Starting phenix.real_space_refine on Thu Aug 6 11:19:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9udk_64071/08_2026/9udk_64071.cif Found real_map, /net/cci-nas-00/data/ceres_data/9udk_64071/08_2026/9udk_64071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9udk_64071/08_2026/9udk_64071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9udk_64071/08_2026/9udk_64071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9udk_64071/08_2026/9udk_64071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9udk_64071/08_2026/9udk_64071.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 18 5.49 5 Mg 6 5.21 5 S 60 5.16 5 C 9182 2.51 5 N 2549 2.21 5 O 2748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14563 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2357 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 1 Chain: "B" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2366 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 1 Chain: "C" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2453 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain breaks: 1 Chain: "D" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2528 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 308} Chain: "E" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2522 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "F" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2145 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.88, per 1000 atoms: 0.20 Number of scatterers: 14563 At special positions: 0 Unit cell: (83.062, 133.318, 127.734, 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 60 16.00 P 18 15.00 Mg 6 11.99 O 2748 8.00 N 2549 7.00 C 9182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 666.0 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3434 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 20 sheets defined 46.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.730A pdb=" N LEU A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.584A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.796A pdb=" N MET A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.523A pdb=" N VAL A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.915A pdb=" N ARG A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.624A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'B' and resid 50 through 64 removed outlier: 3.640A pdb=" N ALA B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.644A pdb=" N HIS B 100 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.639A pdb=" N ILE B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.981A pdb=" N VAL B 226 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 238 through 262 removed outlier: 3.765A pdb=" N VAL B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.563A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.758A pdb=" N ARG B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 299 through 312 removed outlier: 3.878A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.610A pdb=" N GLY C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.918A pdb=" N ALA C 56 " --> pdb=" O GLN C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 127 through 133 removed outlier: 3.742A pdb=" N GLN C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.736A pdb=" N GLU C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.573A pdb=" N MET C 208 " --> pdb=" O ASN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.665A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 262 removed outlier: 4.377A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET C 254 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLN C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.650A pdb=" N ILE C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 302 through 312 removed outlier: 3.761A pdb=" N VAL C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.574A pdb=" N GLN D 133 " --> pdb=" O PRO D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.740A pdb=" N PHE D 152 " --> pdb=" O PRO D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 removed outlier: 3.795A pdb=" N ARG D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 238 through 260 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.585A pdb=" N ALA D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 312 removed outlier: 3.830A pdb=" N VAL D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.672A pdb=" N VAL E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 64 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 134 removed outlier: 3.579A pdb=" N TRP E 130 " --> pdb=" O GLY E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.602A pdb=" N GLY E 146 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 151 through 158 Processing helix chain 'E' and resid 204 through 209 removed outlier: 3.547A pdb=" N ASP E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 removed outlier: 3.823A pdb=" N ASN E 227 " --> pdb=" O ASP E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.614A pdb=" N TYR E 236 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN E 237 " --> pdb=" O LYS E 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 233 through 237' Processing helix chain 'E' and resid 238 through 262 removed outlier: 3.725A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN E 261 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 283 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 302 through 315 removed outlier: 3.562A pdb=" N VAL E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.607A pdb=" N