Starting phenix.real_space_refine on Thu Aug 6 09:50:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8osg_17152/08_2026/8osg_17152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osg_17152/08_2026/8osg_17152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8osg_17152/08_2026/8osg_17152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osg_17152/08_2026/8osg_17152.map" model { file = "/net/cci-nas-00/data/ceres_data/8osg_17152/08_2026/8osg_17152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osg_17152/08_2026/8osg_17152.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8osg_17152/08_2026/8osg_17152.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8osg_17152/08_2026/8osg_17152.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 16 5.49 5 Mg 4 5.21 5 S 51 5.16 5 C 9147 2.51 5 N 2517 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s 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: 14536 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2214 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 4 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2529 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2529 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2529 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2529 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2024 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 11, 'TRANS': 246} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "C" 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: "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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.19 Number of scatterers: 14536 At special positions: 0 Unit cell: (130.284, 138.6, 79.464, 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 51 16.00 P 16 15.00 Mg 4 11.99 O 2801 8.00 N 2517 7.00 C 9147 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: 0.94 Conformation dependent library (CDL) restraints added in 573.2 milliseconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 15 sheets defined 50.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 24 through 36 removed outlier: 3.863A pdb=" N LYS A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.606A pdb=" N THR A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.887A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 211 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 239 removed outlier: 3.608A pdb=" N GLN A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 265 removed outlier: 3.617A pdb=" N GLN A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.643A pdb=" N LEU A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.758A pdb=" N ILE A 294 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 313 through 319 removed outlier: 4.016A pdb=" N ILE A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.525A pdb=" N ARG A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.864A pdb=" N VAL A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.632A pdb=" N ASP B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.619A pdb=" N THR B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.543A pdb=" N SER B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.791A pdb=" N LYS B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.953A pdb=" N SER B 169 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.688A pdb=" N ASP B 209 " --> pdb=" O PRO B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.921A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 227 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.703A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 307 removed outlier: 4.129A pdb=" N ILE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 removed outlier: 3.867A pdb=" N ILE B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR B 322 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.622A pdb=" N LYS C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 31 " --> pdb=" O MET C 27 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.833A pdb=" N ILE C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.836A pdb=" N CYS C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.030A pdb=" N ARG C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 211' Processing helix chain 'C' and resid 222 through 239 removed outlier: 3.613A pdb=" N ASN C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 removed outlier: 3.617A pdb=" N ALA C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 271 through 286 removed outlier: 3.715A pdb=" N ARG C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.556A pdb=" N ASN C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.641A pdb=" N LYS C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 21 removed outlier: 3.643A pdb=" N ALA D 20 " --> pdb=" O PRO D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.860A pdb=" N ALA D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU D 31 " --> pdb=" O MET D 27 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.842A pdb=" N THR D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 116 through 121 removed