Starting phenix.real_space_refine on Sat Jan 25 17:00:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c87_45299/01_2025/9c87_45299_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c87_45299/01_2025/9c87_45299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c87_45299/01_2025/9c87_45299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c87_45299/01_2025/9c87_45299.map" model { file = "/net/cci-nas-00/data/ceres_data/9c87_45299/01_2025/9c87_45299_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c87_45299/01_2025/9c87_45299_trim.cif" } resolution = 3.7 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: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 4 5.21 5 S 204 5.16 5 C 24211 2.51 5 N 6597 2.21 5 O 7405 1.98 5 H 38668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 77104 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 5451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5451 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "B" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "C" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "D" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "E" Number of atoms: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5286 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 1 Chain: "F" Number of atoms: 5010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5010 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 9, 'TRANS': 312} Chain breaks: 2 Chain: "S" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2599 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 10, 'TRANS': 156} Chain: "h" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "i" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "j" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "k" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "l" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "m" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "n" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "p" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "q" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "r" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "s" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "t" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "u" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "v" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MTX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.13, per 1000 atoms: 0.35 Number of scatterers: 77104 At special positions: 0 Unit cell: (146.353, 139.65, 203.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 204 16.00 P 15 15.00 Mg 4 11.99 O 7405 8.00 N 6597 7.00 C 24211 6.00 H 38668 1.00 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: 14.84 Conformation dependent library (CDL) restraints added in 4.9 seconds 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX S 201 " Number of C-beta restraints generated: 9058 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 67 sheets defined 49.9% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.504A pdb=" N HIS A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 100 Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.718A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 158 through 170 removed outlier: 4.320A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.845A pdb=" N ILE A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 190 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 removed outlier: 3.593A pdb=" N GLN A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.530A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.646A pdb=" N GLN A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.816A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.524A pdb=" N ILE A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.770A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.552A pdb=" N ASP A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 387 removed outlier: 4.298A pdb=" N ARG A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N THR A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.712A pdb=" N ILE A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 4.158A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 removed outlier: 3.690A pdb=" N LYS B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.566A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 removed outlier: 4.285A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.501A pdb=" N ARG B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.660A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.856A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.764A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.509A pdb=" N ILE B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.963A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.619A pdb=" N ALA B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.090A pdb=" N ARG B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.589A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.514A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.511A pdb=" N GLN C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.642A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.905A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.642A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.532A pdb=" N GLN C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 removed outlier: 3.563A pdb=" N ASN C 342 " --> pdb=" O GLN C 338 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.829A pdb=" N ALA C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 387 removed outlier: 4.343A pdb=" N ARG C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP C 382 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.723A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.511A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.875A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.557A pdb=" N LYS D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.592A pdb=" N ALA D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.521A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 291 through 297 removed outlier: 3.737A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.646A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.562A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 removed outlier: 4.123A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 removed outlier: 3.556A pdb=" N ASP D 356 " --> pdb=" O ASP D 352 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 387 removed outlier: 3.806A pdb=" N LEU D 372 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP D 382 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N THR D 383 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.717A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.798A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 98 removed outlier: 3.962A pdb=" N VAL E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 136 removed outlier: 3.774A pdb=" N LEU E 136 " --> pdb=" O LEU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 158 through 169 removed outlier: 4.243A pdb=" N ILE E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.524A pdb=" N LEU E 211 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.556A pdb=" N ARG E 261 " --> pdb=" O VAL E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 289 removed outlier: 4.341A pdb=" N GLU E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.537A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.560A pdb=" N LEU E 308 " --> pdb=" O PHE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'E' and resid 332 through 344 removed outlier: 3.671A pdb=" N GLU E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 removed outlier: 3.558A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 387 removed outlier: 4.608A pdb=" N ASP E 382 " --> pdb=" O ALA E 378 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR E 383 " --> pdb=" O ALA E 379 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 399 through 404 removed outlier: 4.211A pdb=" N ILE E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 399 through 404' Processing helix chain 'F' and resid 66 through 78 Processing helix chain 'F' and resid 81 through 101 removed outlier: 3.602A pdb=" N TYR F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 98 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 136 removed outlier: 3.558A pdb=" N ARG F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.751A pdb=" N ILE F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 179 removed outlier: 3.951A pdb=" N ARG F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.506A pdb=" N GLN F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 212 " --> pdb=" O GLN F 208 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 Processing helix chain 'F' and resid 283 through 289 removed outlier: 3.712A pdb=" N LEU F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 298 Processing helix chain 'F' and resid 301 through 307 Processing helix chain 'F' and resid 318 through 328 removed outlier: 3.568A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 344 removed outlier: 3.754A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 removed outlier: 3.713A pdb=" N ASP F 356 " --> pdb=" O ASP F 352 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 removed outlier: 3.991A pdb=" N ARG F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA F 379 " --> pdb=" O ILE F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 399 through 404 removed outlier: 3.544A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 34 Processing helix chain 'S' and resid 43 through 51 Processing helix chain 'S' and resid 77 through 86 removed outlier: 3.714A pdb=" N CYS S 85 " --> pdb=" O ALA S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 103 Processing helix chain 'S' and resid 104 through 107 Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.957A pdb=" N GLU h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 54 Processing helix chain 'h' and resid 69 through 83 removed outlier: 3.648A pdb=" N ILE h 76 " --> pdb=" O ALA h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 105 Processing helix chain 'h' and resid 132 through 158 Processing helix chain 'h' and resid 160 through 168 Processing helix chain 'h' and resid 175 through 183 removed outlier: 3.655A pdb=" N GLU h 181 " --> pdb=" O PRO h 177 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 25 removed outlier: 3.726A pdb=" N LYS i 25 " --> pdb=" O SER i 21 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 54 removed outlier: 3.698A pdb=" N LEU i 42 " --> pdb=" O HIS i 38 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 83 removed outlier: 3.689A pdb=" N GLY i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER i 75 " --> pdb=" O THR i 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE i 76 " --> pdb=" O ALA i 72 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR i 79 " --> pdb=" O SER i 75 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 104 Processing helix chain 'i' and resid 132 through 158 Processing helix chain 'i' and resid 160 through 169 Processing helix chain 'i' and resid 175 through 183 removed outlier: 3.630A pdb=" N GLU i 181 " --> pdb=" O PRO i 177 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR i 182 " --> pdb=" O GLU i 178 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 25 removed outlier: 3.580A pdb=" N LEU j 23 " --> pdb=" O ILE j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 54 Processing helix chain 'j' and resid 69 through 83 removed outlier: 4.019A pdb=" N ILE j 76 " --> pdb=" O ALA j 72 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR j 77 " --> pdb=" O GLY j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 105 removed outlier: 3.511A pdb=" N ALA j 105 " --> pdb=" O PHE j 101 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 158 Processing helix chain 'j' and resid 160 through 169 Processing helix chain 'j' and resid 176 through 183 removed outlier: 3.778A pdb=" N GLU j 181 " --> pdb=" O PRO j 177 " (cutoff:3.500A) Processing helix chain 'k' and resid 19 through 26 removed outlier: 3.650A pdb=" N GLU k 26 " --> pdb=" O ARG k 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 36 through 54 removed outlier: 3.556A pdb=" N GLU k 53 " --> pdb=" O PHE k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 83 removed outlier: 3.758A pdb=" N GLY k 73 " --> pdb=" O VAL k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 