Starting phenix.real_space_refine on Fri May 16 17:06:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osg_17152/05_2025/8osg_17152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osg_17152/05_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_17152/05_2025/8osg_17152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osg_17152/05_2025/8osg_17152.map" model { file = "/net/cci-nas-00/data/ceres_data/8osg_17152/05_2025/8osg_17152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osg_17152/05_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-5687/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: 8.70, per 1000 atoms: 0.60 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 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: 1.38 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: 3.64 Time building geometry restraints manager: 3.74 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.090 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.560 ------------------------------------------------------------------------------- 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 : 1.704 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.2337 time to fit residues: 54.2785 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 : 1.546 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086072 restraints weight = 35129.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.088540 restraints weight = 20277.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.090206 restraints weight = 14526.119| |-----------------------------------------------------------------------------| 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 : 11.208 158.888 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 5.19177 ( 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 : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7896 (tmt) cc_final: 0.7625 (tmt) REVERT: C 146 ASN cc_start: 0.8429 (t0) cc_final: 0.8123 (t0) REVERT: D 138 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6787 (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: 0.9202 (tt) REVERT: F 24 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7234 (pp30) REVERT: F 151 TYR cc_start: 0.8274 (t80) cc_final: 0.7802 (t80) REVERT: F 197 ASN cc_start: 0.7521 (t0) cc_final: 0.7308 (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: 0.2172 time to fit residues: 69.1498 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 : 1.578 ------------------------------------------------------------------------------- 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: 9.9990 chunk 150 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS F 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.114595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086773 restraints weight = 35056.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089283 restraints weight = 20025.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090912 restraints weight = 14284.595| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14756 Z= 0.120 Angle : 0.590 12.137 20003 Z= 0.283 Chirality : 0.042 0.158 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.733 154.293 2124 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.33 % Allowed : 31.54 % Favored : 63.13 % 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: -1.11 (0.20), residues: 1789 helix: 0.79 (0.21), residues: 711 sheet: -0.90 (0.48), residues: 135 loop : -2.01 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.004 0.001 HIS C 214 PHE 0.013 0.001 PHE F 16 TYR 0.015 0.001 TYR D 341 ARG 0.004 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 428) hydrogen bonds : angle 4.64930 ( 1209) covalent geometry : bond 0.00281 (14756) covalent geometry : angle 0.58959 (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 223 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 138 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7784 (tmt) cc_final: 0.7281 (tmt) REVERT: C 146 ASN cc_start: 0.8435 (t0) cc_final: 0.8060 (t0) REVERT: D 138 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6828 (pp20) REVERT: D 331 LYS cc_start: 0.8157 (ptmm) cc_final: 0.7809 (pttp) REVERT: E 27 MET cc_start: 0.7346 (tmm) cc_final: 0.6835 (tmm) REVERT: F 44 MET cc_start: 0.8162 (tpp) cc_final: 0.7903 (tpp) REVERT: F 210 ARG cc_start: 0.7064 (tpm170) cc_final: 0.6829 (tpm170) outliers start: 85 outliers final: 48 residues processed: 210 average time/residue: 0.2309 time to fit residues: 77.2971 Evaluate side-chains 184 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 296 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 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 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 138 GLU 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 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 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 294 ILE 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: 8.9990 chunk 46 optimal weight: 0.0050 chunk 124 optimal weight: 4.9990 chunk 22 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 166 optimal weight: 9.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- 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 E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088997 restraints weight = 34354.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091600 restraints weight = 19556.