Starting phenix.real_space_refine on Sun Dec 29 10:48:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et3_28585/12_2024/8et3_28585_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et3_28585/12_2024/8et3_28585.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/8et3_28585/12_2024/8et3_28585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et3_28585/12_2024/8et3_28585.map" model { file = "/net/cci-nas-00/data/ceres_data/8et3_28585/12_2024/8et3_28585_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et3_28585/12_2024/8et3_28585_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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 128 5.16 5 C 17844 2.51 5 N 4847 2.21 5 O 5477 1.98 5 H 28542 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 56854 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5334 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 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: 5452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5452 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "D" Number of atoms: 5452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5452 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "E" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5304 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 13, 'TRANS': 328} Chain breaks: 1 Chain: "F" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5147 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 3 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: "S" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 145 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'TRANS': 10} Chain: "Y" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1645 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "Z" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1644 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 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} Time building chain proxies: 20.65, per 1000 atoms: 0.36 Number of scatterers: 56854 At special positions: 0 Unit cell: (146.432, 144.768, 181.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 16 15.00 O 5477 8.00 N 4847 7.00 C 17844 6.00 H 28542 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: 11.44 Conformation dependent library (CDL) restraints added in 3.7 seconds 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6692 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 43 sheets defined 50.7% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.700A pdb=" N ILE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 101 Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.647A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 4.097A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.575A pdb=" N ARG A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.984A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.558A pdb=" N HIS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.514A pdb=" N GLN A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.730A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.539A pdb=" N ILE A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.756A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.535A pdb=" N LYS A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 4.227A pdb=" N ARG A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.690A pdb=" N ILE A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.930A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.598A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.154A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.727A pdb=" N ARG B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.433A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.912A pdb=" N HIS B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.884A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.630A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.584A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.513A pdb=" N LEU B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.077A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.651A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.666A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.215A pdb=" N ARG B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.604A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.644A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.615A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.514A pdb=" N GLN C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.666A pdb=" N GLN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 removed outlier: 3.569A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.669A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.616A pdb=" N LEU C 308 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.557A pdb=" N GLN C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.530A pdb=" N ALA C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 4.252A pdb=" N ARG C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 removed outlier: 3.666A pdb=" N ASP C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.787A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.837A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.644A pdb=" N ASN D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.699A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.566A pdb=" N LYS D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.802A pdb=" N ARG D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.567A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 217 removed outlier: 3.537A pdb=" N GLN D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 282 through 289 removed outlier: 3.630A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.500A pdb=" N LEU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.577A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.763A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 