105 Processing helix chain 'k' and resid 132 through 158 Processing helix chain 'k' and resid 160 through 168 Processing helix chain 'k' and resid 175 through 183 Processing helix chain 'l' and resid 19 through 25 removed outlier: 3.545A pdb=" N LYS l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 54 removed outlier: 3.647A pdb=" N ALA l 52 " --> pdb=" O LEU l 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU l 53 " --> pdb=" O PHE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 69 through 83 removed outlier: 3.664A pdb=" N ILE l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 96 through 105 Processing helix chain 'l' and resid 132 through 158 Processing helix chain 'l' and resid 160 through 168 Processing helix chain 'l' and resid 175 through 183 removed outlier: 3.774A pdb=" N GLU l 181 " --> pdb=" O PRO l 177 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 26 removed outlier: 3.758A pdb=" N GLU m 26 " --> pdb=" O ARG m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 54 Processing helix chain 'm' and resid 69 through 83 removed outlier: 3.682A pdb=" N SER m 75 " --> pdb=" O THR m 71 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE m 76 " --> pdb=" O ALA m 72 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR m 77 " --> pdb=" O GLY m 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP m 78 " --> pdb=" O MET m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 105 removed outlier: 3.544A pdb=" N ALA m 105 " --> pdb=" O PHE m 101 " (cutoff:3.500A) Processing helix chain 'm' and resid 132 through 158 Processing helix chain 'm' and resid 160 through 169 Processing helix chain 'm' and resid 176 through 183 removed outlier: 3.508A pdb=" N VAL m 180 " --> pdb=" O ALA m 176 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU m 181 " --> pdb=" O PRO m 177 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR m 182 " --> pdb=" O GLU m 178 " (cutoff:3.500A) Processing helix chain 'n' and resid 19 through 25 removed outlier: 3.665A pdb=" N LYS n 25 " --> pdb=" O SER n 21 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 54 Processing helix chain 'n' and resid 70 through 83 removed outlier: 3.512A pdb=" N SER n 75 " --> pdb=" O THR n 71 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) Processing helix chain 'n' and resid 96 through 102 Processing helix chain 'n' and resid 132 through 158 Processing helix chain 'n' and resid 160 through 169 Processing helix chain 'n' and resid 176 through 183 removed outlier: 3.616A pdb=" N GLU n 181 " --> pdb=" O PRO n 177 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 25 removed outlier: 3.657A pdb=" N LYS p 25 " --> pdb=" O SER p 21 " (cutoff:3.500A) Processing helix chain 'p' and resid 36 through 54 removed outlier: 3.639A pdb=" N LEU p 42 " --> pdb=" O HIS p 38 " (cutoff:3.500A) Processing helix chain 'p' and resid 69 through 81 removed outlier: 3.762A pdb=" N ILE p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 105 Processing helix chain 'p' and resid 132 through 158 Processing helix chain 'p' and resid 160 through 169 Processing helix chain 'p' and resid 175 through 183 removed outlier: 3.536A pdb=" N VAL p 180 " --> pdb=" O ALA p 176 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU p 181 " --> pdb=" O PRO p 177 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 26 removed outlier: 3.780A pdb=" N LEU q 23 " --> pdb=" O ILE q 19 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU q 26 " --> pdb=" O ARG q 22 " (cutoff:3.500A) Processing helix chain 'q' and resid 36 through 54 removed outlier: 3.670A pdb=" N LEU q 42 " --> pdb=" O HIS q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 83 removed outlier: 3.902A pdb=" N ILE q 76 " --> pdb=" O ALA q 72 " (cutoff:3.500A) Processing helix chain 'q' and resid 96 through 105 Processing helix chain 'q' and resid 132 through 158 Processing helix chain 'q' and resid 160 through 169 Processing helix chain 'q' and resid 176 through 183 removed outlier: 3.548A pdb=" N VAL q 180 " --> pdb=" O ALA q 176 " (cutoff:3.500A) Processing helix chain 'r' and resid 18 through 25 Processing helix chain 'r' and resid 36 through 54 removed outlier: 3.542A pdb=" N LEU r 42 " --> pdb=" O HIS r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 69 through 83 removed outlier: 3.795A pdb=" N ILE r 76 " --> pdb=" O ALA r 72 " (cutoff:3.500A) Processing helix chain 'r' and resid 96 through 105 Processing helix chain 'r' and resid 132 through 158 Processing helix chain 'r' and resid 160 through 169 Processing helix chain 'r' and resid 176 through 182 Processing helix chain 's' and resid 19 through 26 removed outlier: 3.687A pdb=" N GLU s 26 " --> pdb=" O ARG s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 36 through 54 removed outlier: 3.551A pdb=" N LEU s 42 " --> pdb=" O HIS s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 83 removed outlier: 3.634A pdb=" N GLY s 73 " --> pdb=" O VAL s 69 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE s 76 " --> pdb=" O ALA s 72 " (cutoff:3.500A) Processing helix chain 's' and resid 96 through 105 removed outlier: 3.826A pdb=" N ALA s 105 " --> pdb=" O PHE s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 132 through 158 Processing helix chain 's' and resid 160 through 168 Processing helix chain 's' and resid 176 through 182 Processing helix chain 't' and resid 19 through 26 removed outlier: 3.763A pdb=" N GLU t 26 " --> pdb=" O ARG t 22 " (cutoff:3.500A) Processing helix chain 't' and resid 36 through 54 removed outlier: 3.694A pdb=" N LEU t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE t 43 " --> pdb=" O MET t 39 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 83 removed outlier: 3.745A pdb=" N ILE t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN t 81 " --> pdb=" O TYR t 77 " (cutoff:3.500A) Processing helix chain 't' and resid 96 through 105 Processing helix chain 't' and resid 132 through 158 Processing helix chain 't' and resid 160 through 168 Processing helix chain 't' and resid 176 through 182 Processing helix chain 'u' and resid 19 through 26 removed outlier: 3.523A pdb=" N LEU u 23 " --> pdb=" O ILE u 19 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS u 25 " --> pdb=" O SER u 21 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU u 26 " --> pdb=" O ARG u 22 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 54 removed outlier: 3.776A pdb=" N ALA u 52 " --> pdb=" O LEU u 48 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU u 53 " --> pdb=" O PHE u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 69 through 83 removed outlier: 3.720A pdb=" N GLY u 73 " --> pdb=" O VAL u 69 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER u 75 " --> pdb=" O THR u 71 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR u 79 " --> pdb=" O SER u 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 96 through 105 Processing helix chain 'u' and resid 132 through 158 removed outlier: 3.515A pdb=" N ILE u 137 " --> pdb=" O THR u 133 " (cutoff:3.500A) Processing helix chain 'u' and resid 160 through 170 removed outlier: 4.054A pdb=" N ARG u 170 " --> pdb=" O ARG u 166 " (cutoff:3.500A) Processing helix chain 'u' and resid 176 through 182 removed outlier: 3.525A pdb=" N VAL u 180 " --> pdb=" O ALA u 176 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU u 181 " --> pdb=" O PRO u 177 " (cutoff:3.500A) Processing helix chain 'v' and resid 19 through 26 removed outlier: 3.572A pdb=" N GLU v 26 " --> pdb=" O ARG v 22 " (cutoff:3.500A) Processing helix chain 'v' and resid 36 through 54 removed outlier: 3.542A pdb=" N GLU v 53 " --> pdb=" O PHE v 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 69 through 83 removed outlier: 3.513A pdb=" N GLY v 73 " --> pdb=" O VAL v 69 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE v 76 " --> pdb=" O ALA v 72 " (cutoff:3.500A) Processing helix chain 'v' and resid 96 through 104 Processing helix chain 'v' and resid 132 through 158 removed outlier: 3.549A pdb=" N ILE v 137 " --> pdb=" O THR v 133 " (cutoff:3.500A) Processing helix chain 'v' and resid 160 through 169 Processing helix chain 'v' and resid 176 through 182 removed outlier: 3.883A pdb=" N VAL v 180 " --> pdb=" O ALA v 176 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU v 181 " --> pdb=" O PRO v 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 144 removed outlier: 6.690A pdb=" N THR A 141 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP A 184 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 143 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 181 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY A 248 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 183 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.597A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 397 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 410 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.306A pdb=" N VAL B 181 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLY B 248 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 183 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 117 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.754A pdb=" N VAL B 238 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 236 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.561A pdb=" N ILE B 398 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 397 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 410 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.987A pdb=" N THR C 141 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASP C 184 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA C 143 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 249 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 219 through 221 removed outlier: 3.848A pdb=" N ALA C 220 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 238 " --> pdb=" O ALA C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 347 through 350 removed outlier: 6.290A pdb=" N ASP C 347 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE C 398 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLU C 349 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 395 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL C 397 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 410 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 140 through 144 removed outlier: 6.875A pdb=" N THR D 141 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP D 184 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA D 143 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU D 116 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 219 through 221 removed outlier: 3.701A pdb=" N VAL D 238 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 347 through 350 removed outlier: 6.436A pdb=" N ASP D 347 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE D 398 " --> pdb=" O ASP D 347 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU D 349 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU D 410 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.563A pdb=" N THR E 141 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL E 181 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY E 248 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE E 115 " --> pdb=" O CYS E 247 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY E 249 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 117 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU E 116 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 349 through 350 removed outlier: 6.996A pdb=" N GLU E 349 " --> pdb=" O ILE E 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 117 through 118 Processing sheet with id=AB6, first strand: chain 'F' and resid 141 through 144 removed outlier: 6.592A pdb=" N THR F 141 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP F 184 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA F 143 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 246 " --> pdb=" O VAL F 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 347 through 349 removed outlier: 7.640A pdb=" N ASP F 347 " --> pdb=" O VAL F 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 60 through 62 Processing sheet with id=AB9, first strand: chain 'S' and resid 134 through 138 removed outlier: 6.931A pdb=" N ILE S 155 " --> pdb=" O VAL S 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 5 through 9 removed outlier: 4.078A pdb=" N ARG h 15 " --> pdb=" O GLU h 