ALA F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 88 Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 127 through 134 Processing helix chain 'F' and resid 143 through 146 Processing helix chain 'F' and resid 147 through 152 removed outlier: 3.579A pdb=" N PHE F 152 " --> pdb=" O PRO F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.633A pdb=" N LEU F 158 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU F 159 " --> pdb=" O GLN F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 159' Processing helix chain 'F' and resid 221 through 233 removed outlier: 3.578A pdb=" N ASN F 227 " --> pdb=" O ASP F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 237 Processing helix chain 'F' and resid 238 through 262 removed outlier: 4.352A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 252 " --> pdb=" O MET F 248 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR F 255 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 261 " --> pdb=" O GLN F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.595A pdb=" N ILE F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 removed outlier: 4.185A pdb=" N ARG F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 298 Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.906A pdb=" N VAL F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 5.730A pdb=" N VAL A 93 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP A 141 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 67 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 14 through 17 removed outlier: 4.033A pdb=" N THR B 14 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.318A pdb=" N VAL B 93 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET B 68 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 113 through 115 removed outlier: 3.677A pdb=" N VAL B 113 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 121 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA7, first strand: chain 'C' and resid 92 through 95 removed outlier: 6.376A pdb=" N VAL C 93 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP C 141 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 95 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 67 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 108 through 111 Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.530A pdb=" N VAL D 93 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP D 141 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL D 95 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU D 138 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR D 184 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE D 140 " --> pdb=" O THR D 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 115 removed outlier: 3.731A pdb=" N GLU D 122 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 164 through 165 Processing sheet with id=AB6, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AB7, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.449A pdb=" N MET E 68 " --> pdb=" O THR E 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 108 through 112 Processing sheet with id=AB9, first strand: chain 'E' and resid 164 through 165 removed outlier: 3.560A pdb=" N LEU E 164 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 14 through 17 removed outlier: 4.057A pdb=" N VAL F 30 " --> pdb=" O VAL F 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 92 through 94 removed outlier: 3.534A pdb=" N VAL F 139 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1485 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: 1.99 Time building geometry restraints manager: 1.51 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: 4883 1.34 - 1.46: 2989 1.46 - 1.58: 6868 1.58 - 1.69: 26 1.69 - 1.81: 108 Bond restraints: 14874 Sorted by residual: bond pdb=" N ASP C 27 " pdb=" CA ASP C 27 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.91e+00 bond pdb=" N SER C 26 " pdb=" CA SER C 26 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.92e+00 bond pdb=" N TYR D 47 " pdb=" CA TYR D 47 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.31e-02 5.83e+03 4.90e+00 bond pdb=" N ASP D 46 " pdb=" CA ASP D 46 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.45e-02 4.76e+03 4.17e+00 bond pdb=" CA SER C 26 " pdb=" CB SER C 26 " ideal model delta sigma weight residual 1.534 1.504 0.030 1.78e-02 3.16e+03 2.88e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 19998 1.85 - 3.69: 245 3.69 - 5.54: 36 5.54 - 7.38: 4 7.38 - 9.23: 3 Bond angle restraints: 20286 Sorted by residual: angle pdb=" CA ASP C 27 " pdb=" C ASP C 27 " pdb=" O ASP C 27 " ideal model delta sigma weight residual 120.43 116.87 3.56 1.09e+00 8.42e-01 1.06e+01 angle pdb=" CB MET B 29 " pdb=" CG MET B 29 " pdb=" SD MET B 29 " ideal model delta sigma weight residual 112.70 121.93 -9.23 3.00e+00 1.11e-01 9.47e+00 angle pdb=" CA SER C 26 " pdb=" C SER C 26 " pdb=" O SER C 26 " ideal model delta sigma weight residual 120.99 117.72 3.27 1.12e+00 7.97e-01 8.51e+00 angle pdb=" N GLY A 76 " pdb=" CA GLY A 76 " pdb=" C GLY A 76 " ideal model delta sigma weight residual 113.18 119.91 -6.73 2.37e+00 1.78e-01 8.05e+00 angle pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sigma weight residual 112.00 108.14 3.86 1.40e+00 5.10e-01 7.60e+00 ... (remaining 20281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7281 17.77 - 35.53: 1154 35.53 - 53.30: 352 53.30 - 71.06: 106 71.06 - 88.83: 32 Dihedral angle restraints: 8925 sinusoidal: 3624 harmonic: 5301 Sorted by residual: dihedral pdb=" CA GLU B 122 " pdb=" C