Processing helix chain 'D' and resid 351 through 366 Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.966A pdb=" N SER D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP D 382 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR D 383 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.647A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.670A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 101 Processing helix chain 'E' and resid 124 through 136 Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.971A pdb=" N ILE E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 179 removed outlier: 3.826A pdb=" N ARG E 178 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 217 removed outlier: 4.127A pdb=" N GLN E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 211 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 Processing helix chain 'E' and resid 280 through 289 removed outlier: 3.808A pdb=" N GLY E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.660A pdb=" N ILE E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.783A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 344 removed outlier: 3.779A pdb=" N GLU E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 Processing helix chain 'E' and resid 368 through 387 removed outlier: 3.557A pdb=" N LEU E 372 " --> pdb=" O GLY E 368 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG E 373 " --> pdb=" O ALA E 369 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA E 379 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP E 382 " --> pdb=" O ALA E 378 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR E 383 " --> pdb=" O ALA E 379 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 405 Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.697A pdb=" N ASP F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 101 Processing helix chain 'F' and resid 124 through 136 removed outlier: 4.206A pdb=" N LEU F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 158 through 169 removed outlier: 3.570A pdb=" N CYS F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 179 Processing helix chain 'F' and resid 185 through 190 removed outlier: 3.825A pdb=" N ILE F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 217 removed outlier: 3.715A pdb=" N GLN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 263 removed outlier: 3.833A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 289 Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.802A pdb=" N LEU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.612A pdb=" N ILE F 305 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 308 " --> pdb=" O PHE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 removed outlier: 3.555A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 345 Processing helix chain 'F' and resid 351 through 366 Processing helix chain 'F' and resid 369 through 380 removed outlier: 4.192A pdb=" N ARG F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 387 removed outlier: 3.547A pdb=" N ASP F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.668A pdb=" N LEU H 23 " --> pdb=" O ILE H 19 " (cutoff:3.500A) removed outlier: 3.955A 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: 3.579A pdb=" N GLY H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.906A 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 131 through 158 Processing helix chain 'H' and resid 160 through 169 Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.634A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS I 25 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 removed outlier: 3.626A pdb=" N GLU I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.569A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR I 79 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 131 through 158 Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 176 through 183 Processing helix chain 'J' and resid 19 through 25 removed outlier: 3.766A 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: 3.799A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 131 through 158 Processing helix chain 'J' and resid 160 through 168 Processing helix chain 'J' and resid 176 through 183 Processing helix chain 'K' and resid 19 through 25 Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.506A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 131 through 158 removed outlier: 3.511A pdb=" N ILE K 137 " --> pdb=" O THR K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 168 Processing helix chain 'K' and resid 176 through 183 Processing helix chain 'L' and resid 19 through 25 removed outlier: 3.605A pdb=" N LYS L 25 " --> pdb=" O SER L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 removed outlier: 3.565A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.703A 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 131 through 158 Processing helix chain 'L' and resid 160 through 168 Processing helix chain 'L' and resid 176 through 183 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.744A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 54 removed outlier: 3.567A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 83 Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 131 through 158 removed outlier: 3.558A pdb=" N ILE M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 170 removed outlier: 4.492A pdb=" N ARG M 170 " --> pdb=" O ARG M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.564A pdb=" N LYS N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.761A pdb=" N GLY N 73 " --> pdb=" O VAL N 69 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 104 Processing helix chain 'N' and resid 131 through 158 Processing helix chain 'N' and resid 160 through 170 removed outlier: 4.332A pdb=" N ARG N 170 " --> pdb=" O ARG