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.313A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER h 65 " --> pdb=" O GLN h 94 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE h 112 " --> pdb=" O VAL h 87 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR h 89 " --> pdb=" O PHE h 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.313A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER h 65 " --> pdb=" O GLN h 94 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG h 118 " --> pdb=" O CYS h 91 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY h 93 " --> pdb=" O ARG h 118 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N MET h 120 " --> pdb=" O GLY h 93 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA h 95 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'h' and resid 125 through 131 removed outlier: 3.660A pdb=" N TYR h 128 " --> pdb=" O TYR p 128 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR p 128 " --> pdb=" O TYR h 128 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'i' and resid 5 through 10 removed outlier: 3.509A pdb=" N ARG i 15 " --> pdb=" O GLU i 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.622A pdb=" N ILE i 29 " --> pdb=" O TYR i 62 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASN i 64 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU i 31 " --> pdb=" O ASN i 64 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG i 118 " --> pdb=" O CYS i 91 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLY i 93 " --> pdb=" O ARG i 118 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N MET i 120 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA i 95 " --> pdb=" O MET i 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.622A pdb=" N ILE i 29 " --> pdb=" O TYR i 62 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASN i 64 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU i 31 " --> pdb=" O ASN i 64 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE i 112 " --> pdb=" O VAL i 87 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR i 89 " --> pdb=" O PHE i 112 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER i 187 " --> pdb=" O ARG i 111 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS i 113 " --> pdb=" O SER i 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'i' and resid 125 through 131 removed outlier: 4.061A pdb=" N TYR i 128 " --> pdb=" O TYR q 128 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR q 128 " --> pdb=" O TYR i 128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY i 130 " --> pdb=" O GLY q 126 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY q 126 " --> pdb=" O GLY i 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'j' and resid 5 through 7 Processing sheet with id=AD1, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.513A pdb=" N ILE j 29 " --> pdb=" O TYR j 62 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN j 64 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU j 31 " --> pdb=" O ASN j 64 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE j 59 " --> pdb=" O SER j 88 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE j 90 " --> pdb=" O ILE j 59 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU j 61 " --> pdb=" O ILE j 90 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET j 92 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE j 63 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN j 94 " --> pdb=" O ILE j 63 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG j 118 " --> pdb=" O CYS j 91 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLY j 93 " --> pdb=" O ARG j 118 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET j 120 " --> pdb=" O GLY j 93 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA j 95 " --> pdb=" O MET j 120 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.513A pdb=" N ILE j 29 " --> pdb=" O TYR j 62 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN j 64 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU j 31 " --> pdb=" O ASN j 64 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE j 59 " --> pdb=" O SER j 88 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE j 90 " --> pdb=" O ILE j 59 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU j 61 " --> pdb=" O ILE j 90 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET j 92 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE j 63 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN j 94 " --> pdb=" O ILE j 63 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N PHE j 112 " --> pdb=" O VAL j 87 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR j 89 " --> pdb=" O PHE j 112 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS j 113 " --> pdb=" O SER j 187 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'j' and resid 125 through 131 removed outlier: 3.627A pdb=" N TYR r 128 " --> pdb=" O TYR j 128 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY j 130 " --> pdb=" O GLY r 126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'k' and resid 5 through 9 Processing sheet with id=AD5, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.163A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N PHE k 112 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR k 89 " --> pdb=" O PHE k 112 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.163A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG k 118 " --> pdb=" O CYS k 91 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLY k 93 " --> pdb=" O ARG k 118 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N MET k 120 " --> pdb=" O GLY k 93 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA k 95 " --> pdb=" O MET k 120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 125 through 131 removed outlier: 3.790A pdb=" N TYR k 128 " --> pdb=" O TYR s 128 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR s 128 " --> pdb=" O TYR k 128 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'l' and resid 5 through 8 removed outlier: 4.147A pdb=" N ARG l 15 " --> pdb=" O GLU l 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.744A pdb=" N ILE l 29 " --> pdb=" O TYR l 62 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASN l 64 " --> pdb=" O ILE l 29 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU l 31 " --> pdb=" O ASN l 64 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG l 118 " --> pdb=" O CYS l 91 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY l 93 " --> pdb=" O ARG l 118 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N MET l 120 " --> pdb=" O GLY l 93 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA l 95 " --> pdb=" O MET l 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL l 119 " --> pdb=" O LEU l 174 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.744A pdb=" N ILE l 29 " --> pdb=" O TYR l 62 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASN l 64 " --> pdb=" O ILE l 29 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU l 31 " --> pdb=" O ASN l 64 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N PHE l 112 " --> pdb=" O VAL l 87 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR l 89 " --> pdb=" O PHE l 112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS l 113 " --> pdb=" O SER l 187 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'l' and resid 125 through 131 removed outlier: 3.806A pdb=" N TYR l 128 " --> pdb=" O TYR t 128 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR t 128 " --> pdb=" O TYR l 128 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'm' and resid 5 through 9 Processing sheet with id=AE4, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.100A pdb=" N ILE m 59 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE m 90 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU m 61 " --> pdb=" O ILE m 90 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET m 92 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE m 63 " --> pdb=" O MET m 92 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN m 94 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER m 65 " --> pdb=" O GLN m 94 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.100A pdb=" N ILE m 59 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE m 90 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU m 61 " --> pdb=" O ILE m 90 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET m 92 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE m 63 " --> pdb=" O MET m 92 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN m 94 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER m 65 " --> pdb=" O GLN m 94 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG m 118 " --> pdb=" O CYS m 91 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLY m 93 " --> pdb=" O ARG m 118 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET m 120 " --> pdb=" O GLY m 93 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA m 95 " --> pdb=" O MET m 120 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'm' and resid 125 through 126 removed outlier: 3.528A pdb=" N GLY m 126 " --> pdb=" O GLY u 130 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY u 130 " --> pdb=" O GLY m 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'm' and resid 130 through 131 removed outlier: 3.626A pdb=" N GLY m 130 " --> pdb=" O GLY u 126 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY u 126 " --> pdb=" O GLY m 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'n' and resid 5 through 10 Processing sheet with id=AE9, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.053A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE n 112 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR n 89 " --> pdb=" O PHE n 112 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'n' and resid 94 through 95 removed outlier: 6.123A pdb=" N ALA n 95 " --> pdb=" O MET n 120 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'n' and resid 125 through 131 removed outlier: 3.756A pdb=" N TYR n 128 " --> pdb=" O TYR v 128 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR v 128 " --> pdb=" O TYR n 128 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'p' and resid 5 through 6 removed outlier: 3.861A pdb=" N PHE p 17 " --> pdb=" O VAL p 6 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'p' and resid 28 through 29 removed outlier: 6.257A pdb=" N ILE p 59 " --> pdb=" O SER p 88 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE p 90 " --> pdb=" O ILE p 59 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU p 61 " --> pdb=" O ILE p 90 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET p 92 " --> pdb=" O LEU p 61 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE p 63 " --> pdb=" O MET p 92 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN p 94 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER p 65 " --> pdb=" O GLN p 94 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG p 118 " --> pdb=" O CYS p 91 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY p 93 " --> pdb=" O ARG p 118 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N MET p 120 " --> pdb=" O GLY p 93 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA p 95 " --> pdb=" O MET p 120 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE p 121 " --> pdb=" O ARG p 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG p 172 " --> pdb=" O ILE p 121 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'p' and resid 28 through 29 removed outlier: 6.257A pdb=" N ILE p 59 " --> pdb=" O SER p 88 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE p 90 " --> pdb=" O ILE p 59 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU p 61 " --> pdb=" O ILE p 90 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET p 92 " --> pdb=" O LEU p 61 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE p 63 " --> pdb=" O MET p 92 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLN p 94 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER p 65 " --> pdb=" O GLN p 94 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE p 112 " --> pdb=" O VAL p 87 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR p 89 " --> pdb=" O PHE p 112 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS p 113 " --> pdb=" O SER p 187 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'q' and resid 5 through 6 removed outlier: 3.644A pdb=" N PHE q 17 " --> pdb=" O VAL q 6 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'q' and resid 28 through 32 removed