Starting phenix.real_space_refine on Fri Jul 3 03:35:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oi6_16887/07_2026/8oi6_16887.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi6_16887/07_2026/8oi6_16887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8oi6_16887/07_2026/8oi6_16887.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oi6_16887/07_2026/8oi6_16887.cif" model { file = "/net/cci-nas-00/data/ceres_data/8oi6_16887/07_2026/8oi6_16887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi6_16887/07_2026/8oi6_16887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oi6_16887/07_2026/8oi6_16887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi6_16887/07_2026/8oi6_16887.map" } resolution = 3.59 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= -0.002 sd= 0.214 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 8 5.49 5 Mg 4 5.21 5 S 83 5.16 5 C 7304 2.51 5 N 1945 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11573 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 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: "B" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 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: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 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: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2767 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 18, 'TRANS': 335} Chain breaks: 1 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: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 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} 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: "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: "D" 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: 2.79, per 1000 atoms: 0.24 Number of scatterers: 11573 At special positions: 0 Unit cell: (94.38, 89.54, 165.77, 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 83 16.00 P 8 15.00 Mg 4 11.99 O 2229 8.00 N 1945 7.00 C 7304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 530.8 milliseconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 22 sheets defined 49.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.569A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.699A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 214 removed outlier: 4.041A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.783A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.599A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.050A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.007A 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 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.531A pdb=" N GLN A 354 " --> 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 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.570A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.293A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.518A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.678A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.797A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.518A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.165A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.958A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.568A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.908A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.680A pdb=" N SER B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.500A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.691A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.810A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.507A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.549A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.733A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.430A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.501A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.980A 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 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.916A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.585A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.567A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.652A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.585A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.746A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.513A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.851A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.550A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.658A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.602A pdb=" N MET D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.019A 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 337 through 349 Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.011A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.565A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.839A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.171A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.667A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.698A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.574A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.654A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.815A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.705A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.071A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.755A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 5.947A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 529 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3734 1.34 - 1.46: 2694 1.46 - 1.58: 5233 1.58 - 1.70: 18 1.70 - 1.82: 143 Bond restraints: 11822 Sorted by residual: bond pdb=" N HYP I 6 " pdb=" CD HYP I 6 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" N HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.33e+02 bond pdb=" CG HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.530 1.371 0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" CG HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.530 1.372 0.158 2.00e-02 2.50e+03 6.23e+01 ... (remaining 11817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15688 1.80 - 3.60: 254 3.60 - 5.39: 66 5.39 - 7.19: 30 7.19 - 8.99: 7 Bond angle restraints: 16045 Sorted by residual: angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.42 -4.42 1.10e+00 8.26e-01 1.61e+01 angle pdb=" N HYP H 6 " pdb=" CD HYP H 6 " pdb=" CG HYP H 6 " ideal model delta sigma weight residual 103.20 109.04 -5.84 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 116.88 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N HYP J 6 " pdb=" CA HYP J 6 " pdb=" CB HYP J 6 " ideal model delta sigma weight residual 103.00 106.86 -3.86 1.10e+00 8.26e-01 1.23e+01 angle pdb=" N HYP I 6 " pdb=" CA HYP I 6 " pdb=" CB HYP I 6 " ideal model delta sigma weight residual 103.00 106.84 -3.84 1.10e+00 8.26e-01 1.22e+01 ... (remaining 16040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 6852 33.98 - 67.96: 220 67.96 - 101.94: 17 101.94 - 135.92: 4 135.92 - 169.90: 3 Dihedral angle restraints: 7096 sinusoidal: 2855 harmonic: 4241 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 130.10 169.90 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 131.78 168.22 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 137.14 162.86 1 2.00e+01 2.50e-03 4.69e+01 ... (remaining 7093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.035: 1789 1.035 - 2.070: 0 2.070 - 3.106: 0 3.106 - 4.141: 0 4.141 - 5.176: 6 Chirality restraints: 1795 Sorted by residual: chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.65 5.18 2.00e-01 2.50e+01 6.70e+02 chirality pdb=" CA DTH I 4 " pdb=" N DTH I 4 " pdb=" C DTH I 4 " pdb=" CB DTH I 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.64 5.16 2.00e-01 2.50e+01 6.66e+02 chirality pdb=" CA DTH J 4 " pdb=" N DTH J 4 " pdb=" C DTH J 4 " pdb=" CB DTH J 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.60 5.13 2.00e-01 2.50e+01 6.57e+02 ... (remaining 1792 not shown) Planarity restraints: 2037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 117 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" CD GLU A 117 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 117 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 117 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 166 " -0.011 2.00e-02 2.50e+03 1.15e-02 2.63e+00 pdb=" CG TYR C 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 166 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 166 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 166 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 166 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 166 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 367 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.022 5.00e-02 4.00e+02 ... (remaining 2034 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 45 2.43 - 3.04: 7139 3.04 - 3.66: 17282 3.66 - 4.28: 26390 4.28 - 4.90: 43999 Nonbonded interactions: 94855 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.808 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.810 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.820 3.620 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.126 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.137 2.170 ... (remaining 94850 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' and (resid 6 through 362 or resid 401 through 402)) selection = (chain 'B' and (resid 6 through 362 or resid 401 through 402)) selection = (chain 'C' and (resid 6 through 362 or resid 401 through 402)) selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.005 