outlier: 4.019A pdb=" N VAL D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 121' Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.876A pdb=" N ASN D 146 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 164 through 170 removed outlier: 4.310A pdb=" N ASP D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 164 through 170' Processing helix chain 'D' and resid 206 through 210 removed outlier: 3.523A pdb=" N ASP D 209 " --> pdb=" O GLN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 239 Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.800A pdb=" N PHE D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 244 " --> pdb=" O PRO D 240 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 239 through 245' Processing helix chain 'D' and resid 247 through 262 removed outlier: 3.739A pdb=" N VAL D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.604A pdb=" N GLU D 267 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 285 removed outlier: 3.599A pdb=" N VAL D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 308 removed outlier: 3.719A pdb=" N LYS D 301 " --> pdb=" O ASN D 297 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 322 removed outlier: 4.467A pdb=" N THR D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.908A pdb=" N GLU D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 removed outlier: 3.548A pdb=" N ALA E 20 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 21 " --> pdb=" O PHE E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 21' Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.894A pdb=" N LYS E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 58 removed outlier: 3.582A pdb=" N THR E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 116 through 121 removed outlier: 4.334A pdb=" N VAL E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 116 through 121' Processing helix chain 'E' and resid 142 through 146 removed outlier: 4.161A pdb=" N ASN E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 removed outlier: 4.269A pdb=" N VAL E 165 " --> pdb=" O HIS E 161 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 210 Processing helix chain 'E' and resid 222 through 239 removed outlier: 4.085A pdb=" N ASN E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 247 removed outlier: 3.635A pdb=" N PHE E 243 " --> pdb=" O ASN E 239 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS E 246 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR E 247 " --> pdb=" O PHE E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 removed outlier: 3.902A pdb=" N ALA E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 265 Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 271 through 285 removed outlier: 3.567A pdb=" N LYS E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 285 " --> pdb=" O VAL E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 308 removed outlier: 4.290A pdb=" N VAL E 295 " --> pdb=" O ARG E 291 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS E 301 " --> pdb=" O ASN E 297 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA E 305 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 306 " --> pdb=" O ALA E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 319 removed outlier: 3.823A pdb=" N ILE E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 removed outlier: 3.515A pdb=" N LEU E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 25 through 37 removed outlier: 3.759A pdb=" N LEU F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 30 " --> pdb=" O GLU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 removed outlier: 3.637A pdb=" N ILE F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 170 removed outlier: 3.804A pdb=" N VAL F 165 " --> pdb=" O HIS F 161 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.768A pdb=" N ASP F 209 " --> pdb=" O PRO F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 239 removed outlier: 3.701A pdb=" N ASN F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 263 removed outlier: 3.670A pdb=" N LEU F 244 " --> pdb=" O PRO F 240 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 246 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR F 247 " --> pdb=" O PHE F 243 " (cutoff:3.500A) Proline residue: F 249 - end of helix removed outlier: 4.007A pdb=" N THR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA F 253 " --> pdb=" O PRO F 249 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS F 263 " --> pdb=" O VAL F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 285 removed outlier: 3.988A pdb=" N LEU F 285 " --> pdb=" O VAL F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 308 removed outlier: 3.811A pdb=" N ILE F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS F 301 " --> pdb=" O ASN F 297 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 removed outlier: 3.572A pdb=" N ILE F 317 " --> pdb=" O THR F 313 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG F 319 " --> pdb=" O ASP F 315 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL F 320 " --> pdb=" O ASP F 316 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR F 322 " --> pdb=" O ARG F 318 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 325 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 removed outlier: 3.641A pdb=" N LYS F 342 " --> pdb=" O ASP F 338 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 110 removed outlier: 7.070A pdb=" N LEU A 150 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.529A pdb=" N VAL B 109 " --> pdb=" O TYR B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.922A pdb=" N THR B 123 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 138 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 174 through 177 removed outlier: 3.862A pdb=" N VAL B 177 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 184 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.573A pdb=" N GLY C 194 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 45 " --> pdb=" O GLY C 194 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N MET C 44 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA7, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.650A pdb=" N ILE C 184 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 108 through 111 removed outlier: 3.900A pdb=" N GLY D 47 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 215 " --> pdb=" O MET D 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 46 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 217 " --> pdb=" O MET D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 66 through 70 Processing sheet with id=AB1, first strand: chain 'D' and resid 174 through 177 removed outlier: 3.700A pdb=" N VAL D 177 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 184 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 43 through 47 removed outlier: 5.786A pdb=" N MET E 44 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE E 217 " --> pdb=" O MET E 44 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET E 46 " --> pdb=" O ILE E 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.728A pdb=" N LYS E 104 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL E 69 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU E 102 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 108 through 111 removed outlier: 6.760A pdb=" N VAL E 109 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU E 150 " --> pdb=" O VAL E 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 192 through 196 removed outlier: 6.238A pdb=" N VAL F 43 " --> pdb=" O GLY F 194 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY F 196 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE F 45 " --> pdb=" O GLY F 196 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET F 46 " --> pdb=" O ALA F 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 109 through 110 removed outlier: 6.620A pdb=" N VAL F 109 " --> pdb=" O TYR F 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 428 hydrogen bonds defined for protein. 1209 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: 1.48 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3953 1.33 - 1.45: 2068 1.45 - 1.57: 8624 1.57 - 1.69: 26 1.69 - 1.81: 85 Bond restraints: 14756 Sorted by residual: bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C5 ADP F 401 " pdb=" C6 ADP F 401 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" N ASP E 78 " pdb=" CA ASP E 78 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.64e+01 bond pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta sigma weight residual 1.457 1.488 -0.031 9.10e-03 1.21e+04 1.19e+01 ... (remaining 14751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 19737 2.66 - 5.32: 213 5.32 - 7.98: 40 7.98 - 10.64: 11 10.64 - 13.31: 2 Bond angle restraints: 20003 Sorted by residual: angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 128.57 11.30 1.00e+00 1.00e+00 1.28e+02 angle pdb=" PA ATP E 401 " pdb=" O3A ATP E 401 " pdb=" PB ATP E 401 " ideal model delta sigma weight residual 136.83 129.97 6.86 1.00e+00 1.00e+00 4.71e+01 angle pdb=" CA GLY E 42 " pdb=" C GLY E 42 " pdb=" O GLY E 42 " ideal model delta sigma weight residual 122.52 118.27 4.25 7.90e-01 1.60e+00 2.90e+01 angle pdb=" C LEU E 203 " pdb=" CA LEU E 203 " pdb=" CB LEU E 203 " ideal model delta sigma weight residual 116.54 110.49 6.05 1.15e+00 7.56e-01 2.77e+01 angle pdb=" CA MET B 44 " pdb=" CB MET B 44 " pdb=" CG MET B 44 " ideal model delta sigma weight residual 114.10 123.39 -9.29 2.00e+00 2.50e-01 2.16e+01 ... (remaining 19998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 8484 30.32 - 60.64: 531 60.64 - 90.96: 32 90.96 - 121.28: 3 121.28 - 151.60: 2 Dihedral angle restraints: 9052 sinusoidal: 3787 harmonic: 5265 Sorted by residual: dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 148.40 151.60 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.34 -145.34 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O2A ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PA ADP F 401 " pdb=" PB ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.39 -116.39 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 9049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1714 0.043 - 0.086: 446 0.086 - 0.129: 158 0.129 - 0.173: 16 0.173 - 0.216: 4 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CA MET D 44 " pdb=" N MET D 44 " pdb=" C MET D 44 " pdb=" CB MET D 44 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LEU F 167 " pdb=" N LEU F 167 " pdb=" C LEU F 167 " pdb=" CB LEU F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA ILE D 337 " pdb=" N ILE D 337 " pdb=" C ILE D 337 " pdb=" CB ILE D 337 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 2335 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 208 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LEU F 208 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU F 208 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP F 209 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 240 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 241 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 239 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO F 240 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 240 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 240 " 0.022 5.00e-02 4.00e+02 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 151 2.59 - 3.17: 11983 3.17 - 3.74: 21250 3.74 - 4.32: 26459 4.32 - 4.90: 43663 Nonbonded interactions: 103506 Sorted by model distance: nonbonded pdb=" O2B ATP D 401 " pdb="MG MG D 402 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP B 87 " pdb=" N GLU B 88 " model vdw 2.115 3.120 nonbonded pdb=" CB SER B 54 " pdb="MG MG B 401 " model vdw 2.131 2.570 nonbonded pdb=" O SER E 279 " pdb=" OG SER E 283 " model vdw 2.161 3.040 nonbonded pdb=" O VAL F 165 " pdb=" OG SER F 169 " model vdw 2.198 3.040 ... (remaining 103501 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 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'B' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'C' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'D' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'E' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'F' and (resid 14 through 65 or resid 103 through 353)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.970 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.004 0.110 14756 Z= 0.235 Angle : 0.743 13.306 20003 Z= 0.420 Chirality : 0.044 0.216 2338 Planarity : 0.004 0.044 2579 Dihedral : 18.173 151.600 5628 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.11 % Favored : 91.84 % Rotamer: Outliers : 0.19 % Allowed : 35.80 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1789 helix: 0.55 (0.21), residues: 659 sheet: -1.02 (0.50), residues: 116 loop : -1.90 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.014 0.001 TYR D 341 PHE 0.011 0.001 PHE A 351 TRP 0.004 0.001 TRP B 174 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.23 (14756) covalent geometry : angle 0.74268 / 0.42 (20003) hydrogen bonds : bond 0.25918 / 16.84 ( 428) hydrogen bonds : angle 7.38144 / 5.07 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.373 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.1016 time to fit residues: 23.8472 Evaluate side-chains 138 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 146 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.0134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.085440 restraints weight = 35296.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087883 restraints weight = 20319.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089496 restraints weight = 14542.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.090528 restraints weight = 11867.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.091172 restraints weight = 10462.760| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14756 Z= 0.160 Angle : 0.653 13.791 20003 Z= 0.316 Chirality : 0.043 0.168 2338 Planarity : 0.005 0.048 2579 Dihedral : 8.355 159.796 2002 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.55 % Favored : 91.39 % Rotamer: Outliers : 5.20 % Allowed : 32.29 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.20), residues: 1789 helix: 0.55 (0.20), residues: 727 sheet: -1.22 (0.44), residues: 154 loop : -2.19 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 189 TYR 0.018 0.001 TYR D 341 PHE 0.016 0.001 PHE B 243 TRP 0.004 0.001 TRP B 174 HIS 0.005 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (14756) covalent geometry : angle 0.65251 / 0.32 (20003) hydrogen bonds : bond 0.05131 / 3.35 ( 428) hydrogen bonds : angle 5.22780 / 3.62 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 138 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8266 (p0) REVERT: B 44 MET cc_start: 0.7962 (tmt) cc_final: 0.7683 (tmt) REVERT: C 40 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8721 (mm) REVERT: C 146 ASN cc_start: 0.8485 (t0) cc_final: 0.8193 (t0) REVERT: E 19 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8207 (t) REVERT: E 113 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9212 (tt) REVERT: F 24 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7345 (pp30) REVERT: F 151 TYR cc_start: 0.8356 (t80) cc_final: 0.7896 (t80) REVERT: F 190 PHE cc_start: 0.8798 (p90) cc_final: 0.8594 (p90) REVERT: F 197 ASN cc_start: 0.7573 (t0) cc_final: 0.7369 (t0) REVERT: F 210 ARG cc_start: 0.7241 (tpm170) cc_final: 0.6862 (tpm170) outliers start: 83 outliers final: 44 residues processed: 209 average time/residue: 0.0882 time to fit residues: 29.0778 Evaluate side-chains 185 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 161 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 152 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.087728 restraints weight = 34812.