outlier: 6.054A pdb=" N ILE q 59 " --> pdb=" O SER q 88 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE q 90 " --> pdb=" O ILE q 59 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU q 61 " --> pdb=" O ILE q 90 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET q 92 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE q 63 " --> pdb=" O MET q 92 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLN q 94 " --> pdb=" O ILE q 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER q 65 " --> pdb=" O GLN q 94 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG q 118 " --> pdb=" O CYS q 91 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY q 93 " --> pdb=" O ARG q 118 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N MET q 120 " --> pdb=" O GLY q 93 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA q 95 " --> pdb=" O MET q 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'q' and resid 28 through 32 removed outlier: 6.054A pdb=" N ILE q 59 " --> pdb=" O SER q 88 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE q 90 " --> pdb=" O ILE q 59 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU q 61 " --> pdb=" O ILE q 90 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET q 92 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE q 63 " --> pdb=" O MET q 92 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLN q 94 " --> pdb=" O ILE q 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER q 65 " --> pdb=" O GLN q 94 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N PHE q 112 " --> pdb=" O VAL q 87 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR q 89 " --> pdb=" O PHE q 112 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER q 187 " --> pdb=" O ARG q 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS q 113 " --> pdb=" O SER q 187 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'r' and resid 28 through 32 removed outlier: 6.461A pdb=" N ILE r 29 " --> pdb=" O TYR r 62 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASN r 64 " --> pdb=" O ILE r 29 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU r 31 " --> pdb=" O ASN r 64 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR r 89 " --> pdb=" O PHE r 112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER r 187 " --> pdb=" O ARG r 111 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'r' and resid 118 through 121 removed outlier: 3.669A pdb=" N ILE r 121 " --> pdb=" O ARG r 172 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 's' and resid 5 through 9 removed outlier: 3.550A pdb=" N GLU s 8 " --> pdb=" O ARG s 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG s 15 " --> pdb=" O GLU s 8 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 's' and resid 28 through 32 removed outlier: 6.606A pdb=" N ILE s 29 " --> pdb=" O TYR s 62 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN s 64 " --> pdb=" O ILE s 29 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU s 31 " --> pdb=" O ASN s 64 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE s 59 " --> pdb=" O SER s 88 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE s 90 " --> pdb=" O ILE s 59 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU s 61 " --> pdb=" O ILE s 90 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N MET s 92 " --> pdb=" O LEU s 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE s 63 " --> pdb=" O MET s 92 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN s 94 " --> pdb=" O ILE s 63 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER s 65 " --> pdb=" O GLN s 94 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG s 118 " --> pdb=" O CYS s 91 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY s 93 " --> pdb=" O ARG s 118 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N MET s 120 " --> pdb=" O GLY s 93 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA s 95 " --> pdb=" O MET s 120 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 's' and resid 28 through 32 removed outlier: 6.606A pdb=" N ILE s 29 " --> pdb=" O TYR s 62 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN s 64 " --> pdb=" O ILE s 29 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU s 31 " --> pdb=" O ASN s 64 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE s 59 " --> pdb=" O SER s 88 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE s 90 " --> pdb=" O ILE s 59 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU s 61 " --> pdb=" O ILE s 90 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N MET s 92 " --> pdb=" O LEU s 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE s 63 " --> pdb=" O MET s 92 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN s 94 " --> pdb=" O ILE s 63 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER s 65 " --> pdb=" O GLN s 94 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N PHE s 112 " --> pdb=" O VAL s 87 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR s 89 " --> pdb=" O PHE s 112 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS s 113 " --> pdb=" O SER s 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 't' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 't' and resid 28 through 31 removed outlier: 6.689A pdb=" N ILE t 29 " --> pdb=" O TYR t 62 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASN t 64 " --> pdb=" O ILE t 29 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU t 31 " --> pdb=" O ASN t 64 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER t 65 " --> pdb=" O MET t 92 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN t 94 " --> pdb=" O SER t 65 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ARG t 118 " --> pdb=" O CYS t 91 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY t 93 " --> pdb=" O ARG t 118 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N MET t 120 " --> pdb=" O GLY t 93 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA t 95 " --> pdb=" O MET t 120 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 't' and resid 28 through 31 removed outlier: 6.689A pdb=" N ILE t 29 " --> pdb=" O TYR t 62 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASN t 64 " --> pdb=" O ILE t 29 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU t 31 " --> pdb=" O ASN t 64 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER t 65 " --> pdb=" O MET t 92 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN t 94 " --> pdb=" O SER t 65 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N PHE t 112 " --> pdb=" O VAL t 87 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR t 89 " --> pdb=" O PHE t 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER t 187 " --> pdb=" O ARG t 111 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'u' and resid 5 through 9 removed outlier: 3.573A pdb=" N ARG u 15 " --> pdb=" O GLU u 8 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'u' and resid 28 through 32 removed outlier: 6.451A pdb=" N THR u 89 " --> pdb=" O PHE u 112 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER u 187 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS u 113 " --> pdb=" O SER u 187 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'u' and resid 94 through 95 removed outlier: 3.538A pdb=" N ARG u 172 " --> pdb=" O ILE u 121 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'v' and resid 5 through 7 Processing sheet with id=AH3, first strand: chain 'v' and resid 28 through 32 removed outlier: 5.346A pdb=" N SER v 65 " --> pdb=" O MET v 92 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLN v 94 " --> pdb=" O SER v 65 " (cutoff:3.500A) removed outlier: 12.208A pdb=" N VAL v 87 " --> pdb=" O PHE v 112 " (cutoff:3.500A) removed outlier: 14.155A pdb=" N LEU v 114 " --> pdb=" O VAL v 87 " (cutoff:3.500A) removed outlier: 12.865A pdb=" N THR v 89 " --> pdb=" O LEU v 114 " (cutoff:3.500A) removed outlier: 13.135A pdb=" N ASN v 116 " --> pdb=" O THR v 89 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N CYS v 91 " --> pdb=" O ASN v 116 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG v 118 " --> pdb=" O CYS v 91 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY v 93 " --> pdb=" O ARG v 118 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N MET v 120 " --> pdb=" O GLY v 93 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA v 95 " --> pdb=" O MET v 120 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'v' and resid 28 through 32 removed outlier: 5.346A pdb=" N SER v 65 " --> pdb=" O MET v 92 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLN v 94 " --> pdb=" O SER v 65 " (cutoff:3.500A) removed outlier: 12.208A pdb=" N VAL v 87 " --> pdb=" O PHE v 112 " (cutoff:3.500A) removed outlier: 14.155A pdb=" N LEU v 114 " --> pdb=" O VAL v 87 " (cutoff:3.500A) removed outlier: 12.865A pdb=" N THR v 89 " --> pdb=" O LEU v 114 " (cutoff:3.500A) removed outlier: 13.135A pdb=" N ASN v 116 " --> pdb=" O THR v 89 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N CYS v 91 " --> pdb=" O ASN v 116 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG v 118 " --> pdb=" O CYS v 91 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY v 93 " --> pdb=" O ARG v 118 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N MET v 120 " --> pdb=" O GLY v 93 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA v 95 " --> pdb=" O MET v 120 " (cutoff:3.500A) 1697 hydrogen bonds defined for protein. 5010 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: 35.35 Time building geometry restraints manager: 18.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 38632 1.03 - 1.23: 39 1.23 - 1.42: 15592 1.42 - 1.62: 23057 1.62 - 1.81: 372 Bond restraints: 77692 Sorted by residual: bond pdb=" C MTX S 201 " pdb=" O MTX S 201 " ideal model delta sigma weight residual 1.230 1.410 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C4 ATP B 500 " pdb=" C5 ATP B 500 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 bond pdb=" C4 ATP A 500 " pdb=" C5 ATP A 500 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.32e+01 bond pdb=" C4 ATP C 500 " pdb=" C5 ATP C 500 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C5 ATP C 500 " pdb=" C6 ATP C 500 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 77687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 140617 3.93 - 7.86: 249 7.86 - 11.79: 11 11.79 - 15.72: 0 15.72 - 19.65: 6 Bond angle restraints: 140883 Sorted by residual: angle pdb=" PB ATP C 500 " pdb=" O3B ATP C 500 " pdb=" PG ATP C 500 " ideal model delta sigma weight residual 139.87 120.22 19.65 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PB ATP A 500 " pdb=" O3B ATP A 500 " pdb=" PG ATP A 500 " ideal model delta sigma weight residual 139.87 120.38 19.49 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB ATP B 500 " pdb=" O3B ATP B 500 " pdb=" PG ATP B 500 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PA ATP B 500 " pdb=" O3A ATP B 500 " pdb=" PB ATP B 500 " ideal model delta sigma weight residual 136.83 119.96 16.87 1.00e+00 1.00e+00 2.85e+02 angle pdb=" PA ATP C 500 " pdb=" O3A ATP C 500 " pdb=" PB ATP C 500 " ideal model delta sigma weight residual 136.83 120.35 16.48 1.00e+00 1.00e+00 2.72e+02 ... (remaining 140878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 32904 17.95 - 35.90: 2434 35.90 - 53.85: 631 53.85 - 71.80: 194 71.80 - 89.75: 25 Dihedral angle restraints: 36188 sinusoidal: 20381 harmonic: 15807 Sorted by residual: dihedral pdb=" CA ASP D 170 " pdb=" CB ASP D 170 " pdb=" CG ASP D 170 " pdb=" OD1 ASP D 170 " ideal model delta sinusoidal sigma weight residual -30.00 -86.42 56.42 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU q 136 " pdb=" CG GLU q 136 " pdb=" CD GLU q 136 " pdb=" OE1 GLU q 136 " ideal model delta sinusoidal sigma weight residual 0.00 84.96 -84.96 1 3.00e+01 1.11e-03 9.73e+00 dihedral pdb=" CB MET r 98 " pdb=" CG MET r 98 " pdb=" SD MET r 98 " pdb=" CE MET r 98 " ideal model delta sinusoidal sigma weight residual -60.00 -119.10 59.10 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 36185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4525 0.040 - 0.081: 1035 0.081 - 0.121: 364 0.121 - 0.162: 118 0.162 - 0.202: 3 Chirality restraints: 6045 Sorted by residual: chirality pdb=" CA GLU E 328 " pdb=" N GLU E 328 " pdb=" C GLU E 328 " pdb=" CB GLU E 328 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE F 246 " pdb=" N ILE F 246 " pdb=" C ILE F 246 " pdb=" CB ILE F 246 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA PRO E 329 " pdb=" N PRO E 329 " pdb=" C PRO E 329 " pdb=" CB