Starting phenix.real_space_refine on Fri Jun 13 04:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osg_17152/06_2025/8osg_17152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osg_17152/06_2025/8osg_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_17152/06_2025/8osg_17152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osg_17152/06_2025/8osg_17152.map" model { file = "/net/cci-nas-00/data/ceres_data/8osg_17152/06_2025/8osg_17152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osg_17152/06_2025/8osg_17152.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.35, per 1000 atoms: 0.64 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: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.49 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: 4.50 Time building geometry restraints manager: 4.19 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: 8539 30.32 - 60.64: 591 60.64 - 90.96: 41 90.96 - 121.28: 3 121.28 - 151.60: 2 Dihedral angle restraints: 9176 sinusoidal: 3911 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 9173 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: 1.440 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.230 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 18.748 151.600 5752 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP B 174 HIS 0.005 0.001 HIS B 214 PHE 0.011 0.001 PHE A 351 TYR 0.014 0.001 TYR D 341 ARG 0.003 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.25918 ( 428) hydrogen bonds : angle 7.38144 ( 1209) covalent geometry : bond 0.00377 (14756) covalent geometry : angle 0.74268 (20003) *********************** 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 : 1.636 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.2406 time to fit residues: 55.3761 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 : 1.796 ------------------------------------------------------------------------------- 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 152 optimal weight: 0.0470 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS F 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.113842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086075 restraints weight = 35129.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.088549 restraints weight = 20304.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.090204 restraints weight = 14510.682| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14756 Z= 0.140 Angle : 0.633 13.410 20003 Z= 0.307 Chirality : 0.042 0.172 2338 Planarity : 0.004 0.048 2579 Dihedral : 11.208 158.887 2126 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.16 % Favored : 91.78 % Rotamer: Outliers : 4.83 % Allowed : 32.60 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1789 helix: 0.57 (0.20), residues: 726 sheet: -1.18 (0.44), residues: 154 loop : -2.16 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 174 HIS 0.004 0.001 HIS C 214 PHE 0.015 0.001 PHE F 16 TYR 0.018 0.001 TYR D 341 ARG 0.004 0.000 ARG A 189 Details of bonding type rmsd hydrogen bonds : bond 0.05279 ( 428) hydrogen bonds : angle 5.19179 ( 1209) covalent geometry : bond 0.00323 (14756) covalent geometry : angle 0.63326 (20003) *********************** 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 216 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 139 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7894 (tmt) cc_final: 0.7625 (tmt) REVERT: C 146 ASN cc_start: 0.8429 (t0) cc_final: 0.8125 (t0) REVERT: D 138 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6789 (pp20) REVERT: D 331 LYS cc_start: 0.8210 (ptmm) cc_final: 0.7897 (ptmm) REVERT: E 113 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9201 (tt) REVERT: F 24 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7233 (pp30) REVERT: F 151 TYR cc_start: 0.8273 (t80) cc_final: 0.7801 (t80) REVERT: F 197 ASN cc_start: 0.7519 (t0) cc_final: 0.7307 (t0) REVERT: F 210 ARG cc_start: 0.7330 (tpm170) cc_final: 0.6964 (tpm170) outliers start: 77 outliers final: 38 residues processed: 205 average time/residue: 0.2220 time to fit residues: 70.4700 Evaluate side-chains 178 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 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 45 ILE Chi-restraints excluded: chain C residue 165 VAL 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 138 GLU 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 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 F residue 19 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 161 optimal weight: 0.0070 chunk 150 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS C 34 ASN F 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.115520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087883 restraints weight = 34735.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090455 restraints weight = 19336.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092208 restraints weight = 13544.954| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1335 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= 0.108 Angle : 0.580 11.933 20003 Z= 0.277 Chirality : 0.041 0.166 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.639 153.400 2124 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.70 % Allowed : 31.79 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1789 helix: 0.80 (0.21), residues: 712 sheet: -0.86 (0.49), residues: 124 loop : -1.97 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 PHE 0.013 0.001 PHE F 16 TYR 0.016 0.001 TYR D 341 ARG 0.005 0.000 ARG E 309 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 428) hydrogen bonds : angle 4.50649 ( 1209) covalent geometry : bond 0.00247 (14756) covalent geometry : angle 0.57958 (20003) *********************** 