N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'Y' and resid 9 through 24 Processing helix chain 'Z' and resid 9 through 24 removed outlier: 3.546A pdb=" N LEU Z 22 " --> pdb=" O TYR Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 46 Processing helix chain 'Z' and resid 56 through 58 No H-bonds generated for 'chain 'Z' and resid 56 through 58' Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 144 removed outlier: 6.075A pdb=" N THR A 141 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP A 184 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA A 143 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 115 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 221 removed outlier: 3.812A pdb=" N ALA A 220 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 238 " --> pdb=" O ALA A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.252A pdb=" N THR B 141 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASP B 184 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA B 143 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.532A pdb=" N VAL B 238 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 222 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 349 removed outlier: 6.854A pdb=" N ILE B 412 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL B 396 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 410 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.224A pdb=" N THR C 141 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASP C 184 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA C 143 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C 115 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLY C 249 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU C 117 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 219 through 222 Processing sheet with id=AA9, first strand: chain 'C' and resid 347 through 349 removed outlier: 6.313A pdb=" N ASP C 347 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 140 through 144 removed outlier: 6.480A pdb=" N THR D 141 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP D 184 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA D 143 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU D 116 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB3, first strand: chain 'D' and resid 347 through 349 Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 removed outlier: 6.137A pdb=" N THR E 141 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU E 116 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 219 through 222 Processing sheet with id=AB6, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.508A pdb=" N VAL E 397 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 410 " --> pdb=" O VAL E 397 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.380A pdb=" N THR F 141 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP F 184 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA F 143 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE F 115 " --> pdb=" O PHE F 245 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS F 247 " --> pdb=" O ILE F 115 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU F 116 " --> pdb=" O ALA F 312 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 219 through 222 Processing sheet with id=AB9, first strand: chain 'F' and resid 347 through 349 removed outlier: 4.048A pdb=" N LYS F 395 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AC2, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.312A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER H 65 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG H 118 " --> pdb=" O CYS H 91 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY H 93 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N MET H 120 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA H 95 " --> pdb=" O MET H 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.312A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER H 65 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 5 through 10 Processing sheet with id=AC5, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.331A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER I 65 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.331A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER I 65 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 5 through 9 removed outlier: 3.745A pdb=" N ARG J 15 " --> pdb=" O GLU J 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 28 through 32 removed outlier: 5.487A pdb=" N SER J 65 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN J 94 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 28 through 32 removed outlier: 5.487A pdb=" N SER J 65 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN J 94 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG J 111 " --> pdb=" O SER J 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AD2, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.621A pdb=" N ILE K 29 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN K 64 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU K 31 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG K 118 " --> pdb=" O CYS K 91 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY K 93 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N MET K 120 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG K 172 " --> pdb=" O ILE K 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.621A pdb=" N ILE K 29 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN K 64 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU K 31 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG K 111 " --> pdb=" O SER K 187 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AD5, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.672A pdb=" N ILE L 29 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN L 64 