PRO E 329 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 6042 not shown) Planarity restraints: 11552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 MTX S 201 " 0.019 2.00e-02 2.50e+03 8.83e-02 2.53e+02 pdb=" C4 MTX S 201 " 0.111 2.00e-02 2.50e+03 pdb=" C4A MTX S 201 " 0.058 2.00e-02 2.50e+03 pdb=" C6 MTX S 201 " 0.026 2.00e-02 2.50e+03 pdb=" C7 MTX S 201 " -0.059 2.00e-02 2.50e+03 pdb=" C8A MTX S 201 " -0.019 2.00e-02 2.50e+03 pdb=" C9 MTX S 201 " 0.041 2.00e-02 2.50e+03 pdb=" N1 MTX S 201 " -0.037 2.00e-02 2.50e+03 pdb=" N3 MTX S 201 " 0.096 2.00e-02 2.50e+03 pdb=" N5 MTX S 201 " 0.077 2.00e-02 2.50e+03 pdb=" N8 MTX S 201 " -0.075 2.00e-02 2.50e+03 pdb=" NA2 MTX S 201 " 0.001 2.00e-02 2.50e+03 pdb=" NA4 MTX S 201 " -0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N MTX S 201 " 0.130 2.00e-02 2.50e+03 8.13e-02 8.26e+01 pdb=" CA MTX S 201 " -0.099 2.00e-02 2.50e+03 pdb=" C MTX S 201 " 0.026 2.00e-02 2.50e+03 pdb=" O MTX S 201 " 0.018 2.00e-02 2.50e+03 pdb=" C11 MTX S 201 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MTX S 201 " -0.041 2.00e-02 2.50e+03 5.20e-02 5.41e+01 pdb=" C11 MTX S 201 " -0.033 2.00e-02 2.50e+03 pdb=" C12 MTX S 201 " 0.023 2.00e-02 2.50e+03 pdb=" C13 MTX S 201 " 0.024 2.00e-02 2.50e+03 pdb=" C14 MTX S 201 " -0.013 2.00e-02 2.50e+03 pdb=" C15 MTX S 201 " -0.067 2.00e-02 2.50e+03 pdb=" C16 MTX S 201 " 0.114 2.00e-02 2.50e+03 pdb=" N10 MTX S 201 " -0.008 2.00e-02 2.50e+03 ... (remaining 11549 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 8267 2.25 - 2.84: 179041 2.84 - 3.42: 202644 3.42 - 4.01: 281811 4.01 - 4.60: 432647 Nonbonded interactions: 1104410 Sorted by model distance: nonbonded pdb=" O ILE n 59 " pdb=" H SER n 88 " model vdw 1.661 2.450 nonbonded pdb=" O ILE i 59 " pdb=" H SER i 88 " model vdw 1.671 2.450 nonbonded pdb=" O ILE k 59 " pdb=" H SER k 88 " model vdw 1.683 2.450 nonbonded pdb=" HD1 HIS s 122 " pdb=" O GLN s 123 " model vdw 1.687 2.450 nonbonded pdb=" O ILE s 59 " pdb=" H SER s 88 " model vdw 1.687 2.450 ... (remaining 1104405 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 65 through 192 or (resid 204 and (name N or name CA or nam \ e C or name O or name HA2 or name HA3)) or resid 205 through 218 or (resid 235 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name CE1 or name CE2 or name CZ or name HA or name HB2 or name HB3 or \ name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) or resid 236 through \ 413)) selection = (chain 'B' and (resid 65 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 127 through 192 or (resid 204 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 05 through 218 or (resid 235 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or n \ ame HZ )) or resid 236 through 413)) selection = (chain 'C' and (resid 65 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 127 through 192 or (resid 204 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 05 through 218 or (resid 235 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or n \ ame HZ )) or resid 236 through 413)) selection = (chain 'D' and (resid 65 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 127 through 192 or (resid 204 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 05 through 218 or (resid 235 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or n \ ame HZ )) or resid 236 through 413)) selection = (chain 'E' and (resid 65 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 127 through 218 or (resid 235 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ or name HA or name HB2 or name HB3 \ or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) or resid 236 throu \ gh 413)) selection = (chain 'F' and (resid 65 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 96 through 125 or (resid 126 and (name N or name CA or name C or n \ ame O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name \ HG21 or name HG22 or name HG23)) or resid 127 through 413)) } ncs_group { reference = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } 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=0.00 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: 1.400 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: 1.000 Extract box with map and model: 2.070 Check model and map are aligned: 0.430 Set scattering table: 0.520 Process input model: 130.060 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.560 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: 0.030 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.180 39024 Z= 0.255 Angle : 0.705 19.655 52716 Z= 0.428 Chirality : 0.043 0.202 6045 Planarity : 0.004 0.088 6835 Dihedral : 12.083 89.751 14861 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.02 % 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: -1.93 (0.11), residues: 4879 helix: -0.71 (0.10), residues: 2219 sheet: -0.74 (0.20), residues: 614 loop : -2.02 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 22 HIS 0.012 0.001 HIS C 230 PHE 0.013 0.001 PHE k 17 TYR 0.011 0.001 TYR E 171 ARG 0.005 0.000 ARG S 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 857 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 857 time to evaluate : 4.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.9415 (t0) cc_final: 0.9052 (t0) REVERT: B 118 ILE cc_start: 0.9133 (mt) cc_final: 0.8868 (tt) REVERT: B 182 TYR cc_start: 0.8600 (t80) cc_final: 0.8356 (t80) REVERT: B 215 ILE cc_start: 0.6785 (mm) cc_final: 0.6398 (mm) REVERT: D 245 PHE cc_start: 0.8409 (m-80) cc_final: 0.8131 (m-80) REVERT: D 413 TYR cc_start: 0.7957 (m-80) cc_final: 0.7703 (m-80) REVERT: E 118 ILE cc_start: 0.9484 (mt) cc_final: 0.9209 (pt) REVERT: E 144 ASP cc_start: 0.7932 (t0) cc_final: 0.7135 (t0) REVERT: E 244 LEU cc_start: 0.9050 (tp) cc_final: 0.8756 (tp) REVERT: E 410 LEU cc_start: 0.8746 (pt) cc_final: 0.8491 (mm) REVERT: E 411 LEU cc_start: 0.7998 (mt) cc_final: 0.7449 (pt) REVERT: F 270 PHE cc_start: 0.6954 (m-80) cc_final: 0.6511 (m-80) REVERT: F 289 GLN cc_start: 0.8649 (tt0) cc_final: 0.8216 (tp40) REVERT: F 350 PHE cc_start: 0.8614 (m-80) cc_final: 0.8295 (m-10) REVERT: h 70 ILE cc_start: 0.9099 (mm) cc_final: 0.8867 (tp) REVERT: h 128 TYR cc_start: 0.8243 (t80) cc_final: 0.7976 (t80) REVERT: i 60 TYR cc_start: 0.7646 (m-80) cc_final: 0.6986 (m-80) REVERT: i 70 ILE cc_start: 0.9101 (mt) cc_final: 0.8877 (mm) REVERT: k 5 MET cc_start: 0.8539 (mmm) cc_final: 0.8336 (mmm) REVERT: k 26 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7910 (tm-30) REVERT: k 193 ASN cc_start: 0.7757 (m-40) cc_final: 0.7372 (t0) REVERT: l 49 PHE cc_start: 0.8647 (t80) cc_final: 0.7969 (t80) REVERT: l 70 ILE cc_start: 0.8784 (mm) cc_final: 0.8030 (tp) REVERT: l 98 MET cc_start: 0.7849 (tpt) cc_final: 0.7386 (tpt) REVERT: m 5 MET cc_start: 0.8104 (mmm) cc_final: 0.7854 (mmm) REVERT: m 64 ASN cc_start: 0.8390 (t0) cc_final: 0.8113 (t0) REVERT: m 128 TYR cc_start: 0.7884 (t80) cc_final: 0.7471 (t80) REVERT: n 134 ASP cc_start: 0.9455 (m-30) cc_final: 0.9105 (m-30) REVERT: p 58 ASP cc_start: 0.8677 (p0) cc_final: 0.8111 (m-30) REVERT: p 77 TYR cc_start: 0.7537 (t80) cc_final: 0.7312 (t80) REVERT: p 81 GLN cc_start: 0.8485 (mm110) cc_final: 0.7971 (mm-40) REVERT: p 167 ASP cc_start: 0.7188 (m-30) cc_final: 0.6534 (m-30) REVERT: q 94 GLN cc_start: 0.8904 (pt0) cc_final: 0.8268 (pm20) REVERT: q 113 CYS cc_start: 0.8921 (p) cc_final: 0.8486 (p) REVERT: q 118 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.7363 (mtt-85) REVERT: r 81 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7079 (tp-100) REVERT: r 108 LYS cc_start: 0.8014 (tptt) cc_final: 0.7781 (mppt) REVERT: s 19 ILE cc_start: 0.5743 (tp) cc_final: 0.5537 (tp) REVERT: s 20 TYR cc_start: 0.8196 (m-80) cc_final: 0.7758 (m-80) REVERT: s 47 MET cc_start: 0.6248 (ptm) cc_final: 0.6016 (ptm) REVERT: s 60 TYR cc_start: 0.7724 (m-80) cc_final: 0.7516 (m-10) REVERT: s 62 TYR cc_start: 0.6905 (m-80) cc_final: 0.6492 (m-10) REVERT: s 113 CYS cc_start: 0.8636 (p) cc_final: 0.8413 (p) REVERT: s 120 MET cc_start: 0.7940 (tmm) cc_final: 0.6809 (tmm) REVERT: s 171 ASP cc_start: 0.8157 (m-30) cc_final: 0.7565 (m-30) REVERT: t 101 PHE cc_start: 0.7237 (t80) cc_final: 0.6975 (t80) REVERT: u 62 TYR cc_start: 0.7135 (m-80) cc_final: 0.6880 (m-10) REVERT: u 91 CYS cc_start: 0.7161 (p) cc_final: 0.6902 (p) REVERT: v 20 TYR cc_start: 0.8503 (m-80) cc_final: 0.8071 (t80) REVERT: v 112 PHE cc_start: 0.8731 (m-80) cc_final: 0.8507 (m-10) REVERT: v 120 MET cc_start: 0.8336 (ttp) cc_final: 0.7891 (tmm) REVERT: v 163 GLN cc_start: 0.8759 (tp40) cc_final: 0.8529 (tm-30) REVERT: v 171 ASP cc_start: 0.8310 (m-30) cc_final: 0.7066 (t0) outliers start: 0 outliers final: 0 residues processed: 857 average time/residue: 1.1156 time to fit residues: 1511.1848 Evaluate side-chains 567 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 4.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 0.5980 chunk 369 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 382 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 443 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN B 342 ASN C 260 HIS C 289 GLN D 230 HIS F 237 GLN F 260 HIS h 150 ASN j 41 ASN k 81 GLN k 193 ASN m 193 ASN p 41 ASN p 150 ASN r 81 GLN ** r 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 123 GLN r 193 ASN s 41 ASN t 41 ASN t 94 GLN t 163 GLN v 191 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.090716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065829 restraints weight = 447429.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068790 restraints weight = 165382.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.070491 restraints weight = 94350.845| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39024 Z= 0.250 Angle : 0.590 8.810 52716 Z= 0.311 Chirality : 0.041 0.160 6045 Planarity : 0.004 0.048 6835 Dihedral : 5.761 77.989 5451 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.80 % Allowed : 7.42 % Favored : 91.78 % Cbeta Deviations : 0.02 % 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 (0.11), residues: 4879 helix: 0.38 (0.10), residues: 2364 sheet: -0.95 (0.18), residues: 737 loop : -1.73 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 133 HIS 0.008 0.001 HIS C 260 PHE 0.019 0.001 PHE B 298 TYR 0.013 0.001 TYR h 182 ARG 0.008 0.000 ARG h 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 610 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 577 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8590 (tm-30) REVERT: A 170 ASP cc_start: 0.9382 (t0) cc_final: 0.8983 (t0) REVERT: B 118 ILE cc_start: 0.9189 (mt) cc_final: 0.8906 (tt) REVERT: B 182 TYR cc_start: 0.8773 (t80) cc_final: 0.8546 (t80) REVERT: D 245 PHE cc_start: 0.8586 (m-80) cc_final: 0.8331 (m-10) REVERT: D 413 TYR cc_start: 0.7880 (m-80) cc_final: 0.7532 (m-80) REVERT: E 118 ILE cc_start: 0.9459 (mt) cc_final: 0.9213 (pt) REVERT: E 191 ARG cc_start: 0.7337 (mtm180) cc_final: 0.7025 (mtp180) REVERT: E 244 LEU cc_start: 0.9132 (tp) cc_final: 0.8886 (tp) REVERT: F 289 GLN cc_start: 0.8714 (tt0) cc_final: 0.8377 (tp40) REVERT: F 350 PHE cc_start: 0.8659 (m-80) cc_final: 0.8383 (m-80) REVERT: h 70 ILE cc_start: 0.8776 (mm) cc_final: 0.8467 (tp) REVERT: j 8 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6599 (tm-30) REVERT: j 15 ARG cc_start: 0.7747 (mpp-170) cc_final: 0.7287 (mtm-85) REVERT: j 178 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8573 (mp0) REVERT: k 26 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7968 (tm-30) REVERT: k 80 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8642 (mtt) REVERT: k 193 ASN cc_start: 0.8017 (m110) cc_final: 0.7614 (t0) REVERT: l 128 TYR cc_start: 0.7862 (t80) cc_final: 0.7162 (t80) REVERT: l 150 ASN cc_start: 0.9338 (m-40) cc_final: 0.9090 (m110) REVERT: m 118 ARG cc_start: 0.8368 (mmt180) cc_final: 0.8002 (mmt180) REVERT: m 128 TYR cc_start: 0.7920 (t80) cc_final: 0.7556 (t80) REVERT: p 58 ASP cc_start: 0.8672 (p0) cc_final: 0.8094 (m-30) REVERT: p 167 ASP cc_start: 0.6668 (m-30) cc_final: 0.6371 (m-30) REVERT: q 94 GLN cc_start: 0.8422 (pt0) cc_final: 0.8107 (pm20) REVERT: q 113 CYS cc_start: 0.9044 (p) cc_final: 0.8550 (p) REVERT: q 120 MET cc_start: 0.7803 (tmm) cc_final: 0.7602 (tmm) REVERT: r 108 LYS cc_start: 0.8046 (tptt) cc_final: 0.7842 (mppt) REVERT: r 116 ASN cc_start: 0.8105 (m110) cc_final: 0.7664 (m110) REVERT: s 20 TYR cc_start: 0.8115 (m-80) cc_final: 0.7821 (m-80) REVERT: s 62 TYR cc_start: 0.6972 (m-80) cc_final: 0.6582 (m-80) REVERT: s 63 ILE cc_start: 0.7466 (mt) cc_final: 0.7179 (mt) REVERT: s 171 ASP cc_start: 0.7984 (m-30) cc_final: 0.7710 (m-30) REVERT: u 91 CYS cc_start: 0.7215 (p) cc_final: 0.6957 (p) REVERT: u 182 TYR cc_start: 0.8582 (t80) cc_final: 0.8326 (t80) REVERT: v 20 TYR cc_start: 0.8562 (m-80) cc_final: 0.8038 (t80) REVERT: v 25 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8505 (mmtm) REVERT: v 92 MET cc_start: 0.6505 (mtp) cc_final: 0.6247 (mtm) REVERT: v 98 MET cc_start: 0.6413 (mmm) cc_final: 0.6121 (tpp) REVERT: v 112 PHE cc_start: 0.8720 (m-80) cc_final: 0.8470 (m-10) REVERT: v 163 GLN cc_start: 0.8764 (tp40) cc_final: 0.8494 (tm-30) outliers start: 33 outliers final: 22 residues processed: 597 average time/residue: 1.0908 time to fit residues: 1040.9473 Evaluate side-chains 528 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 505 time to evaluate : 4.