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.090330 restraints weight = 19560.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092084 restraints weight = 13640.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093223 restraints weight = 10915.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093920 restraints weight = 9515.188| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14756 Z= 0.105 Angle : 0.580 11.789 20003 Z= 0.276 Chirality : 0.041 0.164 2338 Planarity : 0.004 0.049 2579 Dihedral : 7.858 154.066 2000 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.51 % Allowed : 32.41 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.20), residues: 1789 helix: 0.78 (0.21), residues: 711 sheet: -0.90 (0.49), residues: 124 loop : -1.98 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 179 TYR 0.015 0.001 TYR D 341 PHE 0.014 0.001 PHE F 16 TRP 0.002 0.000 TRP B 174 HIS 0.004 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (14756) covalent geometry : angle 0.57978 / 0.28 (20003) hydrogen bonds : bond 0.03933 / 2.57 ( 428) hydrogen bonds : angle 4.53480 / 3.16 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 141 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7769 (tmt) cc_final: 0.7224 (tmt) REVERT: C 146 ASN cc_start: 0.8450 (t0) cc_final: 0.8089 (t0) REVERT: E 27 MET cc_start: 0.7329 (tmm) cc_final: 0.6859 (tmm) REVERT: F 190 PHE cc_start: 0.8812 (p90) cc_final: 0.8521 (p90) REVERT: F 197 ASN cc_start: 0.7575 (t0) cc_final: 0.7313 (t0) REVERT: F 210 ARG cc_start: 0.7007 (tpm170) cc_final: 0.6747 (tpm170) outliers start: 72 outliers final: 36 residues processed: 199 average time/residue: 0.0915 time to fit residues: 29.0881 Evaluate side-chains 173 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 153 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 132 optimal weight: 0.0070 chunk 159 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.084951 restraints weight = 35393.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.087413 restraints weight = 20495.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089033 restraints weight = 14687.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090052 restraints weight = 11957.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090565 restraints weight = 10567.716| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14756 Z= 0.173 Angle : 0.619 11.308 20003 Z= 0.297 Chirality : 0.043 0.165 2338 Planarity : 0.004 0.050 2579 Dihedral : 7.831 152.926 2000 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 5.89 % Allowed : 31.60 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1789 helix: 0.73 (0.21), residues: 723 sheet: -1.24 (0.43), residues: 155 loop : -2.14 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.012 0.001 TYR D 341 PHE 0.014 0.001 PHE F 16 TRP 0.005 0.001 TRP B 174 HIS 0.005 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (14756) covalent geometry : angle 0.61902 / 0.30 (20003) hydrogen bonds : bond 0.04404 / 2.87 ( 428) hydrogen bonds : angle 4.62360 / 3.20 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 132 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7806 (tmt) cc_final: 0.7288 (tmt) REVERT: C 40 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8703 (mm) REVERT: C 146 ASN cc_start: 0.8551 (t0) cc_final: 0.8156 (t0) REVERT: C 229 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8791 (tt) REVERT: E 27 MET cc_start: 0.7415 (tmm) cc_final: 0.6916 (tmm) REVERT: F 44 MET cc_start: 0.8215 (tpp) cc_final: 0.7992 (tpp) REVERT: F 151 TYR cc_start: 0.8344 (t80) cc_final: 0.7947 (t80) REVERT: F 190 PHE cc_start: 0.8843 (p90) cc_final: 0.8494 (p90) REVERT: F 210 ARG cc_start: 0.7043 (tpm170) cc_final: 0.6511 (tpm170) REVERT: F 323 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8559 (tt) outliers start: 94 outliers final: 66 residues processed: 214 average time/residue: 0.0910 time to fit residues: 30.9835 Evaluate side-chains 201 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 132 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 11 optimal weight: 0.0570 chunk 146 optimal weight: 0.0980 chunk 101 optimal weight: 0.1980 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 135 optimal weight: 0.0570 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.118255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.091065 restraints weight = 35983.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093814 restraints weight = 19515.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095579 restraints weight = 13457.