GLU B 122 " pdb=" N PHE B 123 " pdb=" CA PHE B 123 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA MET D 28 " pdb=" C MET D 28 " pdb=" N MET D 29 " pdb=" CA MET D 29 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " pdb=" OD1 ASP C 98 " ideal model delta sinusoidal sigma weight residual -30.00 -86.33 56.33 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 8922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1424 0.033 - 0.066: 615 0.066 - 0.098: 170 0.098 - 0.131: 84 0.131 - 0.164: 6 Chirality restraints: 2299 Sorted by residual: chirality pdb=" CA TYR D 47 " pdb=" N TYR D 47 " pdb=" C TYR D 47 " pdb=" CB TYR D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA ASN B 135 " pdb=" N ASN B 135 " pdb=" C ASN B 135 " pdb=" CB ASN B 135 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ASP D 13 " pdb=" N ASP D 13 " pdb=" C ASP D 13 " pdb=" CB ASP D 13 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2296 not shown) Planarity restraints: 2613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 176 " 0.071 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO D 177 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO D 177 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 177 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 269 " 0.061 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO B 270 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 40 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO E 41 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 41 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 41 " -0.045 5.00e-02 4.00e+02 ... (remaining 2610 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 133 2.49 - 3.09: 10295 3.09 - 3.70: 22980 3.70 - 4.30: 32296 4.30 - 4.90: 52512 Nonbonded interactions: 118216 Sorted by model distance: nonbonded pdb=" O1G ATP E 401 " pdb="MG MG E 402 " model vdw 1.891 2.170 nonbonded pdb=" O3G ATP F 401 " pdb="MG MG F 402 " model vdw 1.914 2.170 nonbonded pdb="MG MG B 403 " pdb=" O3G ATP C 401 " model vdw 1.936 2.170 nonbonded pdb=" O1B ATP A 401 " pdb="MG MG A 402 " model vdw 1.973 2.170 nonbonded pdb=" O1G ATP D 401 " pdb="MG MG D 402 " model vdw 1.976 2.170 ... (remaining 118211 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 10 through 108 or resid 127 through 159 or resid 175 throu \ gh 188 or resid 204 through 319)) selection = (chain 'B' and (resid 10 through 108 or resid 127 through 159 or resid 175 throu \ gh 188 or resid 204 through 319)) selection = (chain 'C' and (resid 10 through 108 or resid 127 through 159 or resid 175 throu \ gh 188 or resid 204 through 319)) selection = (chain 'D' and (resid 10 through 108 or resid 127 through 159 or resid 175 throu \ gh 188 or resid 204 through 319)) selection = (chain 'E' and (resid 10 through 108 or resid 127 through 159 or resid 175 throu \ gh 188 or resid 204 through 319)) selection = (chain 'F' and resid 10 through 319) } 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 individual isotropic 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: 7.300 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.400 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: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.003 0.070 14874 Z= 0.139 Angle : 0.518 9.230 20286 Z= 0.274 Chirality : 0.042 0.164 2299 Planarity : 0.005 0.106 2613 Dihedral : 20.173 88.827 5491 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.39 % Allowed : 38.41 % Favored : 61.20 % 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: -0.62 (0.20), residues: 1792 helix: 0.02 (0.20), residues: 674 sheet: -1.24 (0.36), residues: 232 loop : -0.38 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 51 TYR 0.022 0.001 TYR A 219 PHE 0.009 0.001 PHE D 294 TRP 0.010 0.001 TRP C 90 HIS 0.006 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14874) covalent geometry : angle 0.51791 / 0.27 (20286) hydrogen bonds : bond 0.22204 / 15.22 ( 518) hydrogen bonds : angle 7.35333 / 5.12 ( 1485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 443 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7280 (tpt-90) REVERT: A 132 TYR cc_start: 0.8266 (t80) cc_final: 0.7819 (t80) REVERT: A 154 ILE cc_start: 0.8800 (mm) cc_final: 0.8541 (mm) REVERT: A 164 LEU cc_start: 0.8818 (tp) cc_final: 0.8411 (mp) REVERT: A 248 MET cc_start: 0.8198 (tpp) cc_final: 0.7312 (tpp) REVERT: A 276 TRP cc_start: 0.8645 (t60) cc_final: 0.8102 (t60) REVERT: B 64 ASN cc_start: 0.8384 (t0) cc_final: 0.8128 (t0) REVERT: B 155 GLN cc_start: 0.7149 (tp40) cc_final: 0.6709 (tp40) REVERT: C 208 MET cc_start: 0.8160 (tpp) cc_final: 0.7575 (mmm) REVERT: D 96 ASN cc_start: 0.7967 (t0) cc_final: 0.7611 (m-40) REVERT: D 122 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 136 VAL cc_start: 0.9002 (p) cc_final: 0.8687 (m) REVERT: D 202 GLN cc_start: 0.7862 (mp-120) cc_final: 0.7558 (mm-40) REVERT: E 29 MET cc_start: 0.7160 (mmt) cc_final: 0.6884 (mmt) REVERT: E 254 MET cc_start: 0.8180 (mtp) cc_final: 0.7852 (ttm) REVERT: E 301 LEU cc_start: 0.8756 (mt) cc_final: 0.8490 (tp) REVERT: F 78 SER cc_start: 0.9234 (m) cc_final: 0.8745 (p) REVERT: F 82 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8328 (mt-10) REVERT: F 83 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7018 (tp-100) REVERT: F 208 MET cc_start: 0.5764 (tpt) cc_final: 0.5525 (mmm) REVERT: F 244 ILE cc_start: 0.8065 (mt) cc_final: 0.7643 (mm) outliers start: 6 outliers final: 1 residues processed: 447 average time/residue: 0.1243 time to fit residues: 79.2035 Evaluate side-chains 242 