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain S residue 162 HIS Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain i residue 186 ASP Chi-restraints excluded: chain j residue 91 CYS Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain k residue 190 THR Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 44 VAL Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain p residue 89 THR Chi-restraints excluded: chain p residue 150 ASN Chi-restraints excluded: chain r residue 38 HIS Chi-restraints excluded: chain s residue 54 ASN Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain t residue 70 ILE Chi-restraints excluded: chain t residue 163 GLN Chi-restraints excluded: chain u residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 386 optimal weight: 20.0000 chunk 122 optimal weight: 0.0980 chunk 135 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 338 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 431 optimal weight: 30.0000 chunk 234 optimal weight: 3.9990 chunk 333 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS B 342 ASN C 342 ASN F 72 ASN F 106 ASN S 114 HIS i 163 GLN j 193 ASN k 138 HIS l 191 HIS n 150 ASN p 131 GLN ** p 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 193 ASN r 116 ASN r 129 GLN r 156 HIS v 191 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.088225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.062854 restraints weight = 447790.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065685 restraints weight = 167626.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067307 restraints weight = 96827.779| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39024 Z= 0.281 Angle : 0.552 8.158 52716 Z= 0.288 Chirality : 0.040 0.145 6045 Planarity : 0.004 0.128 6835 Dihedral : 5.785 83.174 5451 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.06 % Allowed : 7.95 % Favored : 90.98 % Cbeta Deviations : 0.02 % 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: -0.48 (0.12), residues: 4879 helix: 0.81 (0.11), residues: 2376 sheet: -1.29 (0.19), residues: 677 loop : -1.37 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 47 HIS 0.010 0.001 HIS C 260 PHE 0.022 0.001 PHE r 173 TYR 0.014 0.001 TYR n 77 ARG 0.019 0.000 ARG k 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 546 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 502 time to evaluate : 4.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8634 (tm-30) REVERT: A 170 ASP cc_start: 0.9413 (t0) cc_final: 0.9010 (t0) REVERT: A 235 PHE cc_start: 0.8773 (m-80) cc_final: 0.8529 (m-10) REVERT: B 118 ILE cc_start: 0.9241 (mt) cc_final: 0.8937 (tt) REVERT: D 160 ASN cc_start: 0.9146 (m110) cc_final: 0.8911 (m110) REVERT: D 298 PHE cc_start: 0.8123 (t80) cc_final: 0.7880 (t80) REVERT: D 413 TYR cc_start: 0.7945 (m-80) cc_final: 0.7715 (m-80) REVERT: E 118 ILE cc_start: 0.9486 (mt) cc_final: 0.9246 (pt) REVERT: E 191 ARG cc_start: 0.7628 (mtm180) cc_final: 0.7320 (mtp180) REVERT: E 244 LEU cc_start: 0.9175 (tp) cc_final: 0.8973 (tp) REVERT: E 258 ILE cc_start: 0.9642 (mt) cc_final: 0.9303 (tp) REVERT: E 363 MET cc_start: 0.9270 (mmm) cc_final: 0.8998 (mmt) REVERT: F 289 GLN cc_start: 0.8755 (tt0) cc_final: 0.8392 (tp40) REVERT: F 350 PHE cc_start: 0.8792 (m-80) cc_final: 0.8581 (m-80) REVERT: h 70 ILE cc_start: 0.8948 (mm) cc_final: 0.8620 (mm) REVERT: h 98 MET cc_start: 0.8835 (tpt) cc_final: 0.8525 (tpt) REVERT: i 37 ASP cc_start: 0.8892 (p0) cc_final: 0.8690 (p0) REVERT: i 60 TYR cc_start: 0.7682 (m-80) cc_final: 0.7365 (m-80) REVERT: j 17 PHE cc_start: 0.7741 (m-10) cc_final: 0.7510 (m-10) REVERT: k 26 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8220 (tm-30) REVERT: k 80 MET cc_start: 0.9042 (mtt) cc_final: 0.8756 (mtt) REVERT: l 46 GLN cc_start: 0.9001 (mt0) cc_final: 0.8785 (mt0) REVERT: l 150 ASN cc_start: 0.9367 (m-40) cc_final: 0.9111 (m110) REVERT: m 128 TYR cc_start: 0.7978 (t80) cc_final: 0.7624 (t80) REVERT: p 81 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7925 (mm-40) REVERT: q 108 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8764 (tptp) REVERT: q 113 CYS cc_start: 0.9166 (p) cc_final: 0.8664 (p) REVERT: q 118 ARG cc_start: 0.6217 (OUTLIER) cc_final: 0.5524 (mtp-110) REVERT: q 120 MET cc_start: 0.7817 (tmm) cc_final: 0.7575 (tmm) REVERT: r 116 ASN cc_start: 0.8360 (m-40) cc_final: 0.8113 (m110) REVERT: s 20 TYR cc_start: 0.8032 (m-80) cc_final: 0.7697 (m-80) REVERT: s 62 TYR cc_start: 0.7109 (m-80) cc_final: 0.6593 (m-10) REVERT: s 84 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7732 (mmtt) REVERT: s 86 ASP cc_start: 0.7536 (m-30) cc_final: 0.7320 (p0) REVERT: s 171 ASP cc_start: 0.8010 (m-30) cc_final: 0.7652 (m-30) REVERT: t 98 MET cc_start: 0.7240 (mmp) cc_final: 0.6673 (tpp) REVERT: u 120 MET cc_start: 0.6927 (tmm) cc_final: 0.6630 (tmm) REVERT: v 110 LYS cc_start: 0.8966 (mttp) cc_final: 0.8757 (mttm) REVERT: v 112 PHE cc_start: 0.8795 (m-80) cc_final: 0.8479 (m-10) REVERT: v 163 GLN cc_start: 0.8820 (tp40) cc_final: 0.8538 (tm-30) outliers start: 44 outliers final: 28 residues processed: 527 average time/residue: 1.0685 time to fit residues: 893.9232 Evaluate side-chains 493 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 464 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain S residue 162 HIS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain i residue 9 GLN Chi-restraints excluded: chain i residue 18 ASP Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 59 ILE Chi-restraints excluded: chain j residue 187 SER Chi-restraints excluded: chain k residue 17 PHE Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain k residue 190 THR Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain p residue 89 THR Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain r residue 79 THR Chi-restraints excluded: chain s residue 41 ASN Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 96 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 484 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 322 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 338 optimal weight: 3.9990 chunk 397 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 HIS F 260 HIS ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN v 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.088469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063047 restraints weight = 444324.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.065923 restraints weight = 165025.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.067575 restraints weight = 94607.848| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39024 Z= 0.186 Angle : 0.487 6.529 52716 Z= 0.249 Chirality : 0.040 0.148 6045 Planarity : 0.003 0.055 6835 Dihedral : 5.618 85.357 5451 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.82 % Allowed : 9.06 % Favored : 90.11 % Cbeta Deviations : 0.02 % 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: -0.16 (0.12), residues: 4879 helix: 1.13 (0.11), residues: 2403 sheet: -1.27 (0.19), residues: 665 loop : -1.27 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP S 133 HIS 0.006 0.001 HIS u 138 PHE 0.030 0.001 PHE S 125 TYR 0.017 0.001 TYR u 128 ARG 0.005 0.000 ARG h 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 532 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 498 time to evaluate : 4.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.9417 (t0) cc_final: 0.9016 (t0) REVERT: B 118 ILE cc_start: 0.9234 (mt) cc_final: 0.8930 (tt) REVERT: B 182 TYR cc_start: 0.8971 (t80) cc_final: 0.8127 (t80) REVERT: B 347 ASP cc_start: 0.8652 (t0) cc_final: 0.7900 (t0) REVERT: C 363 MET cc_start: 0.8723 (mmm) cc_final: 0.8450 (mmm) REVERT: D 160 ASN cc_start: 0.9157 (m110) cc_final: 0.8908 (m110) REVERT: D 413 TYR cc_start: 0.7888 (m-80) cc_final: 0.7536 (m-80) REVERT: E 118 ILE cc_start: 0.9484 (mt) cc_final: 0.9251 (pt) REVERT: E 191 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7350 (mtp180) REVERT: E 244 LEU cc_start: 0.9154 (tp) cc_final: 0.8938 (tp) REVERT: E 258 ILE cc_start: 0.9624 (mt) cc_final: 0.9299 (tp) REVERT: F 289 GLN cc_start: 0.8807 (tt0) cc_final: 0.8347 (tp40) REVERT: h 70 ILE cc_start: 0.8882 (mm) cc_final: 0.8548 (mm) REVERT: i 34 GLN cc_start: 0.8774 (tp40) cc_final: 0.8357 (tp-100) REVERT: i 37 ASP cc_start: 0.8882 (p0) cc_final: 0.8654 (p0) REVERT: i 60 TYR cc_start: 0.7663 (m-80) cc_final: 0.7368 (m-80) REVERT: k 26 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8205 (tm-30) REVERT: k 80 MET cc_start: 0.9012 (mtt) cc_final: 0.8712 (mtt) REVERT: l 46 GLN cc_start: 0.9002 (mt0) cc_final: 0.8772 (mt0) REVERT: l 150 ASN cc_start: 0.9384 (m-40) cc_final: 0.9118 (m110) REVERT: m 128 TYR cc_start: 0.7947 (t80) cc_final: 0.7596 (t80) REVERT: q 108 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8721 (tptp) REVERT: q 113 CYS cc_start: 0.9154 (p) cc_final: 0.8648 (p) REVERT: q 120 MET cc_start: 0.7872 (tmm) cc_final: 0.7667 (tmm) REVERT: s 20 TYR cc_start: 0.8152 (m-80) cc_final: 0.7843 (m-80) REVERT: s 84 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7711 (mmtt) REVERT: s 171 ASP cc_start: 0.7926 (m-30) cc_final: 0.7578 (m-30) REVERT: u 98 MET cc_start: 0.6728 (mmm) cc_final: 0.6264 (tpt) REVERT: u 120 MET cc_start: 0.7017 (tmm) cc_final: 0.6730 (tmm) REVERT: u 182 TYR cc_start: 0.8694 (t80) cc_final: 0.8309 (t80) REVERT: v 110 LYS cc_start: 0.8994 (mttp) cc_final: 0.8743 (mttm) REVERT: v 112 PHE cc_start: 0.8774 (m-80) cc_final: 0.8552 (m-10) REVERT: v 167 ASP cc_start: 0.6854 (m-30) cc_final: 0.6438 (m-30) outliers start: 34 outliers final: 27 residues processed: 518 average time/residue: 1.0301 time to fit residues: 849.1299 Evaluate side-chains 495 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 468 time to evaluate : 4.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain S residue 162 HIS Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain h residue 113 CYS Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 91 CYS Chi-restraints excluded: chain j residue 187 SER Chi-restraints excluded: chain k residue 17 PHE Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain k residue 190 THR Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 91 CYS Chi-restraints excluded: chain p residue 89 THR Chi-restraints excluded: chain p residue 164 ILE Chi-restraints excluded: chain s residue 91 CYS Chi-restraints excluded: chain v residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 419 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN C 260 HIS ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.086574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060865 restraints weight = 449352.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.063619 restraints weight = 169617.