0.163 11828 Z= 0.303 Angle : 0.648 10.099 16063 Z= 0.305 Chirality : 0.299 5.176 1795 Planarity : 0.003 0.040 2031 Dihedral : 16.913 169.900 4356 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 0.24 % Allowed : 17.74 % Favored : 82.02 % 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: 0.35 (0.23), residues: 1418 helix: 0.06 (0.22), residues: 538 sheet: 0.56 (0.37), residues: 212 loop : 0.49 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.028 0.001 TYR C 166 PHE 0.008 0.001 PHE A 124 TRP 0.014 0.001 TRP B 86 HIS 0.011 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.30 (11822) covalent geometry : angle 0.64020 / 0.30 (16045) hydrogen bonds : bond 0.30317 / 20.52 ( 525) hydrogen bonds : angle 8.74333 / 6.25 ( 1329) link_TRANS : bond 0.01252 / 0.67 ( 6) link_TRANS : angle 2.98562 / 1.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.0892 time to fit residues: 12.4325 Evaluate side-chains 84 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN B 173 HIS B 225 GLN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064599 restraints weight = 34008.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066748 restraints weight = 17270.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.068184 restraints weight = 10657.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069149 restraints weight = 7464.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069764 restraints weight = 5722.849| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11828 Z= 0.182 Angle : 0.637 6.678 16063 Z= 0.307 Chirality : 0.048 0.429 1795 Planarity : 0.004 0.034 2031 Dihedral : 11.654 177.924 1643 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.48 % Favored : 98.45 % Rotamer: Outliers : 1.87 % Allowed : 16.11 % Favored : 82.02 % Cbeta Deviations : 0.22 % 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: 0.60 (0.23), residues: 1418 helix: 0.34 (0.22), residues: 580 sheet: 0.49 (0.34), residues: 235 loop : 0.67 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.016 0.001 TYR B 143 PHE 0.014 0.001 PHE C 352 TRP 0.024 0.002 TRP I 1 HIS 0.003 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (11822) covalent geometry : angle 0.63419 / 0.31 (16045) hydrogen bonds : bond 0.04820 / 3.29 ( 525) hydrogen bonds : angle 5.75288 / 4.19 ( 1329) link_TRANS : bond 0.00559 / 0.35 ( 6) link_TRANS : angle 1.84311 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.426 Fit side-chains REVERT: A 80 ASP cc_start: 0.7989 (t0) cc_final: 0.7722 (t0) outliers start: 23 outliers final: 9 residues processed: 99 average time/residue: 0.0833 time to fit residues: 13.4870 Evaluate side-chains 86 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 112 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.074357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063355 restraints weight = 33955.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065562 restraints weight = 17280.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067033 restraints weight = 10680.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.068002 restraints weight = 7500.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068665 restraints weight = 5781.206| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11828 Z= 0.151 Angle : 0.582 7.010 16063 Z= 0.275 Chirality : 0.046 0.331 1795 Planarity : 0.004 0.035 2031 Dihedral : 10.850 161.427 1638 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 2.20 % Allowed : 16.11 % Favored : 81.69 % Cbeta Deviations : 0.22 % 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: 0.71 (0.23), residues: 1418 helix: 0.53 (0.22), residues: 585 sheet: 0.44 (0.34), residues: 253 loop : 0.68 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.015 0.001 TYR B 143 PHE 0.012 0.001 PHE D 31 TRP 0.012 0.001 TRP C 340 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11822) covalent geometry : angle 0.58063 / 0.27 (16045) hydrogen bonds : bond 0.03670 / 2.52 ( 525) hydrogen bonds : angle 5.27466 / 3.84 ( 1329) link_TRANS : bond 0.00118 / 0.06 ( 6) link_TRANS : angle 1.26608 / 0.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.482 Fit side-chains REVERT: A 80 ASP cc_start: 0.7971 (t0) cc_final: 0.7534 (t0) REVERT: B 132 MET cc_start: 0.8198 (ttp) cc_final: 0.7543 (ttp) outliers start: 27 outliers final: 15 residues processed: 101 average time/residue: 0.0861 time to fit residues: 14.0493 Evaluate side-chains 93 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.071485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.060488 restraints weight = 34493.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062610 restraints weight = 17730.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064049 restraints weight = 11056.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.065008 restraints weight = 7820.