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0000 chunk 149 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS A 83 GLN A 133 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN B 80 HIS B 100 HIS B 235 HIS B 237 GLN B 311 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 119 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN E 202 GLN E 324 ASN F 52 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.168390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134112 restraints weight = 22872.825| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.61 r_work: 0.3601 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14874 Z= 0.134 Angle : 0.585 14.181 20286 Z= 0.308 Chirality : 0.043 0.139 2299 Planarity : 0.005 0.071 2613 Dihedral : 10.423 84.123 2197 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.25 % Allowed : 32.97 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1792 helix: -0.06 (0.19), residues: 752 sheet: -1.21 (0.36), residues: 220 loop : -0.40 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 147 TYR 0.017 0.001 TYR C 236 PHE 0.015 0.001 PHE A 259 TRP 0.009 0.001 TRP A 130 HIS 0.010 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (14874) covalent geometry : angle 0.58466 / 0.31 (20286) hydrogen bonds : bond 0.04421 / 3.00 ( 518) hydrogen bonds : angle 5.58730 / 3.91 ( 1485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 257 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.7907 (m90) cc_final: 0.7648 (m-70) REVERT: A 94 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7012 (tpt-90) REVERT: A 139 VAL cc_start: 0.9074 (t) cc_final: 0.8851 (m) REVERT: A 314 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.6079 (m-10) REVERT: B 64 ASN cc_start: 0.8232 (t0) cc_final: 0.8029 (t0) REVERT: B 123 PHE cc_start: 0.5481 (t80) cc_final: 0.4436 (t80) REVERT: B 169 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6482 (tm-30) REVERT: C 163 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6175 (mmt-90) REVERT: C 208 MET cc_start: 0.8127 (tpp) cc_final: 0.7756 (mmm) REVERT: D 105 ASP cc_start: 0.7812 (m-30) cc_final: 0.7471 (m-30) REVERT: D 136 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8350 (m) REVERT: E 174 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7834 (ttp-170) REVERT: F 28 MET cc_start: 0.6870 (tpt) cc_final: 0.6453 (tpt) REVERT: F 99 SER cc_start: 0.6272 (p) cc_final: 0.5631 (t) REVERT: F 134 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7192 (t-90) REVERT: F 147 ARG cc_start: 0.4473 (ttp-170) cc_final: 0.3029 (ttt-90) REVERT: F 181 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6520 (tt) REVERT: F 208 MET cc_start: 0.5492 (OUTLIER) cc_final: 0.5167 (mtt) REVERT: F 240 GLU cc_start: 0.7566 (tp30) cc_final: 0.7349 (tp30) outliers start: 81 outliers final: 36 residues processed: 319 average time/residue: 0.1132 time to fit residues: 52.8324 Evaluate side-chains 258 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 248 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 122 optimal weight: 0.2980 chunk 158 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN E 169 GLN E 324 ASN F 52 GLN F 80 HIS F 142 GLN ** F 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.166320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.131254 restraints weight = 23156.223| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.66 r_work: 0.3556 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14874 Z= 0.133 Angle : 0.549 9.195 20286 Z= 0.286 Chirality : 0.042 0.188 2299 Planarity : 0.005 0.063 2613 Dihedral : 9.940 89.978 2195 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.02 % Allowed : 29.92 % Favored : 64.05 % 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: -0.59 (0.20), residues: 1792 helix: 0.00 (0.19), residues: 744 sheet: -1.13 (0.36), residues: 214 loop : -0.39 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 103 TYR 0.020 0.001 TYR B 143 PHE 0.012 0.001 PHE A 283 TRP 0.014 0.001 TRP A 276 HIS 0.006 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (14874) covalent geometry : angle 0.54863 / 0.29 (20286) hydrogen bonds : bond 0.03810 / 2.57 ( 518) hydrogen bonds : angle 5.34560 / 3.75 ( 1485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 227 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.7971 (m90) cc_final: 0.7629 (m-70) REVERT: A 94 ARG cc_start: 0.8127 (mtt180) cc_final: 0.6996 (tpt-90) REVERT: A 139 VAL cc_start: 0.9074 (t) cc_final: 0.8740 (m) REVERT: A 143 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7042 (t80) REVERT: A 210 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6793 (tpm170) REVERT: A 248 MET cc_start: 0.8524 (mmt) cc_final: 0.7976 (mmt) REVERT: B 169 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6435 (tm-30) REVERT: C 61 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7988 (t80) REVERT: C 163 ARG cc_start: 0.6827 (mtm180) cc_final: 0.6200 (mmt-90) REVERT: D 75 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8631 (p) REVERT: D 136 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8387 (m) REVERT: D 292 LEU cc_start: 0.8887 (mp) cc_final: 0.8585 (mp) REVERT: E 124 LYS cc_start: 0.6726 (mmmt) cc_final: 0.6518 (mmmt) REVERT: E 127 ILE cc_start: 0.9015 (tp) cc_final: 0.8763 (tt) REVERT: E 295 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8329 (mp) REVERT: F 83 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8065 (mm-40) REVERT: F 134 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7168 (t-90) REVERT: F 181 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6630 (tt) REVERT: F 208 MET cc_start: 0.5518 (OUTLIER) cc_final: 0.5136 (mtt) REVERT: F 244 ILE cc_start: 0.8156 (mt) cc_final: 0.7921 (mm) outliers start: 93 outliers final: 49 residues processed: 303 average time/residue: 0.1105 time to fit residues: 49.8436 Evaluate side-chains 265 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 207 GLN C 237 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** F 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.164721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129345 restraints weight = 23030.131| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.76 r_work: 0.3516 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14874 Z= 0.140 Angle : 0.532 7.354 20286 Z= 0.279 Chirality : 0.042 0.147 2299 Planarity : 0.005 0.065 2613 Dihedral : 9.652 88.907 2195 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.51 % Allowed : 29.15 % Favored : 65.35 % 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: -0.60 (0.20), residues: 1792 helix: 0.04 (0.19), residues: 741 sheet: -1.20 (0.35), residues: 236 loop : -0.39 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 174 TYR 0.020 0.001 TYR B 63 PHE 0.030 0.001 PHE D 288 TRP 0.008 0.001 TRP B 130 HIS 0.015 0.001 HIS F 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (14874) covalent geometry : angle 0.53169 / 0.28 (20286) hydrogen bonds : bond 0.03521 / 2.34 ( 518) hydrogen bonds : angle 5.24277 / 3.69 ( 1485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 219 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.7958 (m90) cc_final: 0.7675 (m-70) REVERT: A 77 LYS cc_start: 0.7822 (mttp) cc_final: 0.7407 (mttp) REVERT: A 94 ARG cc_start: 0.8130 (mtt180) cc_final: 0.6973 (tpt-90) REVERT: A 119 GLN cc_start: 0.4536 (OUTLIER) cc_final: 0.3764 (pt0) REVERT: A 132 TYR cc_start: 0.8234 (t80) cc_final: 0.7899 (t80) REVERT: A 139 VAL cc_start: 0.9056 (t) cc_final: 0.8700 (m) REVERT: A 143 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.6943 (t80) REVERT: A 210 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6847 (tpm170) REVERT: A 248 MET cc_start: 0.8534 (mmt) cc_final: 0.8123 (mmt) REVERT: B 169 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: C 61 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8050 (t80) REVERT: C 163 ARG cc_start: 0.6864 (mtm180) cc_final: 0.6269 (mmt-90) REVERT: D 75 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8655 (p) REVERT: D 136 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8441 (m) REVERT: D 208 MET cc_start: 0.8338 (mmm) cc_final: 0.8106 (tpt) REVERT: E 29 MET cc_start: 0.6097 (mmm) cc_final: 0.5837 (mmm) REVERT: E 124 LYS cc_start: 0.6669 (mmmt) cc_final: 0.6465 (mmmt) REVERT: E 127 ILE cc_start: 0.9011 (tp) cc_final: 0.8782 (tt) REVERT: E 141 ASP cc_start: 0.8140 (m-30) cc_final: 0.7822 (m-30) REVERT: E 207 GLN cc_start: 0.8618 (tp40) cc_final: 0.8148 (tp40) REVERT: F 83 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8146 (mm-40) REVERT: F 134 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7151 (t-90) REVERT: F 181 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6688 (tt) REVERT: F 208 MET cc_start: 0.5484 (OUTLIER) cc_final: 0.5083 (mtt) outliers start: 85 outliers final: 61 residues processed: 285 average time/residue: 0.1172 time to fit residues: 50.1266 Evaluate side-chains 268 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 197 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 53 optimal weight: 7.9990 chunk 142 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 90 optimal weight: 0.0270 chunk 107 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 134 HIS ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.167400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130919 restraints weight = 22957.032| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.93 r_work: 0.3558 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14874 Z= 0.116 Angle : 0.522 8.292 20286 Z= 0.274 Chirality : 0.042 0.134 2299 Planarity : 0.005 0.068 2613 Dihedral : 9.374 89.993 2195 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.38 % Allowed : 29.60 % Favored : 65.03 % 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: -0.51 (0.20), residues: 1792 helix: 0.11 (0.19), residues: 747 sheet: -1.15 (0.35), residues: 235 loop : -0.34 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 174 TYR 0.016 0.001 TYR E 236 PHE 0.010 0.001 PHE A 283 TRP 0.014 0.001 TRP A 130 HIS 0.012 0.001 HIS F 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14874) covalent geometry : angle 0.52204 / 0.27 (20286) hydrogen bonds : bond 0.03279 / 2.19 ( 518) hydrogen bonds : angle 5.14591 / 3.62 ( 1485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 210 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: A 73 HIS cc_start: 0.7887 (m90) cc_final: 0.7687 (m-70) REVERT: A 77 LYS cc_start: 0.7707 (mttp) cc_final: 0.7393 (mttp) REVERT: A 94 ARG cc_start: 0.8007 (mtt180) cc_final: 0.6907 (tpt-90) REVERT: A 119 GLN cc_start: 0.4574 (pp30) cc_final: 0.3763 (pt0) REVERT: A 132 TYR cc_start: 0.8321 (t80) cc_final: 0.8053 (t80) REVERT: A 139 VAL cc_start: 0.9051 (t) cc_final: 0.8696 (m) REVERT: A 142 GLN cc_start: 0.7719 (mt0) cc_final: 0.7511 (mm-40) REVERT: A 143 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.6876 (t80) REVERT: A 210 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6905 (tpm170) REVERT: A 248 MET cc_start: 0.8463 (mmt) cc_final: 0.8031 (mmt) REVERT: B 169 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: C 151 MET cc_start: 0.8606 (tpt) cc_final: 0.8402 (mmp) REVERT: C 163 ARG cc_start: 0.6921 (mtm180) cc_final: 0.6293 (mmt-90) REVERT: D 75 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8617 (p) REVERT: D 136 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8410 (m) REVERT: D 208 MET cc_start: 0.8304 (mmm) cc_final: 0.8072 (tpt) REVERT: E 124 LYS cc_start: 0.6804 (mmmt) cc_final: 0.6588 (mmmt) REVERT: E 141 ASP cc_start: 0.8120 (m-30) cc_final: 0.7732 (m-30) REVERT: E 207 GLN cc_start: 0.8523 (tp40) cc_final: 0.8232 (tp40) REVERT: F 83 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8120 (mm-40) REVERT: F 134 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7136 (t-90) REVERT: F 181 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6724 (tt) REVERT: F 208 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.5045 (mtt) outliers start: 83 outliers final: 59 residues processed: 272 average time/residue: 0.1244 time to fit residues: 50.4481 Evaluate side-chains 268 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 132 optimal weight: 0.0970 chunk 15 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.164989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128361 restraints weight = 22919.234| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.01 r_work: 0.3507 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14874 Z= 0.140 Angle : 0.534 6.712 20286 Z= 0.279 Chirality : 0.042 0.154 2299 Planarity : 0.005 0.071 2613 Dihedral : 9.325 89.818 2195 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 6.35 % Allowed : 29.02 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1792 helix: 0.13 (0.19), residues: 743 sheet: -1.17 (0.35), residues: 235 loop : -0.34 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 174 TYR 0.015 0.001 TYR C 310 PHE 0.011 0.001 PHE F 61 TRP 0.012 0.001 TRP A 130 HIS 0.011 0.001 HIS F 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (14874) covalent geometry : angle 0.53391 / 0.28 (20286) hydrogen bonds : bond 0.03325 / 2.21 ( 518) hydrogen bonds : angle 5.15138 / 3.62 ( 1485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 205 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: A 73 HIS cc_start: 0.7890 (m90) cc_final: 0.7672 (m-70) REVERT: A 77 LYS cc_start: 0.7686 (mttp) cc_final: 0.7346 (mttp) REVERT: A 94 ARG cc_start: 0.8039 (mtt180) cc_final: 0.6952 (tpt-90) REVERT: A 119 GLN cc_start: 0.4692 (pp30) cc_final: 0.4038 (pt0) REVERT: A 132 TYR cc_start: 0.8334 (t80) cc_final: 0.8119 (t80) REVERT: A 139 VAL cc_start: 0.9057 (t) cc_final: 0.8693 (m) REVERT: A 143 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.6921 (t80) REVERT: A 210 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6990 (tpm170) REVERT: A 248 MET cc_start: 0.8430 (mmt) cc_final: 0.7908 (mmt) REVERT: B 169 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: C 163 ARG cc_start: 0.6968 (mtm180) cc_final: 0.6337 (mmt-90) REVERT: D 75 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8588 (p) REVERT: D 136 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8437 (m) REVERT: D 208 MET cc_start: 0.8342 (mmm) cc_final: 0.8093 (tpt) REVERT: D 217 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8324 (tp) REVERT: E 80 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7982 (t70) REVERT: E 141 ASP cc_start: 0.8101 (m-30) cc_final: 0.7701 (m-30) REVERT: E 174 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7637 (ttp80) REVERT: E 207 GLN cc_start: 0.8423 (tp40) cc_final: 0.8218 (tp40) REVERT: E 217 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8411 (tt) REVERT: F 134 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7078 (t-90) REVERT: F 181 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6748 (tt) REVERT: F 208 MET cc_start: 0.5407 (OUTLIER) cc_final: 0.5106 (mtt) outliers start: 98 outliers final: 68 residues processed: 278 average time/residue: 0.1230 time to fit residues: 50.2859 Evaluate side-chains 276 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 196 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 38 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 114 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 162 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN F 52 GLN F 80 HIS F 83 GLN F 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.164751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.128599 restraints weight = 22894.654| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.89 r_work: 0.3498 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14874 Z= 0.133 Angle : 0.550 11.795 20286 Z= 0.285 Chirality : 0.042 0.134 2299 Planarity : 0.005 0.070 2613 Dihedral : 9.239 88.990 2195 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 6.02 % Allowed : 29.02 % Favored : 64.96 % 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: -0.47 (0.20), residues: 1792 helix: 0.12 (0.19), residues: 745 sheet: -1.13 (0.35), residues: 235 loop : -0.30 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 19 TYR 0.016 0.001 TYR C 310 PHE 0.013 0.001 PHE F 182 TRP 0.012 0.001 TRP A 130 HIS 0.009 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (14874) covalent geometry : angle 0.55012 / 0.28 (20286) hydrogen bonds : bond 0.03259 / 2.17 ( 518) hydrogen bonds : angle 5.12933 / 3.59 ( 1485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: A 73 HIS cc_start: 0.7861 (m90) cc_final: 0.7600 (m-70) REVERT: A 77 LYS cc_start: 0.7554 (mttp) cc_final: 0.7292 (mttp) REVERT: A 94 ARG cc_start: 0.8018 (mtt180) cc_final: 0.6903 (tpt-90) REVERT: A 119 GLN cc_start: 0.4750 (pp30) cc_final: 0.4164 (pt0) REVERT: A 139 VAL