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU L 31 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER L 65 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLN L 94 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG L 118 " --> pdb=" O CYS L 91 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY L 93 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N MET L 120 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.672A pdb=" N ILE L 29 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN L 64 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU L 31 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER L 65 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLN L 94 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG L 111 " --> pdb=" O SER L 187 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AD8, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.669A pdb=" N ILE M 29 " --> pdb=" O TYR M 62 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN M 64 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU M 31 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG M 118 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLY M 93 " --> pdb=" O ARG M 118 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N MET M 120 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA M 95 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.669A pdb=" N ILE M 29 " --> pdb=" O TYR M 62 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN M 64 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU M 31 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 5 through 9 Processing sheet with id=AE2, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.169A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG N 111 " --> pdb=" O SER N 187 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 118 through 121 Processing sheet with id=AE4, first strand: chain 'Y' and resid 51 through 54 removed outlier: 3.921A pdb=" N ALA Y 92 " --> pdb=" O VAL Y 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 61 through 65 removed outlier: 5.166A pdb=" N LEU Y 63 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU Y 65 " --> pdb=" O GLU Y 69 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLU Y 69 " --> pdb=" O LEU Y 65 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL Y 70 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE Y 79 " --> pdb=" O PHE Y 76 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 50 through 54 removed outlier: 3.669A pdb=" N ALA Z 92 " --> pdb=" O VAL Z 31 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP Z 33 " --> pdb=" O VAL Z 90 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL Z 90 " --> pdb=" O ASP Z 33 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 60 through 65 removed outlier: 7.893A pdb=" N VAL Z 60 " --> pdb=" O ARG Z 75 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ARG Z 75 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASN Z 62 " --> pdb=" O ASN Z 73 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN Z 73 " --> pdb=" O ASN Z 62 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3849 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: 22.34 Time building geometry restraints manager: 13.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 28516 1.06 - 1.28: 4970 1.28 - 1.50: 11320 1.50 - 1.73: 12250 1.73 - 1.95: 226 Bond restraints: 57282 Sorted by residual: bond pdb=" C ASN M 54 " pdb=" N PRO M 55 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.36e+00 bond pdb=" CB PHE F 235 " pdb=" CG PHE F 235 " ideal model delta sigma weight residual 1.502 1.534 -0.032 2.30e-02 1.89e+03 1.93e+00 bond pdb=" C ASN N 54 " pdb=" N PRO N 55 " ideal model delta sigma weight residual 1.339 1.379 -0.040 3.40e-02 8.65e+02 1.37e+00 bond pdb=" C SER N 65 " pdb=" N PRO N 66 " ideal model delta sigma weight residual 1.339 1.379 -0.039 3.40e-02 8.65e+02 1.34e+00 bond pdb=" CB PRO L 85 " pdb=" CG PRO L 85 " ideal model delta sigma weight residual 1.492 1.434 0.058 5.00e-02 4.00e+02 1.33e+00 ... (remaining 57277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 99933 1.36 - 2.72: 3602 2.72 - 4.08: 312 4.08 - 5.45: 120 5.45 - 6.81: 16 Bond angle restraints: 103983 Sorted by residual: angle pdb=" C ILE H 83 " pdb=" N LYS H 84 " pdb=" CA LYS H 84 " ideal model delta sigma weight residual 119.78 123.80 -4.02 1.24e+00 6.50e-01 1.05e+01 angle pdb=" N GLN F 233 " pdb=" CA GLN F 233 " pdb=" C GLN F 233 " ideal model delta sigma weight residual 112.72 116.48 -3.76 1.28e+00 6.10e-01 8.61e+00 angle pdb=" N GLU F 234 " pdb=" CA GLU F 234 " pdb=" C GLU F 234 " ideal model delta sigma weight residual 111.36 114.48 -3.12 1.09e+00 8.42e-01 8.19e+00 angle pdb=" N SER L 65 " pdb=" CA SER L 65 " pdb=" C SER L 65 " ideal model delta sigma weight residual 108.23 112.75 -4.52 1.62e+00 3.81e-01 7.78e+00 angle pdb=" C ASP D 103 " pdb=" N THR D 104 " pdb=" CA THR D 104 " ideal model delta sigma weight residual 122.41 128.18 -5.77 2.09e+00 2.29e-01 7.63e+00 ... (remaining 103978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.09: 25740 30.09 - 60.17: 848 60.17 - 90.26: 54 90.26 - 120.34: 0 120.34 - 150.43: 2 Dihedral angle restraints: 26644 sinusoidal: 15036 harmonic: 11608 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 149.57 150.43 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" O1A AGS D 500 " pdb=" O3A AGS D 500 " pdb=" PA AGS D 500 " pdb=" PB AGS D 500 " ideal model delta sinusoidal sigma weight residual 292.27 150.71 141.56 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" CB GLU M 136 " pdb=" CG GLU M 136 " pdb=" CD GLU M 136 " pdb=" OE1 GLU M 136 " ideal model delta sinusoidal sigma weight residual 0.00 89.60 -89.60 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 26641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3267 0.037 - 0.075: 786 0.075 - 0.112: 305 0.112 - 0.149: 132 0.149 - 0.187: 6 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CB THR D 104 " pdb=" CA THR D 104 " pdb=" OG1 THR D 104 " pdb=" CG2 THR D 104 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA VAL A 222 " pdb=" N VAL A 222 " pdb=" C VAL A 222 " pdb=" CB VAL A 222 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PRO A 224 " pdb=" N PRO A 224 " pdb=" C PRO A 224 " pdb=" CB PRO A 224 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 4493 not shown) Planarity restraints: 8511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 230 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 231 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 222 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 223 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 235 " 0.016 2.00e-02 2.50e+03 9.88e-03 2.93e+00 pdb=" CG PHE F 235 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE F 235 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE F 235 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE F 235 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 235 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 235 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE F 235 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE F 235 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE F 235 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE F 235 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE F 235 " 0.001 2.00e-02 2.50e+03 ... (remaining 8508 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 6644 2.26 - 2.84: 132277 2.84 - 3.43: 146914 3.43 - 4.01: 204281 4.01 - 4.60: 312687 Nonbonded interactions: 802803 Sorted by model distance: nonbonded pdb=" H HIS B 230 " pdb=" OE1 GLN B 233 " model vdw 1.672 2.450 nonbonded pdb=" O LEU A 166 " pdb=" H TYR A 171 " model vdw 1.677 2.450 nonbonded pdb=" O ILE N 59 " pdb=" H SER N 88 " model vdw 1.687 2.450 nonbonded pdb=" OE1 GLN F 233 " pdb=" H GLN F 233 " model vdw 1.690 2.450 nonbonded pdb=" O ILE M 59 " pdb=" H SER M 88 " model vdw 1.704 2.450 ... (remaining 802798 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 151 or resid 157 through 191 or (resid 202 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 \ or name HG23)) or resid 203 through 413)) selection = (chain 'B' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 151 or resid 157 through 191 or ( \ resid 202 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 203 through 413)) selection = (chain 'C' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 151 or resid 157 through 191 or ( \ resid 202 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 203 through 413)) selection = (chain 'D' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 151 or resid 157 through 191 or ( \ resid 202 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 203 through 413)) selection = (chain 'E' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 151 or resid 157 through 191 or ( \ resid 202 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG2 \ 1 or name HG22 or name HG23)) or resid 203 through 413)) selection = (chain 'F' and (resid 65 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 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' } ncs_group { reference = (chain 'Y' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 8 through 111)) selection = chain 'Z' } 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.740 Extract box with map and model: 1.680 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 94.010 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28740 Z= 0.211 Angle : 0.615 6.807 38873 Z= 0.325 Chirality : 0.042 0.187 4496 Planarity : 0.004 0.068 5041 Dihedral : 12.769 150.429 10918 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 3597 helix: 0.51 (0.12), residues: 1663 sheet: 0.32 (0.20), residues: 540 loop : -0.69 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 20 HIS 0.007 0.001 HIS H 122 PHE 0.029 0.001 PHE F 235 TYR 0.007 0.001 TYR B 153 ARG 0.010 0.001 ARG L 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 3.434 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: B 256 LYS cc_start: 0.9388 (mmmm) cc_final: 0.9148 (mmmm) REVERT: B 384 MET cc_start: 0.8947 (mtp) cc_final: 0.8745 (mtp) REVERT: E 142 MET cc_start: 0.7655 (tmm) cc_final: 0.7150 (tmm) REVERT: F 245 PHE cc_start: 0.8695 (m-80) cc_final: 0.8446 (m-80) REVERT: F 384 MET cc_start: 0.9230 (mpp) cc_final: 0.8895 (mpp) REVERT: H 17 PHE cc_start: 0.7975 (m-80) cc_final: 0.7546 (m-80) REVERT: H 171 ASP cc_start: 0.7935 (m-30) cc_final: 0.7339 (t0) REVERT: I 5 MET cc_start: 0.8787 (mmm) cc_final: 0.8414 (mmm) REVERT: I 120 MET cc_start: 0.8646 (ttp) cc_final: 0.8054 (tmm) REVERT: I 171 ASP cc_start: 0.8461 (m-30) cc_final: 0.7580 (t0) REVERT: J 125 LEU cc_start: 0.8847 (mp) cc_final: 0.8627 (mp) REVERT: J 172 ARG cc_start: 0.8383 (ttt90) cc_final: 0.8169 (mmm160) REVERT: K 8 GLU cc_start: 0.8165 (tt0) cc_final: 0.7846 (tt0) REVERT: K 11 SER cc_start: 0.5234 (p) cc_final: 0.5014 (p) REVERT: L 63 ILE cc_start: 0.9366 (mt) cc_final: 0.9132 (tt) REVERT: L 92 MET cc_start: 0.8662 (mtm) cc_final: 0.8182 (mtt) REVERT: L 94 GLN cc_start: 0.8722 (pt0) cc_final: 0.7835 (pm20) REVERT: L 113 CYS cc_start: 0.8529 (t) cc_final: 0.8100 (t) REVERT: M 8 GLU cc_start: 0.7834 (tp30) cc_final: 0.7470 (tp30) REVERT: M 17 PHE cc_start: 0.8172 (m-80) cc_final: 0.7873 (m-80) REVERT: M 113 CYS cc_start: 0.8780 (t) cc_final: 0.8506 (t) REVERT: N 34 GLN cc_start: 0.8961 (mm110) cc_final: 0.8567 (mm-40) REVERT: N 153 MET cc_start: 0.9620 (mtp) cc_final: 0.9401 (ttm) REVERT: Y 43 MET cc_start: 0.7951 (mpp) cc_final: 0.7569 (mmt) REVERT: Y 81 ARG cc_start: 0.5881 (mtp-110) cc_final: 0.5148 (ttt180) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.9137 time to fit residues: 510.6063 Evaluate side-chains 241 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 