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065675 restraints weight = 6048.199| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 11828 Z= 0.269 Angle : 0.675 6.899 16063 Z= 0.324 Chirality : 0.048 0.248 1795 Planarity : 0.004 0.039 2031 Dihedral : 10.373 147.234 1638 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer: Outliers : 2.77 % Allowed : 17.66 % Favored : 79.58 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1418 helix: 0.46 (0.22), residues: 584 sheet: 0.32 (0.34), residues: 252 loop : 0.48 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 290 TYR 0.015 0.002 TYR B 143 PHE 0.017 0.002 PHE C 352 TRP 0.013 0.002 TRP C 340 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.27 (11822) covalent geometry : angle 0.67430 / 0.32 (16045) hydrogen bonds : bond 0.03806 / 2.61 ( 525) hydrogen bonds : angle 5.25841 / 3.82 ( 1329) link_TRANS : bond 0.00217 / 0.13 ( 6) link_TRANS : angle 1.04208 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.459 Fit side-chains REVERT: A 80 ASP cc_start: 0.8078 (t0) cc_final: 0.7499 (t0) REVERT: B 132 MET cc_start: 0.8357 (ttp) cc_final: 0.7757 (ttp) REVERT: D 305 MET cc_start: 0.7972 (tpp) cc_final: 0.7751 (tpp) outliers start: 34 outliers final: 19 residues processed: 106 average time/residue: 0.0860 time to fit residues: 14.7117 Evaluate side-chains 95 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062329 restraints weight = 34017.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064523 restraints weight = 17322.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065987 restraints weight = 10737.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066951 restraints weight = 7544.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067631 restraints weight = 5819.444| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11828 Z= 0.128 Angle : 0.570 7.559 16063 Z= 0.266 Chirality : 0.045 0.235 1795 Planarity : 0.004 0.036 2031 Dihedral : 9.970 143.168 1638 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 1.87 % Allowed : 18.47 % Favored : 79.66 % Cbeta Deviations : 0.22 % 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: 0.74 (0.23), residues: 1418 helix: 0.72 (0.23), residues: 582 sheet: 0.28 (0.34), residues: 253 loop : 0.59 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 116 TYR 0.007 0.001 TYR A 143 PHE 0.011 0.001 PHE D 31 TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (11822) covalent geometry : angle 0.56907 / 0.27 (16045) hydrogen bonds : bond 0.03016 / 2.07 ( 525) hydrogen bonds : angle 4.96094 / 3.61 ( 1329) link_TRANS : bond 0.00126 / 0.08 ( 6) link_TRANS : angle 1.01072 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.524 Fit side-chains REVERT: A 80 ASP cc_start: 0.7999 (t0) cc_final: 0.7409 (t0) REVERT: D 305 MET cc_start: 0.8086 (tpp) cc_final: 0.7804 (tpp) REVERT: H 5 CYS cc_start: 0.6790 (t) cc_final: 0.6010 (m) outliers start: 23 outliers final: 16 residues processed: 98 average time/residue: 0.0840 time to fit residues: 13.4953 Evaluate side-chains 95 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061048 restraints weight = 34376.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063200 restraints weight = 17612.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064629 restraints weight = 10973.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065599 restraints weight = 7767.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066261 restraints weight = 6001.164| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11828 Z= 0.199 Angle : 0.617 11.817 16063 Z= 0.288 Chirality : 0.046 0.239 1795 Planarity : 0.004 0.039 2031 Dihedral : 9.579 137.318 1638 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Rotamer: Outliers : 2.44 % Allowed : 18.39 % Favored : 79.17 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1418 helix: 0.68 (0.23), residues: 582 sheet: 0.26 (0.34), residues: 252 loop : 0.51 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.009 0.001 TYR C 69 PHE 0.012 0.001 PHE C 352 TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (11822) covalent geometry : angle 0.61613 / 0.29 (16045) hydrogen bonds : bond 0.03209 / 2.21 ( 525) hydrogen bonds : angle 4.97329 / 3.61 ( 1329) link_TRANS : bond 0.00134 / 0.08 ( 6) link_TRANS : angle 0.92019 / 0.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.470 Fit side-chains REVERT: A 80 ASP cc_start: 0.8044 (t0) cc_final: 0.7547 (t0) REVERT: B 132 MET cc_start: 0.8191 (ttp) cc_final: 0.7577 (ttp) REVERT: D 180 LEU cc_start: 0.7793 (tp) cc_final: 0.7559 (tp) REVERT: D 305 MET cc_start: 0.8215 (tpp) cc_final: 0.7926 (tpp) REVERT: H 5 CYS cc_start: 0.6940 (t) cc_final: 0.5917 (m) outliers start: 30 outliers final: 24 residues processed: 103 average time/residue: 0.0798 time to fit residues: 13.5669 Evaluate side-chains 102 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 131 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.073403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062449 restraints weight = 33817.