626 (tpp) REVERT: F 215 ASP cc_start: 0.8682 (p0) cc_final: 0.8395 (t70) REVERT: F 231 GLU cc_start: 0.8111 (pt0) cc_final: 0.7749 (pm20) REVERT: B 227 MET cc_start: 0.8405 (tpp) cc_final: 0.8204 (mpp) REVERT: B 325 MET cc_start: 0.7947 (tpp) cc_final: 0.7568 (mmp) REVERT: B 355 MET cc_start: 0.7632 (mmp) cc_final: 0.7250 (mmm) REVERT: E 8 LEU cc_start: 0.8452 (mt) cc_final: 0.8137 (tp) REVERT: E 78 ASN cc_start: 0.6902 (t0) cc_final: 0.6616 (t0) REVERT: E 82 MET cc_start: 0.6925 (tpt) cc_final: 0.6607 (mmp) REVERT: E 107 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5093 (mt-10) REVERT: E 283 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8372 (mmp) REVERT: E 325 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6766 (ptm) REVERT: A 123 MET cc_start: 0.8587 (tpp) cc_final: 0.8307 (mmt) REVERT: A 313 MET cc_start: 0.7186 (mmm) cc_final: 0.6980 (mmm) REVERT: A 317 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7430 (tp) outliers start: 34 outliers final: 26 residues processed: 148 average time/residue: 0.0997 time to fit residues: 24.3951 Evaluate side-chains 152 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE 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 B residue 165 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 B residue 358 THR 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 283 MET Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 325 MET 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 153 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 179 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 103 ASN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.066053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.056579 restraints weight = 88549.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058081 restraints weight = 50819.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.059119 restraints weight = 33958.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.059854 restraints weight = 25090.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.060361 restraints weight = 19943.356| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16468 Z= 0.167 Angle : 0.677 8.373 22348 Z= 0.336 Chirality : 0.044 0.184 2484 Planarity : 0.004 0.049 2849 Dihedral : 7.027 73.098 2321 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.85 % Allowed : 15.82 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.24 (0.19), residues: 2009 helix: 0.53 (0.20), residues: 738 sheet: 0.05 (0.25), residues: 410 loop : 0.08 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.013 0.001 TYR F 217 PHE 0.018 0.002 PHE C 352 TRP 0.014 0.002 TRP B 356 HIS 0.008 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00375 (16466) covalent geometry : angle 0.67685 (22348) hydrogen bonds : bond 0.04139 ( 721) hydrogen bonds : angle 5.36192 ( 1938) Misc. bond : bond 0.00073 ( 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 159 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.8927 (tpp) cc_final: 0.8541 (tpp) REVERT: F 122 MET cc_start: 0.5772 (ttt) cc_final: 0.5416 (mtp) REVERT: F 163 LYS cc_start: 0.7583 (tmtt) cc_final: 0.6752 (pttp) REVERT: F 214 MET cc_start: 0.8027 (tpp) cc_final: 0.7716 (tpp) REVERT: F 215 ASP cc_start: 0.8656 (p0) cc_final: 0.8361 (t70) REVERT: F 231 GLU cc_start: 0.7976 (pt0) cc_final: 0.7644 (pm20) REVERT: B 325 MET cc_start: 0.7884 (tpp) cc_final: 0.7538 (mmp) REVERT: E 8 LEU cc_start: 0.8459 (mt) cc_final: 0.8139 (tp) REVERT: E 65 LEU cc_start: 0.6870 (mt) cc_final: 0.6614 (mt) REVERT: E 78 ASN cc_start: 0.6777 (t0) cc_final: 0.6495 (t0) REVERT: E 82 MET cc_start: 0.6930 (tpt) cc_final: 0.6613 (mmp) REVERT: E 107 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5049 (mt-10) REVERT: E 325 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6719 (ptm) REVERT: A 119 MET cc_start: 0.8850 (ttm) cc_final: 0.8581 (ttt) REVERT: A 317 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7553 (tp) outliers start: 32 outliers final: 25 residues processed: 148 average time/residue: 0.0997 time to fit residues: 24.3856 Evaluate side-chains 155 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 212 ILE 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 165 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 B residue 358 THR 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 289 ILE Chi-restraints excluded: chain E residue 325 MET 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 153 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 161 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 137 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.066810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.057377 restraints weight = 87508.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.058874 restraints weight = 50186.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.059915 restraints weight = 33470.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060656 restraints weight = 24725.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.061170 restraints weight = 19623.736| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16468 Z= 0.132 Angle : 0.642 8.779 22348 Z= 0.317 Chirality : 0.044 0.187 2484 Planarity : 0.004 0.049 2849 Dihedral : 6.801 73.683 2321 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.74 % Allowed : 16.34 % Favored : 81.92 % 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: 0.90 (0.20), residues: 699 sheet: 0.19 (0.25), residues: 410 loop : 0.23 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.013 0.001 TYR E 306 PHE 0.019 0.001 PHE B 223 TRP 0.019 0.002 TRP B 356 HIS 0.007 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00293 (16466) covalent geometry : angle 0.64218 (22348) hydrogen bonds : bond 0.03761 ( 721) hydrogen bonds : angle 5.19628 ( 1938) Misc. bond : bond 0.00066 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2271.54 seconds wall clock time: 40 minutes 19.12 seconds (2419.12 seconds total)