40.0000 chunk 145 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS B 260 HIS D 163 GLN E 260 HIS F 83 GLN F 324 GLN I 163 GLN J 41 ASN K 156 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28740 Z= 0.311 Angle : 0.596 9.663 38873 Z= 0.314 Chirality : 0.041 0.169 4496 Planarity : 0.004 0.049 5041 Dihedral : 6.953 141.002 4011 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.11 % Favored : 97.80 % Rotamer: Outliers : 0.66 % Allowed : 5.08 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 3597 helix: 1.25 (0.12), residues: 1719 sheet: 0.41 (0.20), residues: 553 loop : -0.52 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 20 HIS 0.007 0.001 HIS E 260 PHE 0.015 0.001 PHE E 298 TYR 0.017 0.001 TYR D 171 ARG 0.008 0.000 ARG K 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 3.385 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: E 142 MET cc_start: 0.7871 (tmm) cc_final: 0.7398 (tmm) REVERT: F 245 PHE cc_start: 0.8835 (m-80) cc_final: 0.8399 (m-80) REVERT: H 17 PHE cc_start: 0.8160 (m-80) cc_final: 0.7716 (m-80) REVERT: H 86 ASP cc_start: 0.8519 (m-30) cc_final: 0.7941 (t0) REVERT: H 120 MET cc_start: 0.8520 (ttp) cc_final: 0.8292 (ttp) REVERT: H 171 ASP cc_start: 0.8061 (m-30) cc_final: 0.7787 (t0) REVERT: I 5 MET cc_start: 0.8979 (mmm) cc_final: 0.8583 (mmp) REVERT: J 34 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8233 (mm-40) REVERT: J 172 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7716 (mmm160) REVERT: K 149 MET cc_start: 0.8796 (mmm) cc_final: 0.8515 (mmm) REVERT: M 8 GLU cc_start: 0.8080 (tp30) cc_final: 0.7654 (tp30) REVERT: M 113 CYS cc_start: 0.8748 (t) cc_final: 0.8327 (t) REVERT: M 120 MET cc_start: 0.7865 (ttp) cc_final: 0.7446 (tmm) REVERT: N 34 GLN cc_start: 0.8916 (mm110) cc_final: 0.8683 (mm-40) REVERT: N 74 MET cc_start: 0.9236 (mmm) cc_final: 0.8985 (mmm) REVERT: Y 43 MET cc_start: 0.8004 (mpp) cc_final: 0.7671 (mmt) REVERT: Y 81 ARG cc_start: 0.5681 (mtp-110) cc_final: 0.5013 (ttt180) outliers start: 20 outliers final: 15 residues processed: 248 average time/residue: 0.8723 time to fit residues: 325.4084 Evaluate side-chains 234 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 256 LYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 324 GLN Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Z residue 19 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 353 optimal weight: 40.0000 chunk 291 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS B 237 GLN B 331 ASN C 83 GLN C 94 ASN C 324 GLN J 138 HIS Y 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 28740 Z= 0.388 Angle : 0.581 9.743 38873 Z= 0.304 Chirality : 0.041 0.186 4496 Planarity : 0.004 0.040 5041 Dihedral : 6.813 127.852 4011 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.66 % Allowed : 5.87 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 3597 helix: 1.27 (0.12), residues: 1736 sheet: 0.32 (0.20), residues: 555 loop : -0.51 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 20 HIS 0.012 0.001 HIS N 122 PHE 0.011 0.001 PHE A 270 TYR 0.011 0.001 TYR A 337 ARG 0.006 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 3.418 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: E 142 MET cc_start: 0.7882 (tmm) cc_final: 0.7428 (tmm) REVERT: H 120 MET cc_start: 0.8711 (ttp) cc_final: 0.8475 (ttp) REVERT: H 162 GLU cc_start: 0.9425 (mp0) cc_final: 0.9087 (pp20) REVERT: I 171 ASP cc_start: 0.8645 (m-30) cc_final: 0.7830 (t0) REVERT: J 36 GLU cc_start: 0.8808 (pt0) cc_final: 0.8510 (pm20) REVERT: J 172 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7753 (mmm160) REVERT: K 149 MET cc_start: 0.8800 (mmm) cc_final: 0.8423 (mmm) REVERT: M 8 GLU cc_start: 0.8248 (tp30) cc_final: 0.7786 (tp30) REVERT: M 113 CYS cc_start: 0.8808 (t) cc_final: 0.8368 (t) REVERT: N 34 GLN cc_start: 0.8967 (mm110) cc_final: 0.8711 (mm-40) REVERT: N 146 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8703 (tttp) REVERT: N 150 ASN cc_start: 0.8563 (m110) cc_final: 0.8254 (m110) REVERT: Y 43 MET cc_start: 0.8030 (mpp) cc_final: 0.7647 (mmt) outliers start: 20 outliers final: 17 residues processed: 227 average time/residue: 0.8514 time to fit residues: 296.3734 Evaluate side-chains 215 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 260 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 18 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 40.0000 chunk 328 optimal weight: 5.9990 chunk 347 optimal weight: 30.0000 chunk 171 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN L 41 ASN ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28740 Z= 0.228 Angle : 0.494 7.968 38873 Z= 0.254 Chirality : 0.040 0.151 4496 Planarity : 0.003 0.035 5041 Dihedral : 6.630 120.859 4011 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.56 % Allowed : 6.43 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3597 helix: 1.63 (0.12), residues: 1737 sheet: 0.39 (0.21), residues: 568 loop : -0.33 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 20 HIS 0.003 0.001 HIS N 156 PHE 0.012 0.001 PHE L 17 TYR 0.024 0.001 TYR A 171 ARG 0.006 0.000 ARG J 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 3.494 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: E 142 MET cc_start: 0.7835 (tmm) cc_final: 0.7376 (tmm) REVERT: H 171 ASP cc_start: 0.8173 (m-30) cc_final: 0.7696 (t0) REVERT: I 171 ASP cc_start: 0.8727 (m-30) cc_final: 0.7922 (t0) REVERT: J 34 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8051 (mm-40) REVERT: J 172 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7747 (mmm160) REVERT: K 149 MET cc_start: 0.8783 (mmm) cc_final: 0.8413 (mmm) REVERT: L 113 CYS cc_start: 0.8590 (t) cc_final: 0.8172 (t) REVERT: M 14 GLU cc_start: 0.8432 (pm20) cc_final: 0.8172 (pm20) REVERT: M 98 MET cc_start: 0.9151 (mmm) cc_final: 0.8788 (mmm) REVERT: M 113 CYS cc_start: 0.8751 (t) cc_final: 0.8289 (t) REVERT: N 5 