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 217 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 142 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7765 (tmt) cc_final: 0.7224 (tmt) REVERT: C 146 ASN cc_start: 0.8416 (t0) cc_final: 0.8049 (t0) REVERT: D 331 LYS cc_start: 0.8183 (ptmm) cc_final: 0.7834 (pttp) REVERT: E 27 MET cc_start: 0.7284 (tmm) cc_final: 0.6804 (tmm) REVERT: E 179 ARG cc_start: 0.8504 (mmp80) cc_final: 0.8272 (mmp80) REVERT: F 34 ASN cc_start: 0.8400 (m-40) cc_final: 0.8163 (m-40) REVERT: F 197 ASN cc_start: 0.7522 (t0) cc_final: 0.7245 (t0) REVERT: F 210 ARG cc_start: 0.6987 (tpm170) cc_final: 0.6495 (tpm170) outliers start: 75 outliers final: 38 residues processed: 204 average time/residue: 0.2470 time to fit residues: 79.5326 Evaluate side-chains 176 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 81 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 166 LEU 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 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 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 31 LEU Chi-restraints excluded: chain E residue 48 ASP 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 19 THR Chi-restraints excluded: chain F residue 43 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 7 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 134 optimal weight: 0.0010 chunk 14 optimal weight: 0.5980 chunk 166 optimal weight: 7.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.116672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089079 restraints weight = 34385.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091642 restraints weight = 19506.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093361 restraints weight = 13745.621| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1628 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= 0.100 Angle : 0.563 11.040 20003 Z= 0.268 Chirality : 0.041 0.177 2338 Planarity : 0.004 0.050 2579 Dihedral : 10.294 149.469 2124 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.33 % Allowed : 32.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1789 helix: 0.73 (0.20), residues: 732 sheet: -0.79 (0.51), residues: 112 loop : -1.98 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 PHE 0.015 0.001 PHE E 347 TYR 0.015 0.001 TYR D 341 ARG 0.003 0.000 ARG A 189 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 428) hydrogen bonds : angle 4.12987 ( 1209) covalent geometry : bond 0.00230 (14756) covalent geometry : angle 0.56262 (20003) *********************** 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 218 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7749 (tmt) cc_final: 0.7151 (tmt) REVERT: C 146 ASN cc_start: 0.8388 (t0) cc_final: 0.8033 (t0) REVERT: D 331 LYS cc_start: 0.8085 (ptmm) cc_final: 0.7722 (pttp) REVERT: E 24 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: E 27 MET cc_start: 0.7302 (tmm) cc_final: 0.6735 (tmm) REVERT: F 44 MET cc_start: 0.8132 (tpp) cc_final: 0.7865 (tpp) REVERT: F 197 ASN cc_start: 0.7576 (t0) cc_final: 0.7313 (t0) REVERT: F 210 ARG cc_start: 0.6989 (tpm170) cc_final: 0.6703 (tpm170) REVERT: F 229 ILE cc_start: 0.8930 (mt) cc_final: 0.8450 (tp) REVERT: F 323 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8470 (tt) outliers start: 69 outliers final: 45 residues processed: 203 average time/residue: 0.2188 time to fit residues: 70.7598 Evaluate side-chains 185 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 312 VAL 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 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 45 ILE 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 56 THR 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 E residue 24 GLN 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 F residue 109 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 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 179 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 87 optimal weight: 0.0670 chunk 68 optimal weight: 0.0870 chunk 36 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 34 ASN ** 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 = 0.3726 r_free = 0.3726 target = 0.116893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089306 restraints weight = 35000.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091919 restraints weight = 19768.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093655 restraints weight = 13877.223| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1740 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= 0.101 Angle : 0.572 10.696 20003 Z= 0.273 Chirality : 0.041 0.150 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.204 146.540 2124 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.01 % Allowed : 33.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1789 helix: 0.81 (0.20), residues: 732 sheet: -0.76 (0.52), residues: 112 loop : -1.96 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 PHE 0.012 0.001 PHE F 16 TYR 0.016 0.001 TYR D 341 ARG 0.006 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 428) hydrogen bonds : angle 3.99544 ( 1209) covalent geometry : bond 0.00236 (14756) covalent geometry : angle 0.57225 (20003) *********************** 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 203 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 139 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: A 349 ARG cc_start: 0.8989 (mmm160) cc_final: 0.8695 (tpt90) REVERT: B 44 MET cc_start: 0.7670 (tmt) cc_final: 0.7076 (tmt) REVERT: B 91 GLN cc_start: 0.8865 (pp30) cc_final: 0.8560 (pm20) REVERT: C 146 ASN cc_start: 0.8351 (t0) cc_final: 0.7942 (t0) REVERT: D 331 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7766 (pttp) REVERT: E 27 MET cc_start: 0.7259 (tmm) cc_final: 0.6740 (tmm) REVERT: E 217 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8211 (tp) REVERT: F 197 ASN cc_start: 0.7628 (t0) cc_final: 0.7349 (t0) REVERT: F 210 ARG cc_start: 0.6978 (tpm170) cc_final: 0.6661 (tpm170) REVERT: F 229 ILE cc_start: 0.8905 (mt) cc_final: 0.8436 (tp) REVERT: F 323 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8475 (tt) outliers start: 64 outliers final: 45 residues processed: 191 average time/residue: 0.2236 time to fit residues: 67.0796 Evaluate side-chains 185 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 281 VAL 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 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 183 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 45 ILE 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 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 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 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 217 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 219 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 129 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 161 HIS D 186 HIS E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086734 restraints weight = 35104.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.089251 restraints weight = 20237.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090919 restraints weight = 14346.524| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14756 Z= 0.145 Angle : 0.605 10.699 20003 Z= 0.289 Chirality : 0.042 0.152 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.216 144.726 2124 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.51 % Allowed : 31.85 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1789 helix: 0.86 (0.21), residues: 737 sheet: -0.91 (0.46), residues: 147 loop : -2.09 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.004 0.001 HIS D 186 PHE 0.018 0.001 PHE F 190 TYR 0.022 0.001 TYR B 341 ARG 0.005 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 428) hydrogen bonds : angle 4.14946 ( 1209) covalent geometry : bond 0.00348 (14756) covalent geometry : angle 0.60458 (20003) *********************** 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 210 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 138 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: B 44 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7230 (tmt) REVERT: B 64 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8235 (mp) REVERT: C 26 GLU cc_start: 0.7789 (tp30) cc_final: 0.7327 (mm-30) REVERT: C 146 ASN cc_start: 0.8469 (t0) cc_final: 0.8051 (t0) REVERT: D 331 LYS cc_start: 0.8144 (ptmm) cc_final: 0.7815 (pttp) REVERT: E 24 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: E 27 MET cc_start: 0.7415 (tmm) cc_final: 0.6797 (tmm) REVERT: F 210 ARG cc_start: 0.6943 (tpm170) cc_final: 0.6517 (tpm170) REVERT: F 323 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8543 (tt) outliers start: 72 outliers final: 52 residues processed: 197 average time/residue: 0.2062 time to fit residues: 65.3345 Evaluate side-chains 192 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 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 175 ASN Chi-restraints excluded: chain B residue 177 VAL 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 296 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL 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 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 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 24 GLN 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 F residue 60 LEU Chi-restraints excluded: chain F residue 109 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 146 optimal weight: 0.0570 chunk 180 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3691 r_free = 0.3691 target = 0.114631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086864 restraints weight = 35171.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089384 restraints weight = 20073.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091063 restraints weight = 14264.077| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14756 Z= 0.130 Angle : 0.603 11.260 20003 Z= 0.287 Chirality : 0.042 0.143 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.188 144.156 2124 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.76 % Allowed : 31.66 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1789 helix: 0.87 (0.21), residues: 736 sheet: -0.93 (0.45), residues: 147 loop : -2.11 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 174 HIS 0.004 0.001 HIS C 214 PHE 0.015 0.001 PHE F 16 TYR 0.019 0.001 TYR B 341 ARG 0.004 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 428) hydrogen bonds : angle 4.09994 ( 1209) covalent geometry : bond 0.00312 (14756) covalent geometry : angle 0.60313 (20003) *********************** 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 214 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 138 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8447 (mm-30) REVERT: A 237 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: B 44 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7186 (tmt) REVERT: B 64 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 91 GLN cc_start: 0.8857 (pp30) cc_final: 0.8553 (pm20) REVERT: C 26 GLU cc_start: 0.7745 (tp30) cc_final: 0.7295 (mm-30) REVERT: C 146 ASN cc_start: 0.8470 (t0) cc_final: 0.8025 (t0) REVERT: D 331 LYS cc_start: 0.8138 (ptmm) cc_final: 0.7833 (pttp) REVERT: E 27 MET cc_start: 0.7467 (tmm) cc_final: 0.6891 (tmm) REVERT: E 91 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: F 210 ARG cc_start: 