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064633 restraints weight = 17201.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066080 restraints weight = 10664.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067058 restraints weight = 7503.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067729 restraints weight = 5775.528| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11828 Z= 0.114 Angle : 0.565 8.049 16063 Z= 0.260 Chirality : 0.044 0.228 1795 Planarity : 0.003 0.036 2031 Dihedral : 9.247 132.921 1638 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % Rotamer: Outliers : 1.63 % Allowed : 19.28 % Favored : 79.09 % Cbeta Deviations : 0.22 % 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: 0.82 (0.23), residues: 1418 helix: 0.80 (0.23), residues: 589 sheet: 0.24 (0.33), residues: 253 loop : 0.66 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.009 0.001 TYR A 143 PHE 0.012 0.001 PHE D 31 TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (11822) covalent geometry : angle 0.56448 / 0.26 (16045) hydrogen bonds : bond 0.02789 / 1.92 ( 525) hydrogen bonds : angle 4.78932 / 3.48 ( 1329) link_TRANS : bond 0.00161 / 0.10 ( 6) link_TRANS : angle 0.92260 / 0.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7989 (t0) cc_final: 0.7465 (t0) REVERT: B 132 MET cc_start: 0.8119 (ttp) cc_final: 0.7485 (ttp) REVERT: C 82 MET cc_start: 0.8503 (tpt) cc_final: 0.8255 (tpt) REVERT: D 180 LEU cc_start: 0.7616 (tp) cc_final: 0.7377 (tp) REVERT: D 305 MET cc_start: 0.8219 (tpp) cc_final: 0.7962 (tpp) REVERT: H 5 CYS cc_start: 0.6715 (t) cc_final: 0.5923 (m) outliers start: 20 outliers final: 16 residues processed: 98 average time/residue: 0.0848 time to fit residues: 13.6292 Evaluate side-chains 96 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 34 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 45 optimal weight: 0.0970 chunk 85 optimal weight: 4.9990 chunk 75 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.075413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064582 restraints weight = 34192.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066749 restraints weight = 17255.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.068191 restraints weight = 10614.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.069170 restraints weight = 7446.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069745 restraints weight = 5719.026| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11828 Z= 0.092 Angle : 0.567 10.634 16063 Z= 0.259 Chirality : 0.043 0.224 1795 Planarity : 0.003 0.036 2031 Dihedral : 8.818 134.020 1638 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 19.04 % Favored : 79.17 % Cbeta Deviations : 0.22 % 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: 0.96 (0.23), residues: 1418 helix: 0.90 (0.23), residues: 591 sheet: 0.27 (0.33), residues: 253 loop : 0.78 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.008 0.001 TYR A 143 PHE 0.012 0.001 PHE D 31 TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (11822) covalent geometry : angle 0.56639 / 0.26 (16045) hydrogen bonds : bond 0.02568 / 1.76 ( 525) hydrogen bonds : angle 4.65335 / 3.38 ( 1329) link_TRANS : bond 0.00221 / 0.13 ( 6) link_TRANS : angle 0.90546 / 0.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.479 Fit side-chains REVERT: A 80 ASP cc_start: 0.7959 (t0) cc_final: 0.7421 (t0) REVERT: B 118 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7574 (tptm) REVERT: C 82 MET cc_start: 0.8480 (tpt) cc_final: 0.8215 (tpt) REVERT: D 227 MET cc_start: 0.8845 (mmm) cc_final: 0.8508 (mmm) REVERT: D 305 MET cc_start: 0.8201 (tpp) cc_final: 0.7955 (tpp) REVERT: H 5 CYS cc_start: 0.6691 (t) cc_final: 0.5989 (m) outliers start: 22 outliers final: 16 residues processed: 98 average time/residue: 0.0869 time to fit residues: 13.8081 Evaluate side-chains 96 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 140 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.074880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064032 restraints weight = 33831.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.066179 restraints weight = 17237.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.067593 restraints weight = 10656.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068554 restraints weight = 7531.