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.065209 restraints weight = 99050.885| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 39024 Z= 0.309 Angle : 0.537 6.495 52716 Z= 0.281 Chirality : 0.040 0.143 6045 Planarity : 0.003 0.059 6835 Dihedral : 5.699 85.608 5451 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.11 % Allowed : 9.89 % Favored : 89.00 % Cbeta Deviations : 0.02 % 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: -0.15 (0.12), residues: 4879 helix: 1.16 (0.11), residues: 2379 sheet: -0.92 (0.19), residues: 740 loop : -1.44 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 133 HIS 0.013 0.001 HIS C 260 PHE 0.026 0.001 PHE t 17 TYR 0.014 0.001 TYR u 128 ARG 0.013 0.000 ARG m 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 508 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 462 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.8658 (m-30) REVERT: A 170 ASP cc_start: 0.9474 (t0) cc_final: 0.9098 (t0) REVERT: B 347 ASP cc_start: 0.8754 (t0) cc_final: 0.8222 (t0) REVERT: C 363 MET cc_start: 0.8785 (mmm) cc_final: 0.8434 (mmm) REVERT: D 160 ASN cc_start: 0.9169 (m110) cc_final: 0.8927 (m110) REVERT: D 413 TYR cc_start: 0.7834 (m-80) cc_final: 0.7445 (m-80) REVERT: E 118 ILE cc_start: 0.9494 (mt) cc_final: 0.9278 (pt) REVERT: E 191 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7570 (mtp180) REVERT: E 258 ILE cc_start: 0.9634 (mt) cc_final: 0.9292 (tp) REVERT: E 363 MET cc_start: 0.9335 (mmm) cc_final: 0.9103 (mmt) REVERT: h 70 ILE cc_start: 0.9047 (mm) cc_final: 0.8738 (mm) REVERT: i 34 GLN cc_start: 0.8845 (tp40) cc_final: 0.8470 (tp40) REVERT: i 37 ASP cc_start: 0.8955 (p0) cc_final: 0.8632 (p0) REVERT: i 60 TYR cc_start: 0.7705 (m-80) cc_final: 0.7365 (m-80) REVERT: k 26 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8196 (tm-30) REVERT: k 80 MET cc_start: 0.9073 (mtt) cc_final: 0.8783 (mtt) REVERT: m 128 TYR cc_start: 0.7819 (t80) cc_final: 0.7430 (t80) REVERT: q 113 CYS cc_start: 0.9183 (p) cc_final: 0.8677 (p) REVERT: q 120 MET cc_start: 0.7783 (tmm) cc_final: 0.7553 (tmm) REVERT: s 171 ASP cc_start: 0.7911 (m-30) cc_final: 0.7552 (m-30) REVERT: t 153 MET cc_start: 0.9149 (mmm) cc_final: 0.8712 (mmm) REVERT: u 34 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8595 (tm-30) REVERT: u 98 MET cc_start: 0.6959 (mmm) cc_final: 0.6460 (tpt) REVERT: u 120 MET cc_start: 0.6978 (tmm) cc_final: 0.6661 (tmm) REVERT: v 112 PHE cc_start: 0.8860 (m-80) cc_final: 0.8629 (m-10) outliers start: 46 outliers final: 35 residues processed: 491 average time/residue: 1.0391 time to fit residues: 814.5082 Evaluate side-chains 477 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 441 time to evaluate : 4.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain S residue 162 HIS Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain i residue 18 ASP Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 187 SER Chi-restraints excluded: chain k residue 17 PHE Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain k residue 190 THR Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 91 CYS Chi-restraints excluded: chain m residue 91 CYS Chi-restraints excluded: chain p residue 80 MET Chi-restraints excluded: chain p residue 89 THR Chi-restraints excluded: chain s residue 41 ASN Chi-restraints excluded: chain s residue 91 CYS Chi-restraints excluded: chain u residue 143 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 220 optimal weight: 40.0000 chunk 286 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 182 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.086970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061321 restraints weight = 443801.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.064135 restraints weight = 165800.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065748 restraints weight = 95736.916| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39024 Z= 0.205 Angle : 0.494 7.099 52716 Z= 0.252 Chirality : 0.040 0.179 6045 Planarity : 0.003 0.061 6835 Dihedral : 5.607 80.179 5451 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.02 % Allowed : 9.96 % Favored : 89.03 % Cbeta Deviations : 0.02 % 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: 0.04 (0.12), residues: 4879 helix: 1.32 (0.11), residues: 2384 sheet: -0.94 (0.18), residues: 758 loop : -1.31 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 133 HIS 0.003 0.001 HIS n 156 PHE 0.020 0.001 PHE S 125 TYR 0.014 0.001 TYR u 128 ARG 0.013 0.000 ARG m 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 504 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 462 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.8643 (m-30) REVERT: A 170 ASP cc_start: 0.9487 (t0) cc_final: 0.9114 (t0) REVERT: B 347 ASP cc_start: 0.8725 (t0) cc_final: 0.8167 (t0) REVERT: C 205 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: C 363 MET cc_start: 0.8792 (mmm) cc_final: 0.8432 (tpp) REVERT: D 160 ASN cc_start: 0.9171 (m110) cc_final: 0.8917 (m110) REVERT: D 413 TYR cc_start: 0.7834 (m-80) cc_final: 0.7447 (m-80) REVERT: E 118 ILE cc_start: 0.9525 (mt) cc_final: 0.9284 (pt) REVERT: E 191 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7611 (mtp180) REVERT: E 258 ILE cc_start: 0.9634 (mt) cc_final: 0.9284 (tp) REVERT: S 109 LYS cc_start: 0.7377 (mtpt) cc_final: 0.7130 (mttp) REVERT: S 140 PHE cc_start: 0.8674 (p90) cc_final: 0.8377 (p90) REVERT: h 70 ILE cc_start: 0.8995 (mm) cc_final: 0.8674 (mm) REVERT: i 37 ASP cc_start: 0.8952 (p0) cc_final: 0.8650 (p0) REVERT: i 60 TYR cc_start: 0.7677 (m-80) cc_final: 0.7360 (m-80) REVERT: k 26 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8208 (tm-30) REVERT: k 80 MET cc_start: 0.9028 (mtt) cc_final: 0.8703 (mtt) REVERT: l 46 GLN cc_start: 0.9023 (mt0) cc_final: 0.8791 (mt0) REVERT: m 128 TYR cc_start: 0.7926 (t80) cc_final: 0.7540 (t80) REVERT: p 17 PHE cc_start: 0.6920 (m-80) cc_final: 0.6440 (m-80) REVERT: q 108 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8819 (tptp) REVERT: q 113 CYS cc_start: 0.9153 (p) cc_final: 0.8649 (p) REVERT: q 120 MET cc_start: 0.7817 (tmm) cc_final: 0.7577 (tmm) REVERT: s 104 THR cc_start: 0.6627 (OUTLIER) cc_final: 0.6066 (t) REVERT: s 171 ASP cc_start: 0.7943 (m-30) cc_final: 0.7565 (m-30) REVERT: u 98 MET cc_start: 0.6797 (mmm) cc_final: 0.6272 (tpt) REVERT: u 120 MET cc_start: 0.7095 (tmm) cc_final: 0.6766 (tmm) REVERT: v 56 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8032 (mp0) REVERT: v 112 PHE cc_start: 0.8872 (m-80) cc_final: 0.8657 (m-10) outliers start: 42 outliers final: 35 residues processed: 489 average time/residue: 1.0377 time to fit residues: 814.8286 Evaluate side-chains 488 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 450 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain S residue 162 HIS Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain i residue 18 ASP Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 187 SER Chi-restraints excluded: chain k residue 17 PHE Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain l residue 91 CYS Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 91 CYS Chi-restraints excluded: chain p residue 89 THR Chi-restraints excluded: chain p residue 120 MET Chi-restraints excluded: chain p residue 121 ILE Chi-restraints excluded: chain s residue 41 ASN Chi-restraints excluded: chain s residue 91 CYS Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain u residue 143 LEU Chi-restraints excluded: chain v residue 110 LYS Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 359 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 379 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 362 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 296 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN C 342 ASN D 260 HIS E 315 ASN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 159 GLN ** q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN v 129 GLN v 191 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.085068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059450 restraints weight = 450471.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062160 restraints weight = 169103.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063725 restraints weight = 98425.957| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 39024 Z= 0.346 Angle : 0.566 7.504 52716 Z= 0.295 Chirality : 0.041 0.139 6045 Planarity : 0.004 0.063 6835 Dihedral : 5.741 69.269 5451 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.28 % Allowed : 10.30 % Favored : 88.42 % Cbeta Deviations : 0.02 % 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: -0.29 (0.12), residues: 4879 helix: 1.03 (0.10), residues: 2390 sheet: -1.02 (0.18), residues: 765 loop : -1.48 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 133 HIS 0.007 0.001 HIS j 122 PHE 0.032 0.002 PHE r 173 TYR 0.011 0.001 TYR B 182 ARG 0.013 0.000 ARG m 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 493 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 440 time to evaluate : 4.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9304 (OUTLIER) cc_final: 0.8658 (m-30) REVERT: A 170 ASP cc_start: 0.9520 (t0) cc_final: 0.9177 (t0) REVERT: B 347 ASP cc_start: 0.8818 (t0) cc_final: 0.8227 (t0) REVERT: D 160 ASN cc_start: 0.9178 (m110) cc_final: 0.8928 (m110) REVERT: D 413 TYR cc_start: 0.7909 (m-80) cc_final: 0.7508 (m-80) REVERT: E 118 ILE cc_start: 0.9526 (mt) cc_final: 0.9292 (pt) REVERT: S 140 PHE cc_start: 0.8732 (p90) cc_final: 0.8415 (p90) REVERT: h 70 ILE cc_start: 0.9115 (mm) cc_final: 0.8825 (mm) REVERT: i 34 GLN cc_start: 0.8844 (tp40) cc_final: 0.8455 (tp40) REVERT: i 37 ASP cc_start: 0.8944 (p0) cc_final: 0.8576 (p0) REVERT: i 60 TYR cc_start: 0.7812 (m-80) cc_final: 0.7490 (m-80) REVERT: k 26 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8226 (tm-30) REVERT: k 46 GLN cc_start: 0.8737 (mt0) cc_final: 0.8413 (mt0) REVERT: k 80 MET cc_start: 0.9114 (mtt) cc_final: 0.8786 (mtt) REVERT: m 128 TYR cc_start: 0.7812 (t80) cc_final: 0.7362 (t80) REVERT: p 17 PHE cc_start: 0.7645 (m-80) cc_final: 0.7369 (m-80) REVERT: p 120 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7325 (tmm) REVERT: q 113 CYS cc_start: 0.9166 (p) cc_final: 0.8636 (p) REVERT: q 120 MET cc_start: 0.7854 (tmm) cc_final: 0.7607 (tmm) REVERT: s 104 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.6119 (t) REVERT: s 171 ASP cc_start: 0.7943 (m-30) cc_final: 0.7562 (m-30) REVERT: u 98 MET cc_start: 0.7001 (mmm) cc_final: 0.6496 (tpt) REVERT: u 108 LYS cc_start: 0.8837 (tppp) cc_final: 0.8473 (tptt) REVERT: u 120 MET cc_start: 0.7104 (tmm) cc_final: 0.6787 (tmm) outliers start: 53 outliers final: 41 residues processed: 475 average time/residue: 1.0480 time to fit residues: 794.9964 Evaluate side-chains 475 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 431 time to evaluate : 4.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 162 HIS Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain i residue 18 ASP Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 187 SER Chi-restraints excluded: chain k residue 17 PHE Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 91 CYS Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 91 CYS Chi-restraints excluded: chain p residue 89 THR Chi-restraints excluded: chain p residue 120 MET Chi-restraints excluded: chain p residue 121 ILE Chi-restraints excluded: chain s residue 41 ASN Chi-restraints excluded: chain s residue 54 ASN Chi-restraints excluded: chain s residue 91 CYS Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain u residue 143 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 421 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 477 optimal weight: 20.0000 chunk 252 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 403 optimal weight: 20.0000 chunk 269 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 ASN ** q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN v 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.084741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059205 restraints weight = 449417.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.061928 restraints weight = 167810.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063487 restraints weight = 97184.861| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 39024 Z= 0.317 Angle : 0.554 8.523 52716 Z= 0.288 Chirality : 0.041 0.194 6045 Planarity : 0.004 0.075 6835 Dihedral : 5.763 65.172 5451 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.16 % Allowed : 10.83 % Favored : 88.01 % Cbeta Deviations : 0.02 % 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: -0.35 (0.12), residues: 4879 helix: 0.98 (0.10), residues: 2395 sheet: -1.09 (0.18), residues: 767 loop : -1.50 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 133 HIS 0.007 0.001 HIS p 122 PHE 0.031 0.002 PHE r 173 TYR 0.027 0.001 TYR B 171 ARG 0.016 0.000 ARG m 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 486 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 438 time to evaluate : 4.