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093305 restraints weight = 13852.762| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1598 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 11.049 20003 Z= 0.269 Chirality : 0.041 0.180 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.310 150.230 2124 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.95 % Allowed : 32.85 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.03 (0.20), residues: 1789 helix: 0.81 (0.21), residues: 718 sheet: -0.78 (0.52), residues: 112 loop : -1.93 (0.19), residues: 959 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 0.018 0.001 TYR D 341 ARG 0.003 0.000 ARG A 189 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 428) hydrogen bonds : angle 4.14976 ( 1209) covalent geometry : bond 0.00226 (14756) covalent geometry : angle 0.56333 (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 208 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7714 (tmt) cc_final: 0.7156 (tmt) REVERT: C 146 ASN cc_start: 0.8376 (t0) cc_final: 0.8010 (t0) REVERT: D 138 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6819 (pp20) REVERT: D 331 LYS cc_start: 0.8125 (ptmm) cc_final: 0.7761 (pttp) REVERT: E 24 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: E 27 MET cc_start: 0.7297 (tmm) cc_final: 0.6725 (tmm) REVERT: F 44 MET cc_start: 0.8124 (tpp) cc_final: 0.7858 (tpp) REVERT: F 197 ASN cc_start: 0.7585 (t0) cc_final: 0.7333 (t0) REVERT: F 210 ARG cc_start: 0.6981 (tpm170) cc_final: 0.6697 (tpm170) REVERT: F 229 ILE cc_start: 0.8914 (mt) cc_final: 0.8418 (tp) REVERT: F 323 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8474 (tt) outliers start: 63 outliers final: 39 residues processed: 193 average time/residue: 0.2082 time to fit residues: 63.4346 Evaluate side-chains 180 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 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 336 SER 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 304 THR Chi-restraints excluded: chain B residue 325 LEU 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 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 219 THR 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: 3.9990 chunk 25 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087615 restraints weight = 35316.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.090167 restraints weight = 20030.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091862 restraints weight = 14143.591| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14756 Z= 0.118 Angle : 0.580 10.740 20003 Z= 0.277 Chirality : 0.042 0.153 2338 Planarity : 0.004 0.050 2579 Dihedral : 10.278 148.114 2124 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.26 % Allowed : 32.54 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.04 (0.20), residues: 1789 helix: 0.86 (0.21), residues: 726 sheet: -0.85 (0.49), residues: 124 loop : -2.02 (0.19), residues: 939 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 0.012 0.001 PHE F 16 TYR 0.015 0.001 TYR D 341 ARG 0.003 0.000 ARG A 189 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 428) hydrogen bonds : angle 4.13492 ( 1209) covalent geometry : bond 0.00284 (14756) covalent geometry : angle 0.58047 (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 204 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 136 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: A 349 ARG cc_start: 0.9018 (mmm160) cc_final: 0.8709 (tpt90) REVERT: B 44 MET cc_start: 0.7764 (tmt) cc_final: 0.7203 (tmt) REVERT: C 146 ASN cc_start: 0.8412 (t0) cc_final: 0.7987 (t0) REVERT: D 138 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6847 (pp20) REVERT: D 331 LYS cc_start: 0.8094 (ptmm) cc_final: 0.7721 (pttp) REVERT: E 27 MET cc_start: 0.7316 (tmm) cc_final: 0.6782 (tmm) REVERT: F 190 PHE cc_start: 0.8822 (p90) cc_final: 0.8575 (p90) REVERT: F 210 ARG cc_start: 0.6927 (tpm170) cc_final: 0.6594 (tpm170) REVERT: F 323 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8531 (tt) outliers start: 68 outliers final: 52 residues processed: 192 average time/residue: 0.2012 time to fit residues: 61.7604 Evaluate side-chains 190 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 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 304 THR Chi-restraints excluded: chain C residue 45 ILE 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 138 GLU 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 184 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: 5.9990 chunk 180 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 104 optimal weight: 0.0980 chunk 152 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087528 restraints weight = 34763.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090088 restraints weight = 19737.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.091776 restraints weight = 13969.980| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14756 Z= 0.115 Angle : 0.577 10.683 20003 Z= 0.275 Chirality : 0.041 0.147 2338 Planarity : 0.004 0.049 2579 Dihedral : 10.200 145.947 2124 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.89 % Allowed : 32.10 % Favored : 63.01 % 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: -1.07 (0.20), residues: 1789 helix: 0.86 (0.21), residues: 732 sheet: -0.82 (0.49), residues: 124 loop : -2.08 (0.19), residues: 933 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 0.014 0.001 PHE E 347 TYR 0.019 0.001 TYR B 341 ARG 0.004 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 428) hydrogen bonds : angle 4.07052 ( 1209) covalent geometry : bond 0.00276 (14756) covalent geometry : angle 0.57737 (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 216 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8428 (mm-30) REVERT: A 237 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: B 44 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7207 (tmt) REVERT: B 64 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 91 GLN cc_start: 0.8849 (pp30) cc_final: 0.8549 (pm20) REVERT: C 146 ASN cc_start: 0.8416 (t0) cc_final: 0.7985 (t0) REVERT: D 138 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: D 331 LYS cc_start: 0.8052 (ptmm) cc_final: 0.7772 (pttp) REVERT: E 27 MET cc_start: 0.7378 (tmm) cc_final: 0.6749 (tmm) REVERT: F 210 ARG cc_start: 0.6985 (tpm170) cc_final: 0.6587 (tpm170) REVERT: F 229 ILE cc_start: 0.8917 (mt) cc_final: 0.8392 (tp) REVERT: F 323 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8526 (tt) outliers start: 78 outliers final: 54 residues processed: 203 average time/residue: 0.2144 time to fit residues: 68.7817 Evaluate side-chains 197 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 137 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 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 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 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 138 GLU 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 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 146 optimal weight: 0.2980 chunk 180 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 142 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 49 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.116648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.088939 restraints weight = 34918.