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096715 restraints weight = 10751.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097416 restraints weight = 9374.242| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14756 Z= 0.101 Angle : 0.580 10.894 20003 Z= 0.273 Chirality : 0.041 0.183 2338 Planarity : 0.004 0.048 2579 Dihedral : 7.449 148.907 2000 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.76 % Allowed : 32.92 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.20), residues: 1789 helix: 0.85 (0.21), residues: 716 sheet: -0.86 (0.49), residues: 124 loop : -2.00 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.017 0.001 TYR D 341 PHE 0.015 0.001 PHE F 236 TRP 0.002 0.000 TRP C 174 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (14756) covalent geometry : angle 0.57954 / 0.27 (20003) hydrogen bonds : bond 0.02923 / 1.93 ( 428) hydrogen bonds : angle 4.05189 / 2.84 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 146 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8976 (mmm160) cc_final: 0.8702 (tpt90) REVERT: B 44 MET cc_start: 0.7709 (tmt) cc_final: 0.7092 (tmt) REVERT: B 91 GLN cc_start: 0.8890 (pp30) cc_final: 0.8617 (pm20) REVERT: C 146 ASN cc_start: 0.8390 (t0) cc_final: 0.7967 (t0) REVERT: E 19 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.8054 (t) REVERT: E 27 MET cc_start: 0.7313 (tmm) cc_final: 0.6765 (tmm) REVERT: F 44 MET cc_start: 0.8156 (tpp) cc_final: 0.7924 (tpp) REVERT: F 190 PHE cc_start: 0.8813 (p90) cc_final: 0.8445 (p90) REVERT: F 197 ASN cc_start: 0.7624 (t0) cc_final: 0.7375 (t0) REVERT: F 210 ARG cc_start: 0.6963 (tpm170) cc_final: 0.6625 (tpm170) REVERT: F 229 ILE cc_start: 0.8895 (mt) cc_final: 0.8415 (tp) REVERT: F 323 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8457 (tt) outliers start: 60 outliers final: 43 residues processed: 193 average time/residue: 0.1068 time to fit residues: 32.3951 Evaluate side-chains 183 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 89 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 75 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.1752 > 50:) chunk 40 optimal weight: 0.0570 chunk 105 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 24 GLN F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.116473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.088835 restraints weight = 34766.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091413 restraints weight = 19703.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093129 restraints weight = 13863.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094244 restraints weight = 11170.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094875 restraints weight = 9776.292| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14756 Z= 0.098 Angle : 0.575 11.303 20003 Z= 0.269 Chirality : 0.041 0.159 2338 Planarity : 0.004 0.050 2579 Dihedral : 7.295 144.792 2000 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.20 % Allowed : 32.92 % Favored : 62.88 % 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: -0.94 (0.20), residues: 1789 helix: 0.94 (0.21), residues: 718 sheet: -0.78 (0.49), residues: 124 loop : -1.93 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 179 TYR 0.015 0.001 TYR D 341 PHE 0.015 0.001 PHE E 347 TRP 0.003 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (14756) covalent geometry : angle 0.57461 / 0.27 (20003) hydrogen bonds : bond 0.02952 / 1.95 ( 428) hydrogen bonds : angle 3.95455 / 2.79 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 142 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: B 44 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7108 (tmt) REVERT: B 64 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8211 (mp) REVERT: C 40 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8565 (mm) REVERT: C 146 ASN cc_start: 0.8410 (t0) cc_final: 0.7991 (t0) REVERT: E 24 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: E 27 MET cc_start: 0.7343 (tmm) cc_final: 0.6755 (tmm) REVERT: F 210 ARG cc_start: 0.6948 (tpm170) cc_final: 0.6574 (tpm170) REVERT: F 323 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8474 (tt) outliers start: 67 outliers final: 45 residues processed: 198 average time/residue: 0.1060 time to fit residues: 33.3028 Evaluate side-chains 189 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 63 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086872 restraints weight = 34885.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089342 restraints weight = 20056.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090992 restraints weight = 14217.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.092059 restraints weight = 11564.