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069190 restraints weight = 5824.795| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11828 Z= 0.110 Angle : 0.566 8.164 16063 Z= 0.258 Chirality : 0.044 0.228 1795 Planarity : 0.003 0.035 2031 Dihedral : 8.608 135.899 1638 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 1.63 % Allowed : 19.20 % Favored : 79.17 % Cbeta Deviations : 0.22 % 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: 0.96 (0.23), residues: 1418 helix: 0.90 (0.23), residues: 594 sheet: 0.30 (0.33), residues: 250 loop : 0.76 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.016 0.001 TYR C 166 PHE 0.012 0.001 PHE D 31 TRP 0.016 0.001 TRP A 86 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (11822) covalent geometry : angle 0.56590 / 0.26 (16045) hydrogen bonds : bond 0.02579 / 1.77 ( 525) hydrogen bonds : angle 4.62382 / 3.36 ( 1329) link_TRANS : bond 0.00179 / 0.10 ( 6) link_TRANS : angle 0.88245 / 0.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.651 Fit side-chains REVERT: A 80 ASP cc_start: 0.7993 (t0) cc_final: 0.7449 (t0) REVERT: B 118 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7609 (tptm) REVERT: B 132 MET cc_start: 0.7932 (ttp) cc_final: 0.7181 (ttp) REVERT: D 305 MET cc_start: 0.8225 (tpp) cc_final: 0.7957 (tpp) REVERT: H 5 CYS cc_start: 0.6797 (t) cc_final: 0.5969 (m) outliers start: 20 outliers final: 16 residues processed: 96 average time/residue: 0.0890 time to fit residues: 13.8836 Evaluate side-chains 94 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 114 optimal weight: 0.0020 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.063359 restraints weight = 33818.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065549 restraints weight = 17221.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067000 restraints weight = 10657.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067930 restraints weight = 7498.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.068613 restraints weight = 5829.622| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11828 Z= 0.112 Angle : 0.574 9.006 16063 Z= 0.260 Chirality : 0.044 0.225 1795 Planarity : 0.003 0.036 2031 Dihedral : 8.415 138.811 1638 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.95 % Rotamer: Outliers : 1.55 % Allowed : 19.37 % Favored : 79.09 % Cbeta Deviations : 0.22 % 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: 1.00 (0.23), residues: 1418 helix: 0.90 (0.22), residues: 594 sheet: 0.29 (0.33), residues: 250 loop : 0.83 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.008 0.001 TYR A 69 PHE 0.012 0.001 PHE D 31 TRP 0.022 0.002 TRP A 86 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (11822) covalent geometry : angle 0.57338 / 0.26 (16045) hydrogen bonds : bond 0.02560 / 1.76 ( 525) hydrogen bonds : angle 4.60334 / 3.33 ( 1329) link_TRANS : bond 0.00176 / 0.10 ( 6) link_TRANS : angle 0.88439 / 0.60 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.489 Fit side-chains REVERT: A 80 ASP cc_start: 0.8009 (t0) cc_final: 0.7514 (t0) REVERT: B 118 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7622 (tptm) REVERT: B 132 MET cc_start: 0.7881 (ttp) cc_final: 0.7128 (ttp) REVERT: D 44 MET cc_start: 0.6981 (ttp) cc_final: 0.6586 (ttp) REVERT: D 227 MET cc_start: 0.8767 (mmm) cc_final: 0.8464 (mmm) REVERT: D 305 MET cc_start: 0.8237 (tpp) cc_final: 0.7971 (tpp) REVERT: H 5 CYS cc_start: 0.6806 (t) cc_final: 0.5990 (m) outliers start: 19 outliers final: 16 residues processed: 93 average time/residue: 0.0899 time to fit residues: 13.4989 Evaluate side-chains 94 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 106 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 131 optimal weight: 0.0870 chunk 142 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.073433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062485 restraints weight = 33974.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.064661 restraints weight = 17419.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066114 restraints weight = 10811.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067079 restraints weight = 7626.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.067718 restraints weight = 5884.729| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11828 Z= 0.145 Angle : 0.588 8.729 16063 Z= 0.270 Chirality : 0.045 0.223 1795 Planarity : 0.003 0.037 2031 Dihedral : 8.297 138.163 1638 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer: Outliers : 1.38 % Allowed : 19.45 % Favored : 79.17 % Cbeta Deviations : 0.22 % 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: 0.95 (0.23), residues: 1418 helix: 0.88 (0.23), residues: 594 sheet: 0.25 (0.33), residues: 250 loop : 0.80 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 147 TYR 0.017 0.001 TYR C 166 PHE 0.011 0.001 PHE D 31 TRP 0.029 0.002 TRP A 86 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (11822) covalent geometry : angle 0.58761 / 0.27 (16045) hydrogen bonds : bond 0.02754 / 1.89 ( 525) hydrogen bonds : angle 4.66699 / 3.37 ( 1329) link_TRANS : bond 0.00154 / 0.09 ( 6) link_TRANS : angle 0.87821 / 0.59 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.39 seconds wall clock time: 30 minutes 46.05 seconds (1846.05 seconds total)