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091491 restraints weight = 19879.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093176 restraints weight = 14032.701| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14756 Z= 0.101 Angle : 0.581 11.724 20003 Z= 0.274 Chirality : 0.041 0.138 2338 Planarity : 0.004 0.050 2579 Dihedral : 10.071 142.964 2124 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.26 % Allowed : 32.41 % 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: -1.00 (0.20), residues: 1789 helix: 0.83 (0.20), residues: 742 sheet: -0.72 (0.52), residues: 112 loop : -1.99 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 174 HIS 0.003 0.001 HIS C 214 PHE 0.017 0.001 PHE F 190 TYR 0.016 0.001 TYR D 341 ARG 0.004 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 428) hydrogen bonds : angle 3.91688 ( 1209) covalent geometry : bond 0.00235 (14756) covalent geometry : angle 0.58067 (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 207 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 139 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: B 44 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7125 (tmt) REVERT: B 64 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8238 (mp) REVERT: C 26 GLU cc_start: 0.7715 (tp30) cc_final: 0.7279 (mm-30) REVERT: C 146 ASN cc_start: 0.8370 (t0) cc_final: 0.7967 (t0) REVERT: D 138 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6796 (pp20) REVERT: D 331 LYS cc_start: 0.8055 (ptmm) cc_final: 0.7727 (pttp) REVERT: E 27 MET cc_start: 0.7358 (tmm) cc_final: 0.6812 (tmm) REVERT: E 91 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: F 210 ARG cc_start: 0.6906 (tpm170) cc_final: 0.6519 (tpm170) REVERT: F 229 ILE cc_start: 0.8908 (mt) cc_final: 0.8434 (tp) outliers start: 68 outliers final: 52 residues processed: 195 average time/residue: 0.2164 time to fit residues: 66.2657 Evaluate side-chains 191 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 134 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 317 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 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 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 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 138 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 147 optimal weight: 0.0070 chunk 7 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 139 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.117422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089889 restraints weight = 34459.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.092490 restraints weight = 19491.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094215 restraints weight = 13648.061| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1960 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= 0.098 Angle : 0.578 11.206 20003 Z= 0.271 Chirality : 0.041 0.169 2338 Planarity : 0.004 0.050 2579 Dihedral : 9.912 138.485 2124 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.70 % Allowed : 31.97 % 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: -0.96 (0.20), residues: 1789 helix: 0.89 (0.20), residues: 746 sheet: -0.71 (0.50), residues: 124 loop : -2.01 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 174 HIS 0.005 0.001 HIS D 186 PHE 0.017 0.001 PHE E 347 TYR 0.021 0.001 TYR B 341 ARG 0.007 0.000 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 428) hydrogen bonds : angle 3.77757 ( 1209) covalent geometry : bond 0.00229 (14756) covalent geometry : angle 0.57776 (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 219 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 144 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: B 44 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7109 (tmt) REVERT: B 64 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8142 (mp) REVERT: B 91 GLN cc_start: 0.8848 (pp30) cc_final: 0.8553 (pm20) REVERT: C 26 GLU cc_start: 0.7626 (tp30) cc_final: 0.7209 (mm-30) REVERT: C 146 ASN cc_start: 0.8358 (t0) cc_final: 0.7957 (t0) REVERT: D 138 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6850 (pp20) REVERT: D 331 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7763 (pttp) REVERT: E 27 MET cc_start: 0.7374 (tmm) cc_final: 0.6864 (tmm) REVERT: E 217 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8309 (tp) REVERT: F 210 ARG cc_start: 0.6995 (tpm170) cc_final: 0.6569 (tpm170) outliers start: 75 outliers final: 56 residues processed: 207 average time/residue: 0.2108 time to fit residues: 68.4753 Evaluate side-chains 194 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 133 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 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 183 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 165 VAL 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 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain 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 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 43 VAL 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 317 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 170 optimal weight: 0.5980 chunk 49 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.117600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.090041 restraints weight = 34677.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092644 restraints weight = 19529.