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092730 restraints weight = 10139.823| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14756 Z= 0.142 Angle : 0.613 11.097 20003 Z= 0.288 Chirality : 0.042 0.157 2338 Planarity : 0.004 0.049 2579 Dihedral : 7.357 143.834 2000 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.58 % Allowed : 32.54 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1789 helix: 0.97 (0.21), residues: 726 sheet: -1.05 (0.45), residues: 144 loop : -2.03 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 179 TYR 0.020 0.001 TYR B 341 PHE 0.018 0.001 PHE F 190 TRP 0.004 0.001 TRP B 174 HIS 0.004 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (14756) covalent geometry : angle 0.61270 / 0.29 (20003) hydrogen bonds : bond 0.03489 / 2.29 ( 428) hydrogen bonds : angle 4.09511 / 2.87 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 139 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: B 44 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7225 (tmt) REVERT: B 64 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 91 GLN cc_start: 0.8849 (pp30) cc_final: 0.8541 (pm20) REVERT: C 26 GLU cc_start: 0.7744 (tp30) cc_final: 0.7277 (mm-30) REVERT: C 146 ASN cc_start: 0.8486 (t0) cc_final: 0.8065 (t0) REVERT: C 325 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8551 (tt) REVERT: E 19 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8043 (t) REVERT: E 27 MET cc_start: 0.7420 (tmm) cc_final: 0.6885 (tmm) REVERT: E 91 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: F 44 MET cc_start: 0.8151 (tpp) cc_final: 0.7925 (tpp) REVERT: F 151 TYR cc_start: 0.8333 (t80) cc_final: 0.7940 (t80) REVERT: F 190 PHE cc_start: 0.8842 (p90) cc_final: 0.8581 (p90) REVERT: F 204 ARG cc_start: 0.8225 (ptp-170) cc_final: 0.8020 (ptp-170) REVERT: F 210 ARG cc_start: 0.6846 (tpm170) cc_final: 0.6421 (tpm170) REVERT: F 323 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8511 (tt) outliers start: 73 outliers final: 53 residues processed: 200 average time/residue: 0.0981 time to fit residues: 30.9348 Evaluate side-chains 195 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 20 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.115592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088080 restraints weight = 34769.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090527 restraints weight = 19968.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092167 restraints weight = 14206.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093265 restraints weight = 11519.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093823 restraints weight = 10125.507| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14756 Z= 0.107 Angle : 0.593 11.996 20003 Z= 0.278 Chirality : 0.041 0.158 2338 Planarity : 0.004 0.049 2579 Dihedral : 7.293 142.803 2000 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.26 % Allowed : 32.92 % Favored : 62.82 % 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: -0.94 (0.20), residues: 1789 helix: 1.00 (0.21), residues: 724 sheet: -0.91 (0.48), residues: 132 loop : -2.00 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 179 TYR 0.021 0.001 TYR B 341 PHE 0.017 0.001 PHE E 347 TRP 0.002 0.000 TRP B 174 HIS 0.004 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (14756) covalent geometry : angle 0.59264 / 0.28 (20003) hydrogen bonds : bond 0.03095 / 2.04 ( 428) hydrogen bonds : angle 3.93939 / 2.77 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 137 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7195 (tmt) REVERT: B 64 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8253 (mp) REVERT: C 26 GLU cc_start: 0.7660 (tp30) cc_final: 0.7284 (mm-30) REVERT: C 146 ASN cc_start: 0.8444 (t0) cc_final: 0.8007 (t0) REVERT: E 19 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8026 (t) REVERT: E 27 MET cc_start: 0.7397 (tmm) cc_final: 0.6829 (tmm) REVERT: E 91 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: F 190 PHE cc_start: 0.8833 (p90) cc_final: 0.8567 (p90) REVERT: F 210 ARG cc_start: 0.6868 (tpm170) cc_final: 0.6428 (tpm170) REVERT: F 229 ILE cc_start: 0.8912 (mt) cc_final: 0.8416 (tp) REVERT: F 323 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8530 (tt) outliers start: 68 outliers final: 53 residues processed: 196 average time/residue: 0.0960 time to fit residues: 29.3169 Evaluate side-chains 193 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 135 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 17 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.116304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.088670 restraints weight = 34784.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091233 restraints weight = 19748.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092993 restraints weight = 14006.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094067 restraints weight = 11273.