cc_start: 0.9043 (t) cc_final: 0.8652 (m) REVERT: A 143 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7097 (t80) REVERT: A 159 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: A 210 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6852 (tpm170) REVERT: A 248 MET cc_start: 0.8437 (mmt) cc_final: 0.8021 (mmt) REVERT: B 169 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: C 163 ARG cc_start: 0.6916 (mtm180) cc_final: 0.6292 (mmt-90) REVERT: C 212 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8911 (m) REVERT: D 75 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8599 (p) REVERT: D 136 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8444 (m) REVERT: D 208 MET cc_start: 0.8327 (mmm) cc_final: 0.8093 (tpt) REVERT: E 29 MET cc_start: 0.6131 (mmm) cc_final: 0.5802 (mmm) REVERT: E 80 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.8038 (t70) REVERT: E 141 ASP cc_start: 0.8098 (m-30) cc_final: 0.7682 (m-30) REVERT: E 174 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7612 (ttp80) REVERT: E 207 GLN cc_start: 0.8423 (tp40) cc_final: 0.8215 (tp40) REVERT: E 217 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8398 (tt) REVERT: F 134 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7054 (t-90) REVERT: F 181 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6759 (tt) REVERT: F 208 MET cc_start: 0.5454 (OUTLIER) cc_final: 0.5086 (mtt) outliers start: 93 outliers final: 65 residues processed: 269 average time/residue: 0.1202 time to fit residues: 48.1799 Evaluate side-chains 268 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 190 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 142 GLN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.163553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126943 restraints weight = 22942.047| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.74 r_work: 0.3487 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14874 Z= 0.162 Angle : 0.576 11.941 20286 Z= 0.299 Chirality : 0.043 0.149 2299 Planarity : 0.005 0.072 2613 Dihedral : 9.295 88.252 2195 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 6.02 % Allowed : 28.69 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1792 helix: 0.07 (0.19), residues: 753 sheet: -1.13 (0.36), residues: 225 loop : -0.34 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 19 TYR 0.014 0.001 TYR B 63 PHE 0.013 0.001 PHE F 140 TRP 0.011 0.001 TRP A 130 HIS 0.010 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (14874) covalent geometry : angle 0.57629 / 0.30 (20286) hydrogen bonds : bond 0.03504 / 2.34 ( 518) hydrogen bonds : angle 5.18759 / 3.65 ( 1485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: A 73 HIS cc_start: 0.7744 (m90) cc_final: 0.7343 (m-70) REVERT: A 77 LYS cc_start: 0.7567 (mttp) cc_final: 0.7271 (mttp) REVERT: A 94 ARG cc_start: 0.8016 (mtt180) cc_final: 0.6904 (tpt-90) REVERT: A 119 GLN cc_start: 0.4781 (pp30) cc_final: 0.4240 (pt0) REVERT: A 139 VAL cc_start: 0.9051 (t) cc_final: 0.8660 (m) REVERT: A 143 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.6829 (t80) REVERT: A 248 MET cc_start: 0.8382 (mmt) cc_final: 0.7903 (mmt) REVERT: B 169 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6453 (tm-30) REVERT: C 163 ARG cc_start: 0.6926 (mtm180) cc_final: 0.6310 (mmt-90) REVERT: D 75 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8566 (p) REVERT: D 136 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8478 (m) REVERT: D 208 MET cc_start: 0.8355 (mmm) cc_final: 0.8131 (tpt) REVERT: D 217 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8243 (tp) REVERT: E 80 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8084 (t70) REVERT: E 141 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: F 134 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7042 (t-90) REVERT: F 181 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6773 (tt) REVERT: F 208 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.5054 (mtt) outliers start: 93 outliers final: 65 residues processed: 272 average time/residue: 0.1079 time to fit residues: 44.0060 Evaluate side-chains 269 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 193 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 155 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.165181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130311 restraints weight = 22905.125| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.64 r_work: 0.3514 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14874 Z= 0.127 Angle : 0.566 10.723 20286 Z= 0.295 Chirality : 0.042 0.152 2299 Planarity : 0.005 0.071 2613 Dihedral : 8.999 89.942 2195 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.47 % Allowed : 30.38 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1792 helix: 0.09 (0.19), residues: 745 sheet: -1.05 (0.36), residues: 225 loop : -0.32 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 19 TYR 0.018 0.001 TYR C 310 PHE 0.019 0.001 PHE F 140 TRP 0.013 0.001 TRP A 130 HIS 0.009 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14874) covalent geometry : angle 0.56643 / 0.29 (20286) hydrogen bonds : bond 0.03284 / 2.19 ( 518) hydrogen bonds : angle 5.10736 / 3.60 ( 1485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 195 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: A 73 HIS cc_start: 0.7645 (m90) cc_final: 0.7254 (m-70) REVERT: A 94 ARG cc_start: 0.7978 (mtt180) cc_final: 0.6873 (tpt-90) REVERT: A 119 GLN cc_start: 0.4816 (pp30) cc_final: 0.4233 (pt0) REVERT: A 139 VAL cc_start: 0.9051 (t) cc_final: 0.8647 (m) REVERT: A 143 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 218 ASN cc_start: 0.6814 (t0) cc_final: 0.6014 (p0) REVERT: A 248 MET cc_start: 0.8378 (mmt) cc_final: 0.7934 (mmt) REVERT: B 169 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: B 234 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8338 (mmtm) REVERT: B 254 MET cc_start: 0.7809 (ptp) cc_final: 0.7016 (tpt) REVERT: C 163 ARG cc_start: 0.6882 (mtm180) cc_final: 0.6282 (mmt-90) REVERT: C 235 HIS cc_start: 0.7131 (p90) cc_final: 0.6906 (p90) REVERT: D 136 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8418 (m) REVERT: D 217 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8405 (tp) REVERT: E 28 MET cc_start: 0.6435 (mmm) cc_final: 0.5934 (mmt) REVERT: E 29 MET cc_start: 0.6219 (mmm) cc_final: 0.5754 (mmm) REVERT: E 80 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.8021 (t70) REVERT: E 141 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: E 174 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7682 (ttp80) REVERT: F 134 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7049 (t-90) REVERT: F 181 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6738 (tt) REVERT: F 208 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.5060 (mtt) outliers start: 69 outliers final: 54 residues processed: 248 average time/residue: 0.1091 time to fit residues: 40.5904 Evaluate side-chains 253 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.0010 chunk 10 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 124 optimal weight: 4.9990 chunk 82 optimal weight: 0.0070 chunk 123 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 235 HIS C 237 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN F 52 GLN F 80 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.166418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131264 restraints weight = 22888.030| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.64 r_work: 0.3549 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14874 Z= 0.110 Angle : 0.562 9.906 20286 Z= 0.292 Chirality : 0.042 0.158 2299 Planarity : 0.004 0.069 2613 Dihedral : 8.628 88.270 2195 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.89 % Allowed : 31.02 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1792 helix: 0.13 (0.19), residues: 747 sheet: -0.87 (0.38), residues: 215 loop : -0.23 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 19 TYR 0.023 0.001 TYR B 63 PHE 0.010 0.001 PHE F 61 TRP 0.013 0.001 TRP A 130 HIS 0.008 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14874) covalent geometry : angle 0.56164 / 0.29 (20286) hydrogen bonds : bond 0.03077 / 2.06 ( 518) hydrogen bonds : angle 5.05141 / 3.55 ( 1485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: A 73 HIS cc_start: 0.7618 (m90) cc_final: 0.7186 (m-70) REVERT: A 94 ARG cc_start: 0.7938 (mtt180) cc_final: 0.6818 (tpt-90) REVERT: A 139 VAL cc_start: 0.9060 (t) cc_final: 0.8670 (m) REVERT: A 143 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6568 (t80) REVERT: A 248 MET cc_start: 0.8359 (mmt) cc_final: 0.7910 (mmt) REVERT: B 169 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: B 234 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8361 (mmtm) REVERT: B 254 MET cc_start: 0.7824 (ptp) cc_final: 0.6996 (tpt) REVERT: C 163 ARG cc_start: 0.6791 (mtm180) cc_final: 0.6223 (mmt-90) REVERT: D 136 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8347 (m) REVERT: D 217 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8397 (tp) REVERT: E 29 MET cc_start: 0.6210 (mmm) cc_final: 0.5776 (mmm) REVERT: E 80 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.7942 (t70) REVERT: E 141 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: E 174 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7700 (ttp80) REVERT: F 134 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.6984 (t-90) REVERT: F 181 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6729 (tt) REVERT: F 208 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.5042 (mtt) outliers start: 60 outliers final: 45 residues processed: 244 average time/residue: 0.1137 time to fit residues: 41.7099 Evaluate side-chains 249 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 90 TRP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 208 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 131 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS C 119 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 80 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.163873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.127856 restraints weight = 23005.222| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.94 r_work: 0.3481 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14874 Z= 0.152 Angle : 0.573 9.716 20286 Z= 0.300 Chirality : 0.043 0.162 2299 Planarity : 0.005 0.073 2613 Dihedral : 8.723 89.288 2195 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.27 % Allowed : 30.63 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1792 helix: 0.14 (0.19), residues: 740 sheet: -1.14 (0.36), residues: 222 loop : -0.20 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 19 TYR 0.024 0.001 TYR A 33 PHE 0.023 0.001 PHE F 61 TRP 0.011 0.001 TRP A 130 HIS 0.013 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (14874) covalent geometry : angle 0.57338 / 0.30 (20286) hydrogen bonds : bond 0.03341 / 2.23 ( 518) hydrogen bonds : angle 5.13248 / 3.62 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.43 seconds wall clock time: 57 minutes 31.66 seconds (3451.66 seconds total)