0.6883 (tpm170) cc_final: 0.6454 (tpm170) REVERT: F 229 ILE cc_start: 0.8933 (mt) cc_final: 0.8423 (tp) REVERT: F 323 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8540 (tt) outliers start: 76 outliers final: 62 residues processed: 201 average time/residue: 0.2024 time to fit residues: 64.9470 Evaluate side-chains 203 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 135 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 199 GLU 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 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 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 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 44 MET 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 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 183 SER 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 31 LEU 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 19 THR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 109 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 147 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 122 optimal weight: 0.2980 chunk 139 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 161 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3710 r_free = 0.3710 target = 0.115859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.088236 restraints weight = 34591.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090804 restraints weight = 19556.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.092501 restraints weight = 13792.563| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.002 0.050 14756 Z= 0.105 Angle : 0.598 12.090 20003 Z= 0.280 Chirality : 0.041 0.141 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.078 142.235 2124 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.45 % Allowed : 31.91 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1789 helix: 0.86 (0.20), residues: 743 sheet: -0.75 (0.49), residues: 124 loop : -2.05 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 PHE 0.016 0.001 PHE E 347 TYR 0.016 0.001 TYR D 341 ARG 0.005 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 428) hydrogen bonds : angle 3.93330 ( 1209) covalent geometry : bond 0.00249 (14756) covalent geometry : angle 0.59761 (20003) *********************** 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 209 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 138 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8320 (mm-30) REVERT: B 44 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7173 (tmt) REVERT: B 64 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 146 ASN cc_start: 0.8414 (t0) cc_final: 0.8018 (t0) REVERT: C 325 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8492 (tt) REVERT: D 331 LYS cc_start: 0.8117 (ptmm) cc_final: 0.7814 (pttp) REVERT: E 27 MET cc_start: 0.7435 (tmm) cc_final: 0.6864 (tmm) REVERT: E 91 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: F 190 PHE cc_start: 0.8820 (p90) cc_final: 0.8587 (p90) REVERT: F 210 ARG cc_start: 0.6946 (tpm170) cc_final: 0.6489 (tpm170) REVERT: F 229 ILE cc_start: 0.8907 (mt) cc_final: 0.8418 (tp) REVERT: F 323 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8481 (tt) outliers start: 71 outliers final: 59 residues processed: 199 average time/residue: 0.2117 time to fit residues: 67.0016 Evaluate side-chains 198 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 199 GLU 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 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 153 ASP 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 227 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 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 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 183 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 31 LEU 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 F residue 19 THR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 109 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 317 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 168 optimal weight: 0.0980 chunk 8 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 141 optimal weight: 0.1980 chunk 5 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 178 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.117618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090357 restraints weight = 34604.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093073 restraints weight = 18772.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094837 restraints weight = 12907.808| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14756 Z= 0.101 Angle : 0.592 12.496 20003 Z= 0.278 Chirality : 0.041 0.140 2338 Planarity : 0.004 0.049 2579 Dihedral : 9.872 137.897 2124 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.45 % Allowed : 33.17 % Favored : 63.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.20), residues: 1789 helix: 0.88 (0.20), residues: 751 sheet: -0.68 (0.52), residues: 112 loop : -1.98 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 174 HIS 0.005 0.001 HIS C 214 PHE 0.016 0.001 PHE F 236 TYR 0.017 0.001 TYR D 341 ARG 0.005 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.02608 ( 428) hydrogen bonds : angle 3.72976 ( 1209) covalent geometry : bond 0.00232 (14756) covalent geometry : angle 0.59226 (20003) *********************** 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: 55 poor density : 145 time to evaluate : 2.997 Fit side-chains revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8366 (mm-30) REVERT: A 237 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: B 44 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7068 (tmt) REVERT: B 64 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (mp) REVERT: B 91 GLN cc_start: 0.8863 (pp30) cc_final: 0.8550 (pm20) REVERT: C 26 GLU cc_start: 0.7560 (tp30) cc_final: 0.7307 (mm-30) REVERT: C 146 ASN cc_start: 0.8383 (t0) cc_final: 0.7988 (t0) REVERT: C 325 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8468 (tt) REVERT: D 331 LYS cc_start: 0.8104 (ptmm) cc_final: 0.7796 (pttp) REVERT: E 27 MET cc_start: 0.7379 (tmm) cc_final: 0.6805 (tmm) REVERT: E 91 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: F 210 ARG cc_start: 0.6852 (tpm170) cc_final: 0.6416 (tpm170) REVERT: F 229 ILE cc_start: 0.8898 (mt) cc_final: 0.8405 (tp) outliers start: 55 outliers final: 41 residues processed: 191 average time/residue: 0.2532 time to fit residues: 75.2162 Evaluate side-chains 183 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain A residue 199 GLU 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 268 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR 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 220 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 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 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 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 F residue 19 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 219 THR 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 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 6 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 64 optimal weight: 0.0040 chunk 88 optimal weight: 0.0570 chunk 147 optimal weight: 0.0000 chunk 84 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 161 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.117836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090548 restraints weight = 34806.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093243 restraints weight = 18872.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095066 restraints weight = 12988.123| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2096 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= 0.100 Angle : 0.597 12.603 20003 Z= 0.278 Chirality : 0.041 0.138 2338 Planarity : 0.004 0.049 2579 Dihedral : 9.800 135.040 2124 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.07 % Allowed : 33.67 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1789 helix: 0.95 (0.20), residues: 747 sheet: -0.64 (0.52), residues: 112 loop : -1.97 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 174 HIS 0.003 0.001 HIS C 214 PHE 0.020 0.001 PHE E 347 TYR 0.017 0.001 TYR D 341 ARG 0.006 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.02619 ( 428) hydrogen bonds : angle 3.67165 ( 1209) covalent geometry : bond 0.00233 (14756) covalent geometry : angle 0.59694 (20003) ********************** 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 195 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6977 (tpp) cc_final: 0.6568 (tpp) REVERT: A 199 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: A 237 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: B 44 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7067 (tmt) REVERT: B 64 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 91 GLN cc_start: 0.8855 (pp30) cc_final: 0.8553 (pm20) REVERT: B 239 ASN cc_start: 0.8516 (t0) cc_final: 0.7961 (m110) REVERT: C 146 ASN cc_start: 0.8380 (t0) cc_final: 0.7989 (t0) REVERT: C 325 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8463 (tt) REVERT: D 331 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7764 (pttp) REVERT: E 27 MET cc_start: 0.7421 (tmm) cc_final: 0.6863 (tmm) REVERT: E 91 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: F 210 ARG cc_start: 0.6959 (tpm170) cc_final: 0.6511 (tpm170) REVERT: F 229 ILE cc_start: 0.8887 (mt) cc_final: 0.8391 (tp) outliers start: 49 outliers final: 38 residues processed: 186 average time/residue: 0.2083 time to fit residues: 62.1090 Evaluate side-chains 184 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 2.057 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain A residue 199 GLU 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 295 VAL Chi-restraints excluded: chain B residue 304 THR 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 220 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 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 209 ASP Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL 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 F residue 19 THR Chi-restraints excluded: chain F residue 219 THR 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 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 95 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.085407 restraints weight = 35441.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087871 restraints weight = 20397.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089493 restraints weight = 14617.991| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14756 Z= 0.179 Angle : 0.671 12.223 20003 Z= 0.317 Chirality : 0.044 0.144 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.065 136.448 2124 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.70 % Allowed : 32.85 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1789 helix: 0.84 (0.20), residues: 749 sheet: -0.99 (0.44), residues: 155 loop : -2.10 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.005 0.001 HIS B 327 PHE 0.017 0.001 PHE F 236 TYR 0.021 0.001 TYR B 341 ARG 0.003 0.000 ARG C 326 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 428) hydrogen bonds : angle 4.15490 ( 1209) covalent geometry : bond 0.00432 (14756) covalent geometry : angle 0.67069 (20003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4592.79 seconds wall clock time: 81 minutes 27.86 seconds (4887.86 seconds total)