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094639 restraints weight = 9883.983| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14756 Z= 0.101 Angle : 0.595 12.418 20003 Z= 0.275 Chirality : 0.041 0.155 2338 Planarity : 0.004 0.049 2579 Dihedral : 7.179 139.829 2000 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.82 % Allowed : 33.10 % Favored : 63.07 % 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: -0.98 (0.20), residues: 1789 helix: 0.87 (0.20), residues: 750 sheet: -0.69 (0.50), residues: 124 loop : -2.04 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 179 TYR 0.017 0.001 TYR B 341 PHE 0.015 0.001 PHE F 236 TRP 0.003 0.000 TRP C 174 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (14756) covalent geometry : angle 0.59523 / 0.27 (20003) hydrogen bonds : bond 0.02915 / 1.93 ( 428) hydrogen bonds : angle 3.82901 / 2.70 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7177 (tmt) REVERT: B 64 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8245 (mp) REVERT: B 91 GLN cc_start: 0.8859 (pp30) cc_final: 0.8549 (pm20) REVERT: C 146 ASN cc_start: 0.8434 (t0) cc_final: 0.8022 (t0) REVERT: C 325 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8459 (tt) REVERT: E 19 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7988 (t) REVERT: E 27 MET cc_start: 0.7375 (tmm) cc_final: 0.6861 (tmm) REVERT: E 91 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: F 190 PHE cc_start: 0.8814 (p90) cc_final: 0.8560 (p90) REVERT: F 210 ARG cc_start: 0.6713 (tpm170) cc_final: 0.6318 (tpm170) REVERT: F 229 ILE cc_start: 0.8888 (mt) cc_final: 0.8399 (tp) REVERT: F 323 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8605 (tt) outliers start: 61 outliers final: 49 residues processed: 193 average time/residue: 0.0897 time to fit residues: 27.4056 Evaluate side-chains 186 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 76 optimal weight: 0.0060 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 34 ASN E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.088266 restraints weight = 34763.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090754 restraints weight = 19859.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092441 restraints weight = 14085.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093517 restraints weight = 11410.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093998 restraints weight = 10011.613| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14756 Z= 0.110 Angle : 0.604 12.562 20003 Z= 0.282 Chirality : 0.041 0.152 2338 Planarity : 0.004 0.049 2579 Dihedral : 7.149 137.851 2000 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.64 % Allowed : 33.42 % Favored : 62.95 % 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: -0.97 (0.20), residues: 1789 helix: 0.90 (0.20), residues: 751 sheet: -0.91 (0.46), residues: 141 loop : -2.03 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 189 TYR 0.018 0.001 TYR B 341 PHE 0.019 0.001 PHE E 347 TRP 0.003 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (14756) covalent geometry : angle 0.60423 / 0.28 (20003) hydrogen bonds : bond 0.03058 / 2.02 ( 428) hydrogen bonds : angle 3.85545 / 2.71 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7220 (tmt) REVERT: B 64 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8247 (mp) REVERT: B 91 GLN cc_start: 0.8846 (pp30) cc_final: 0.8521 (pm20) REVERT: B 239 ASN cc_start: 0.8512 (t0) cc_final: 0.7900 (m110) REVERT: C 26 GLU cc_start: 0.7558 (tp30) cc_final: 0.7237 (mm-30) REVERT: C 146 ASN cc_start: 0.8431 (t0) cc_final: 0.8007 (t0) REVERT: C 325 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8510 (tt) REVERT: E 19 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7970 (t) REVERT: E 27 MET cc_start: 0.7428 (tmm) cc_final: 0.6849 (tmm) REVERT: E 91 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: F 190 PHE cc_start: 0.8841 (p90) cc_final: 0.8582 (p90) REVERT: F 210 ARG cc_start: 0.6756 (tpm170) cc_final: 0.6368 (tpm170) REVERT: F 229 ILE cc_start: 0.8895 (mt) cc_final: 0.8405 (tp) REVERT: F 323 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8587 (tt) outliers start: 58 outliers final: 50 residues processed: 188 average time/residue: 0.0787 time to fit residues: 23.8447 Evaluate side-chains 193 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.116092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088413 restraints weight = 34746.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090951 restraints weight = 20068.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092612 restraints weight = 14305.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093551 restraints weight = 11608.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094329 restraints weight = 10280.502| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14756 Z= 0.108 Angle : 0.601 12.974 20003 Z= 0.279 Chirality : 0.041 0.150 2338 Planarity : 0.004 0.049 2579 Dihedral : 7.095 136.289 2000 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.70 % Allowed : 33.35 % Favored : 62.95 % 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: -0.93 (0.20), residues: 1789 helix: 0.93 (0.21), residues: 746 sheet: -0.89 (0.46), residues: 141 loop : -2.00 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 189 TYR 0.017 0.001 TYR B 341 PHE 0.019 0.001 PHE F 236 TRP 0.002 0.000 TRP E 174 HIS 0.003 0.001 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (14756) covalent geometry : angle 0.60056 / 0.28 (20003) hydrogen bonds : bond 0.03028 / 2.00 ( 428) hydrogen bonds : angle 3.81167 / 2.68 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.79 seconds wall clock time: 37 minutes 5.92 seconds (2225.92 seconds total)