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9342 (OUTLIER) cc_final: 0.8701 (m-30) REVERT: A 170 ASP cc_start: 0.9520 (t0) cc_final: 0.9214 (t0) REVERT: B 285 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 347 ASP cc_start: 0.8830 (t0) cc_final: 0.8235 (t0) REVERT: D 160 ASN cc_start: 0.9175 (m110) cc_final: 0.8920 (m110) REVERT: D 413 TYR cc_start: 0.7880 (m-80) cc_final: 0.7474 (m-80) REVERT: E 118 ILE cc_start: 0.9527 (mt) cc_final: 0.9289 (pt) REVERT: E 258 ILE cc_start: 0.9644 (mt) cc_final: 0.9248 (tp) REVERT: F 350 PHE cc_start: 0.8764 (m-80) cc_final: 0.8511 (m-80) REVERT: S 109 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7500 (mttp) REVERT: S 140 PHE cc_start: 0.8745 (p90) cc_final: 0.8453 (p90) REVERT: h 70 ILE cc_start: 0.9133 (mm) cc_final: 0.8919 (mm) REVERT: i 34 GLN cc_start: 0.8774 (tp40) cc_final: 0.8410 (tp40) REVERT: i 37 ASP cc_start: 0.8982 (p0) cc_final: 0.8573 (p0) REVERT: i 60 TYR cc_start: 0.7798 (m-80) cc_final: 0.7483 (m-80) REVERT: j 17 PHE cc_start: 0.7618 (m-10) cc_final: 0.7295 (m-80) REVERT: k 5 MET cc_start: 0.9041 (mmm) cc_final: 0.8819 (mmm) REVERT: k 26 GLU cc_start: 0.8802 (mm-30) cc_final: 0.7966 (tm-30) REVERT: k 46 GLN cc_start: 0.8682 (mt0) cc_final: 0.8472 (mt0) REVERT: l 5 MET cc_start: 0.8736 (mmt) cc_final: 0.8327 (mmm) REVERT: m 128 TYR cc_start: 0.7807 (t80) cc_final: 0.7322 (t80) REVERT: n 128 TYR cc_start: 0.7676 (t80) cc_final: 0.7466 (t80) REVERT: p 120 MET cc_start: 0.7679 (tmm) cc_final: 0.7243 (tmm) REVERT: q 113 CYS cc_start: 0.9181 (p) cc_final: 0.8652 (p) REVERT: q 120 MET cc_start: 0.7909 (tmm) cc_final: 0.7645 (tmm) REVERT: s 104 THR cc_start: 0.6536 (OUTLIER) cc_final: 0.6158 (t) REVERT: s 171 ASP cc_start: 0.7933 (m-30) cc_final: 0.7546 (m-30) REVERT: u 98 MET cc_start: 0.7004 (mmm) cc_final: 0.6441 (tpt) REVERT: u 108 LYS cc_start: 0.8834 (tppp) cc_final: 0.8468 (tptt) REVERT: u 120 MET cc_start: 0.7177 (tmm) cc_final: 0.6841 (tmm) outliers start: 48 outliers final: 39 residues processed: 473 average time/residue: 1.0239 time to fit residues: 778.4483 Evaluate side-chains 468 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 427 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 162 HIS Chi-restraints excluded: chain h residue 39 MET Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain i residue 18 ASP Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain j residue 187 SER Chi-restraints excluded: chain k residue 17 PHE Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 91 CYS Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 91 CYS Chi-restraints excluded: chain p residue 89 THR Chi-restraints excluded: chain s residue 41 ASN Chi-restraints excluded: chain s residue 54 ASN Chi-restraints excluded: chain s residue 91 CYS Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain u residue 143 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 347 optimal weight: 3.9990 chunk 408 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 433 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 472 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 404 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN v 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.084945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059274 restraints weight = 451206.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.061990 restraints weight = 169301.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063559 restraints weight = 98657.500| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 39024 Z= 0.269 Angle : 0.532 9.195 52716 Z= 0.274 Chirality : 0.040 0.146 6045 Planarity : 0.003 0.073 6835 Dihedral : 5.702 64.512 5451 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.99 % Allowed : 11.22 % Favored : 87.79 % Cbeta Deviations : 0.02 % 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: -0.23 (0.12), residues: 4879 helix: 1.10 (0.10), residues: 2396 sheet: -1.00 (0.18), residues: 798 loop : -1.51 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 133 HIS 0.007 0.001 HIS p 122 PHE 0.023 0.001 PHE r 173 TYR 0.032 0.001 TYR u 128 ARG 0.016 0.000 ARG m 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 482 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 441 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9329 (OUTLIER) cc_final: 0.8679 (m-30) REVERT: A 170 ASP cc_start: 0.9522 (t0) cc_final: 0.9182 (t0) REVERT: B 347 ASP cc_start: 0.8848 (t0) cc_final: 0.8257 (t0) REVERT: C 363 MET cc_start: 0.8886 (tpp) cc_final: 0.8664 (mmt) REVERT: D 160 ASN cc_start: 0.9176 (m110) cc_final: 0.8910 (m110) REVERT: D 413 TYR cc_start: 0.7840 (m-80) cc_final: 0.7456 (m-80) REVERT: E 118 ILE cc_start: 0.9519 (mt) cc_final: 0.9305 (pt) REVERT: F 350 PHE cc_start: 0.8790 (m-80) cc_final: 0.8551 (m-80) REVERT: S 109 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7511 (mttp) REVERT: S 140 PHE cc_start: 0.8760 (p90) cc_final: 0.8488 (p90) REVERT: h 70 ILE cc_start: 0.9129 (mm) cc_final: 0.8915 (mm) REVERT: i 34 GLN cc_start: 0.8779 (tp40) cc_final: 0.8414 (tp40) REVERT: i 37 ASP cc_start: 0.8976 (p0) cc_final: 0.8586 (p0) REVERT: i 60 TYR cc_start: 0.7772 (m-80) cc_final: 0.7497 (m-80) REVERT: i 92 MET cc_start: 0.8262 (ttp) cc_final: 0.8039 (tmm) REVERT: j 17 PHE cc_start: 0.7500 (m-10) cc_final: 0.7193 (m-10) REVERT: k 26 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8141 (tm-30) REVERT: k 80 MET cc_start: 0.9116 (mtt) cc_final: 0.8755 (mtt) REVERT: l 46 GLN cc_start: 0.9045 (mt0) cc_final: 0.8826 (mt0) REVERT: m 128 TYR cc_start: 0.7822 (t80) cc_final: 0.7357 (t80) REVERT: n 128 TYR cc_start: 0.7697 (t80) cc_final: 0.7483 (t80) REVERT: p 120 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7225 (tmm) REVERT: q 113 CYS cc_start: 0.9183 (p) cc_final: 0.8642 (p) REVERT: q 120 MET cc_start: 0.7989 (tmm) cc_final: 0.7713 (tmm) REVERT: q 149 MET cc_start: 0.8588 (tpp) cc_final: 0.8149 (mmt) REVERT: s 104 THR cc_start: 0.6555 (OUTLIER) cc_final: 0.6035 (t) REVERT: s 171 ASP cc_start: 0.7923 (m-30) cc_final: 0.7543 (m-30) REVERT: t 149 MET cc_start: 0.8495 (tmm) cc_final: 0.8102 (mmm) REVERT: t 153 MET cc_start: 0.9125 (mmm) cc_final: 0.8650 (mmm) REVERT: u 98 MET cc_start: 0.7019 (mmm) cc_final: 0.6474 (tpt) REVERT: u 108 LYS cc_start: 0.8824 (tppp) cc_final: 0.8458 (tptt) REVERT: u 120 MET cc_start: 0.7183 (tmm) cc_final: 0.6843 (tmm) outliers start: 41 outliers final: 34 residues processed: 469 average time/residue: 1.0393 time to fit residues: 784.8413 Evaluate side-chains 471 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 434 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain i residue 18 ASP Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 187 SER Chi-restraints excluded: chain k residue 17 PHE Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 91 CYS Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 91 CYS Chi-restraints excluded: chain p residue 120 MET Chi-restraints excluded: chain p residue 121 ILE Chi-restraints excluded: chain s residue 41 ASN Chi-restraints excluded: chain s residue 91 CYS Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain u residue 143 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 416 optimal weight: 2.9990 chunk 429 optimal weight: 10.0000 chunk 301 optimal weight: 0.6980 chunk 184 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 450 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 129 GLN ** k 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.085525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059955 restraints weight = 444115.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062695 restraints weight = 166012.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.064285 restraints weight = 96550.214| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39024 Z= 0.191 Angle : 0.509 9.649 52716 Z= 0.256 Chirality : 0.040 0.157 6045 Planarity : 0.003 0.081 6835 Dihedral : 5.568 63.950 5451 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.89 % Allowed : 11.55 % Favored : 87.55 % Cbeta Deviations : 0.02 % 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: 0.02 (0.12), residues: 4879 helix: 1.34 (0.11), residues: 2403 sheet: -0.93 (0.18), residues: 798 loop : -1.41 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 22 HIS 0.007 0.001 HIS p 122 PHE 0.026 0.001 PHE r 173 TYR 0.029 0.001 TYR u 128 ARG 0.018 0.000 ARG m 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 488 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 451 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9355 (OUTLIER) cc_final: 0.8685 (m-30) REVERT: A 170 ASP cc_start: 0.9534 (t0) cc_final: 0.9217 (t0) REVERT: B 347 ASP cc_start: 0.8876 (t0) cc_final: 0.8302 (t0) REVERT: C 363 MET cc_start: 0.8856 (tpp) cc_final: 0.8622 (mmt) REVERT: D 160 ASN cc_start: 0.9175 (m110) cc_final: 0.8903 (m110) REVERT: D 413 TYR cc_start: 0.7845 (m-80) cc_final: 0.7453 (m-80) REVERT: F 350 PHE cc_start: 0.8772 (m-80) cc_final: 0.8532 (m-80) REVERT: S 109 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7563 (mttp) REVERT: S 140 PHE cc_start: 0.8777 (p90) cc_final: 0.8517 (p90) REVERT: h 70 ILE cc_start: 0.9081 (mm) cc_final: 0.8860 (mm) REVERT: i 34 GLN cc_start: 0.8738 (tp40) cc_final: 0.8354 (tp40) REVERT: i 37 ASP cc_start: 0.8960 (p0) cc_final: 0.8569 (p0) REVERT: i 60 TYR cc_start: 0.7747 (m-80) cc_final: 0.7491 (m-80) REVERT: i 92 MET cc_start: 0.8264 (ttp) cc_final: 0.8015 (tmm) REVERT: j 17 PHE cc_start: 0.7534 (m-10) cc_final: 0.7313 (m-10) REVERT: k 12 ARG cc_start: 0.7265 (ttp80) cc_final: 0.7034 (tpm170) REVERT: k 26 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8169 (tm-30) REVERT: l 46 GLN cc_start: 0.9079 (mt0) cc_final: 0.8872 (mt0) REVERT: m 128 TYR cc_start: 0.7858 (t80) cc_final: 0.7326 (t80) REVERT: p 120 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7194 (tmm) REVERT: q 113 CYS cc_start: 0.9137 (p) cc_final: 0.8655 (p) REVERT: q 120 MET cc_start: 0.8014 (tmm) cc_final: 0.7727 (tmm) REVERT: r 153 MET cc_start: 0.7760 (mmm) cc_final: 0.7442 (tpp) REVERT: s 104 THR cc_start: 0.6537 (OUTLIER) cc_final: 0.6051 (t) REVERT: s 171 ASP cc_start: 0.7905 (m-30) cc_final: 0.7482 (m-30) REVERT: t 149 MET cc_start: 0.8495 (tmm) cc_final: 0.8100 (mmm) REVERT: t 153 MET cc_start: 0.9124 (mmm) cc_final: 0.8638 (mmm) REVERT: u 98 MET cc_start: 0.6937 (mmm) cc_final: 0.6406 (tpt) REVERT: u 120 MET cc_start: 0.7200 (tmm) cc_final: 0.6856 (tmm) outliers start: 37 outliers final: 32 residues processed: 474 average time/residue: 1.0513 time to fit residues: 811.6144 Evaluate side-chains 472 residues out of total 4137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 437 time to evaluate : 4.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain h residue 91 CYS Chi-restraints excluded: chain i residue 18 ASP Chi-restraints excluded: chain i residue 91 CYS Chi-restraints excluded: chain j residue 41 ASN Chi-restraints excluded: chain j residue 187 SER Chi-restraints excluded: chain k residue 17 PHE Chi-restraints excluded: chain k residue 43 ILE Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain l residue 18 ASP Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain l residue 91 CYS Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 91 CYS Chi-restraints excluded: chain p residue 120 MET Chi-restraints excluded: chain p residue 121 ILE Chi-restraints excluded: chain s residue 41 ASN Chi-restraints excluded: chain s residue 91 CYS Chi-restraints excluded: chain s residue 104 THR Chi-restraints excluded: chain u residue 143 LEU Chi-restraints excluded: chain v residue 119 VAL Chi-restraints excluded: chain v residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 262 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 382 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 163 GLN ** q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 81 GLN ** u 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.084923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059369 restraints weight = 447613.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.062100 restraints weight = 166611.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063677 restraints weight = 96368.846| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39024 Z= 0.251 Angle : 0.524 9.566 52716 Z= 0.268 Chirality : 0.040 0.144 6045 Planarity : 0.003 0.078 6835 Dihedral : 5.575 63.508 5451 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.94 % Allowed : 11.77 % Favored : 87.29 % Cbeta Deviations : 0.02 % 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: -0.04 (0.12), residues: 4879 helix: 1.32 (0.11), residues: 2399 sheet: -1.06 (0.17), residues: 871 loop : -1.43 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 22 HIS 0.007 0.001 HIS p 122 PHE 0.033 0.001 PHE S 125 TYR 0.025 0.001 TYR u 128 ARG 0.016 0.000 ARG m 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22641.82 seconds wall clock time: 390 minutes 25.58 seconds (23425.58 seconds total)