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094376 restraints weight = 13698.781| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2040 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 : 0.600 11.914 20003 Z= 0.281 Chirality : 0.041 0.131 2338 Planarity : 0.004 0.049 2579 Dihedral : 9.840 135.907 2124 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.76 % Allowed : 32.66 % 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: -0.92 (0.20), residues: 1789 helix: 0.91 (0.20), residues: 746 sheet: -0.66 (0.50), residues: 124 loop : -1.99 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 174 HIS 0.003 0.001 HIS A 161 PHE 0.018 0.001 PHE F 190 TYR 0.017 0.001 TYR D 341 ARG 0.003 0.000 ARG E 90 Details of bonding type rmsd hydrogen bonds : bond 0.02720 ( 428) hydrogen bonds : angle 3.75690 ( 1209) covalent geometry : bond 0.00234 (14756) covalent geometry : angle 0.59972 (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: 60 poor density : 140 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: A 237 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: B 44 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7117 (tmt) REVERT: B 64 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 91 GLN cc_start: 0.8844 (pp30) cc_final: 0.8547 (pm20) REVERT: B 239 ASN cc_start: 0.8527 (t0) cc_final: 0.7940 (m110) REVERT: C 146 ASN cc_start: 0.8373 (t0) cc_final: 0.7976 (t0) REVERT: D 138 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6876 (pp20) REVERT: D 331 LYS cc_start: 0.8072 (ptmm) cc_final: 0.7756 (pttp) REVERT: E 27 MET cc_start: 0.7371 (tmm) cc_final: 0.6820 (tmm) REVERT: F 210 ARG cc_start: 0.6949 (tpm170) cc_final: 0.6560 (tpm170) outliers start: 60 outliers final: 50 residues processed: 189 average time/residue: 0.2051 time to fit residues: 62.5425 Evaluate side-chains 189 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 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 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 116 THR 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 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain 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 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 317 ILE Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 6 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 0.0270 chunk 147 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.9244 ------------------------------------------------------------------------------- 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** E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.117043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089434 restraints weight = 34922.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092054 restraints weight = 19672.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093756 restraints weight = 13821.106| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14756 Z= 0.106 Angle : 0.605 12.744 20003 Z= 0.282 Chirality : 0.041 0.132 2338 Planarity : 0.004 0.049 2579 Dihedral : 9.803 133.473 2124 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.82 % Allowed : 32.66 % 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: -0.89 (0.20), residues: 1789 helix: 0.96 (0.21), residues: 746 sheet: -0.64 (0.50), residues: 124 loop : -2.00 (0.19), residues: 919 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 0.018 0.001 PHE E 347 TYR 0.017 0.001 TYR D 341 ARG 0.002 0.000 ARG A 189 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 428) hydrogen bonds : angle 3.78156 ( 1209) covalent geometry : bond 0.00253 (14756) covalent geometry : angle 0.60506 (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: 61 poor density : 134 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7052 (tpp) cc_final: 0.6686 (tpp) REVERT: A 199 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8321 (mm-30) REVERT: A 237 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: B 44 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7150 (tmt) REVERT: B 64 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8161 (mp) REVERT: B 91 GLN cc_start: 0.8841 (pp30) cc_final: 0.8540 (pm20) REVERT: B 239 ASN cc_start: 0.8531 (t0) cc_final: 0.7964 (m110) REVERT: C 146 ASN cc_start: 0.8397 (t0) cc_final: 0.7988 (t0) REVERT: C 325 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8521 (tt) REVERT: D 138 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6875 (pp20) REVERT: D 331 LYS cc_start: 0.8187 (ptmm) cc_final: 0.7866 (pttp) REVERT: E 27 MET cc_start: 0.7387 (tmm) cc_final: 0.6863 (tmm) REVERT: F 190 PHE cc_start: 0.8793 (p90) cc_final: 0.8576 (p90) REVERT: F 210 ARG cc_start: 0.6953 (tpm170) cc_final: 0.6532 (tpm170) outliers start: 61 outliers final: 53 residues processed: 185 average time/residue: 0.2002 time to fit residues: 60.2439 Evaluate side-chains 191 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 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 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL 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 329 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 138 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain 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 F residue 19 THR 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 317 ILE Chi-restraints excluded: chain F residue 322 THR 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: 0.9990 chunk 162 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 160 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.117086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.089434 restraints weight = 34758.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092042 restraints weight = 19667.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.093767 restraints weight = 13848.403| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14756 Z= 0.105 Angle : 0.605 12.426 20003 Z= 0.283 Chirality : 0.041 0.130 2338 Planarity : 0.004 0.049 2579 Dihedral : 9.760 131.485 2124 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.08 % Allowed : 32.41 % 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: -0.88 (0.20), residues: 1789 helix: 0.94 (0.20), residues: 750 sheet: -0.60 (0.50), residues: 123 loop : -1.98 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 174 HIS 0.004 0.001 HIS C 214 PHE 0.018 0.001 PHE F 236 TYR 0.017 0.001 TYR D 341 ARG 0.003 0.000 ARG C 326 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 428) hydrogen bonds : angle 3.73627 ( 1209) covalent geometry : bond 0.00251 (14756) covalent geometry : angle 0.60530 (20003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4031.26 seconds wall clock time: 71 minutes 21.07 seconds (4281.07 seconds total)