MET cc_start: 0.8780 (mmm) cc_final: 0.8108 (mmm) REVERT: N 34 GLN cc_start: 0.8967 (mm110) cc_final: 0.8681 (mm-40) REVERT: N 60 TYR cc_start: 0.8908 (m-80) cc_final: 0.8681 (m-80) REVERT: N 74 MET cc_start: 0.9255 (mmm) cc_final: 0.8946 (mmp) REVERT: N 150 ASN cc_start: 0.8642 (m110) cc_final: 0.8258 (m110) REVERT: Y 43 MET cc_start: 0.8035 (mpp) cc_final: 0.7613 (mmt) outliers start: 17 outliers final: 13 residues processed: 213 average time/residue: 0.8671 time to fit residues: 283.0761 Evaluate side-chains 207 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 296 optimal weight: 50.0000 chunk 240 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 312 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28740 Z= 0.265 Angle : 0.510 10.154 38873 Z= 0.259 Chirality : 0.040 0.231 4496 Planarity : 0.003 0.039 5041 Dihedral : 6.539 117.206 4011 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.59 % Allowed : 6.82 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3597 helix: 1.72 (0.12), residues: 1745 sheet: 0.39 (0.21), residues: 570 loop : -0.29 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 20 HIS 0.003 0.001 HIS N 122 PHE 0.012 0.001 PHE L 101 TYR 0.010 0.001 TYR A 337 ARG 0.004 0.000 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 3.425 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: E 142 MET cc_start: 0.7870 (tmm) cc_final: 0.7402 (tmm) REVERT: H 86 ASP cc_start: 0.8507 (m-30) cc_final: 0.7931 (t0) REVERT: H 120 MET cc_start: 0.8734 (ttp) cc_final: 0.8168 (ttp) REVERT: H 162 GLU cc_start: 0.9440 (mp0) cc_final: 0.9115 (pp20) REVERT: H 171 ASP cc_start: 0.8348 (m-30) cc_final: 0.7725 (t0) REVERT: I 171 ASP cc_start: 0.8752 (m-30) cc_final: 0.7946 (t0) REVERT: J 34 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8124 (mm-40) REVERT: J 172 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7764 (mmm160) REVERT: L 113 CYS cc_start: 0.8574 (t) cc_final: 0.8203 (t) REVERT: L 120 MET cc_start: 0.6820 (mmp) cc_final: 0.6370 (mmp) REVERT: M 8 GLU cc_start: 0.8235 (tp30) cc_final: 0.7870 (tp30) REVERT: M 113 CYS cc_start: 0.8774 (t) cc_final: 0.8316 (t) REVERT: N 34 GLN cc_start: 0.8996 (mm110) cc_final: 0.8716 (mm-40) REVERT: N 74 MET cc_start: 0.9274 (mmm) cc_final: 0.8902 (mmm) REVERT: Y 43 MET cc_start: 0.8040 (mpp) cc_final: 0.7635 (mmt) outliers start: 18 outliers final: 13 residues processed: 208 average time/residue: 0.8778 time to fit residues: 279.6605 Evaluate side-chains 207 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.9990 chunk 313 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 348 optimal weight: 50.0000 chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 331 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN H 9 GLN L 41 ASN Y 73 ASN ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28740 Z= 0.225 Angle : 0.484 9.262 38873 Z= 0.247 Chirality : 0.040 0.151 4496 Planarity : 0.003 0.038 5041 Dihedral : 6.481 115.832 4011 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.56 % Allowed : 7.38 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.14), residues: 3597 helix: 1.86 (0.12), residues: 1747 sheet: 0.33 (0.23), residues: 500 loop : -0.24 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 20 HIS 0.003 0.001 HIS M 156 PHE 0.017 0.001 PHE M 101 TYR 0.011 0.001 TYR D 182 ARG 0.003 0.000 ARG Y 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 3.443 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: E 142 MET cc_start: 0.7857 (tmm) cc_final: 0.7394 (tmm) REVERT: H 60 TYR cc_start: 0.9025 (m-80) cc_final: 0.8591 (m-80) REVERT: H 120 MET cc_start: 0.8708 (ttp) cc_final: 0.8347 (ttp) REVERT: H 171 ASP cc_start: 0.8398 (m-30) cc_final: 0.7883 (t0) REVERT: I 120 MET cc_start: 0.8799 (ttp) cc_final: 0.8240 (ttt) REVERT: I 171 ASP cc_start: 0.8795 (m-30) cc_final: 0.7989 (t0) REVERT: J 34 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8256 (mm110) REVERT: J 172 ARG cc_start: 0.8054 (ttt90) cc_final: 0.7792 (mmm160) REVERT: K 120 MET cc_start: 0.8040 (ttt) cc_final: 0.7193 (tmm) REVERT: L 113 CYS cc_start: 0.8538 (t) cc_final: 0.8153 (t) REVERT: M 113 CYS cc_start: 0.8740 (t) cc_final: 0.8271 (t) REVERT: N 34 GLN cc_start: 0.9007 (mm110) cc_final: 0.8716 (mm-40) REVERT: Y 43 MET cc_start: 0.8026 (mpp) cc_final: 0.7611 (mmt) outliers start: 17 outliers final: 14 residues processed: 203 average time/residue: 0.8945 time to fit residues: 278.3150 Evaluate side-chains 204 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 194 optimal weight: 0.0770 chunk 346 optimal weight: 50.0000 chunk 217 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28740 Z= 0.226 Angle : 0.488 8.837 38873 Z= 0.248 Chirality : 0.040 0.147 4496 Planarity : 0.003 0.038 5041 Dihedral : 6.444 116.251 4011 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.59 % Allowed : 7.75 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 3597 helix: 1.92 (0.12), residues: 1745 sheet: 0.34 (0.23), residues: 510 loop : -0.21 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 20 HIS 0.003 0.001 HIS M 156 PHE 0.013 0.001 PHE L 101 TYR 0.009 0.001 TYR A 337 ARG 0.007 0.000 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 3.431 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: E 142 MET cc_start: 0.7878 (tmm) cc_final: 0.7423 (tmm) REVERT: E 260 HIS cc_start: 0.9157 (OUTLIER) cc_final: 0.8889 (t70) REVERT: H 60 TYR cc_start: 0.9018 (m-80) cc_final: 0.8687 (m-80) REVERT: H 86 ASP cc_start: 0.8441 (m-30) cc_final: 0.7972 (t0) REVERT: H 120 MET cc_start: 0.8738 (ttp) cc_final: 0.8154 (ttp) REVERT: H 162 GLU cc_start: 0.9457 (mp0) cc_final: 0.9022 (pm20) REVERT: H 171 ASP cc_start: 0.8436 (m-30) cc_final: 0.7822 (t0) REVERT: I 120 MET cc_start: 0.8819 (ttp) cc_final: 0.8201 (ttt) REVERT: I 171 ASP cc_start: 0.8801 (m-30) cc_final: 0.7976 (t0) REVERT: K 120 MET cc_start: 0.8058 (ttt) cc_final: 0.7196 (tmm) REVERT: L 113 CYS cc_start: 0.8487 (t) cc_final: 0.8122 (t) REVERT: M 113 CYS cc_start: 0.8731 (t) cc_final: 0.8271 (t) REVERT: N 34 GLN cc_start: 0.9010 (mm110) cc_final: 0.8731 (mm-40) REVERT: N 182 TYR cc_start: 0.8405 (t80) cc_final: 0.8168 (t80) REVERT: Y 43 MET cc_start: 0.8036 (mpp) cc_final: 0.7610 (mmt) outliers start: 18 outliers final: 15 residues processed: 205 average time/residue: 0.9268 time to fit residues: 292.2048 Evaluate side-chains 210 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 260 HIS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Z residue 19 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 272 optimal weight: 0.0980 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN E 94 ASN E 101 ASN H 46 GLN L 41 ASN ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28740 Z= 0.263 Angle : 0.500 7.042 38873 Z= 0.256 Chirality : 0.040 0.148 4496 Planarity : 0.003 0.038 5041 Dihedral : 6.483 116.893 4011 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.66 % Allowed : 7.81 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 3597 helix: 1.88 (0.12), residues: 1751 sheet: 0.40 (0.23), residues: 491 loop : -0.35 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 20 HIS 0.004 0.001 HIS M 156 PHE 0.018 0.001 PHE L 101 TYR 0.010 0.001 TYR A 337 ARG 0.005 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 3.543 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: E 142 MET cc_start: 0.7894 (tmm) cc_final: 0.7456 (tmm) REVERT: H 60 TYR cc_start: 0.9036 (m-80) cc_final: 0.8709 (m-80) REVERT: H 86 ASP cc_start: 0.8447 (m-30) cc_final: 0.7912 (t0) REVERT: H 120 MET cc_start: 0.8759 (ttp) cc_final: 0.8160 (tpp) REVERT: I 120 MET cc_start: 0.8821 (ttp) cc_final: 0.8104 (ttt) REVERT: I 171 ASP cc_start: 0.8810 (m-30) cc_final: 0.7999 (t0) REVERT: J 34 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8251 (mm-40) REVERT: J 172 ARG cc_start: 0.8380 (tpp80) cc_final: 0.8108 (mmm160) REVERT: K 120 MET cc_start: 0.8034 (ttt) cc_final: 0.7193 (tmm) REVERT: L 113 CYS cc_start: 0.8511 (t) cc_final: 0.8151 (t) REVERT: M 113 CYS cc_start: 0.8714 (t) cc_final: 0.8242 (t) REVERT: N 34 GLN cc_start: 0.9026 (mm110) cc_final: 0.8748 (mm-40) REVERT: Y 43 MET cc_start: 0.8022 (mpp) cc_final: 0.7634 (mmt) outliers start: 20 outliers final: 19 residues processed: 210 average time/residue: 0.9088 time to fit residues: 292.6939 Evaluate side-chains 214 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Z residue 19 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 40.0000 chunk 332 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 253 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 292 optimal weight: 9.9990 chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 GLN L 41 ASN ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28740 Z= 0.289 Angle : 0.519 8.032 38873 Z= 0.266 Chirality : 0.040 0.167 4496 Planarity : 0.003 0.037 5041 Dihedral : 6.537 117.386 4011 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.69 % Allowed : 7.91 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.14), residues: 3597 helix: 1.87 (0.12), residues: 1744 sheet: 0.39 (0.23), residues: 489 loop : -0.38 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 20 HIS 0.005 0.001 HIS K 156 PHE 0.014 0.001 PHE L 101 TYR 0.010 0.001 TYR A 337 ARG 0.005 0.000 ARG L 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 3.857 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: E 142 MET cc_start: 0.7876 (tmm) cc_final: 0.7435 (tmm) REVERT: H 60 TYR cc_start: 0.9045 (m-80) cc_final: 0.8718 (m-80) REVERT: H 86 ASP cc_start: 0.8462 (m-30) cc_final: 0.7949 (t0) REVERT: H 120 MET cc_start: 0.8738 (ttp) cc_final: 0.8169 (tpp) REVERT: H 162 GLU cc_start: 0.9495 (mp0) cc_final: 0.9119 (pm20) REVERT: I 120 MET cc_start: 0.8841 (ttp) cc_final: 0.8142 (ttt) REVERT: I 171 ASP cc_start: 0.8849 (m-30) cc_final: 0.8023 (t0) REVERT: J 34 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8285 (mm-40) REVERT: K 118 ARG cc_start: 0.8547 (ptp-170) cc_final: 0.8148 (ptp-170) REVERT: K 120 MET cc_start: 0.8114 (ttt) cc_final: 0.7229 (tmm) REVERT: L 113 CYS cc_start: 0.8475 (t) cc_final: 0.8115 (t) REVERT: M 60 TYR cc_start: 0.8915 (m-80) cc_final: 0.8071 (m-80) REVERT: N 34 GLN cc_start: 0.9026 (mm110) cc_final: 0.8749 (mm-40) REVERT: Y 25 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7733 (tm-30) REVERT: Y 43 MET cc_start: 0.8004 (mpp) cc_final: 0.7591 (mmt) outliers start: 21 outliers final: 21 residues processed: 204 average time/residue: 0.9372 time to fit residues: 292.4403 Evaluate side-chains 211 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 324 GLN Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Z residue 19 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 8.9990 chunk 341 optimal weight: 40.0000 chunk 208 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 chunk 358 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 28740 Z= 0.292 Angle : 0.640 59.179 38873 Z= 0.356 Chirality : 0.040 0.154 4496 Planarity : 0.003 0.037 5041 Dihedral : 6.538 117.381 4011 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.66 % Allowed : 7.94 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.14), residues: 3597 helix: 1.86 (0.12), residues: 1744 sheet: 0.39 (0.23), residues: 489 loop : -0.38 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 20 HIS 0.005 0.001 HIS K 156 PHE 0.013 0.001 PHE L 101 TYR 0.010 0.001 TYR A 337 ARG 0.005 0.000 ARG L 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7194 Ramachandran restraints generated. 3597 Oldfield, 0 Emsley, 3597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 3.575 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: E 142 MET cc_start: 0.7889 (tmm) cc_final: 0.7450 (tmm) REVERT: H 60 TYR cc_start: 0.9044 (m-80) cc_final: 0.8717 (m-80) REVERT: H 86 ASP cc_start: 0.8462 (m-30) cc_final: 0.7949 (t0) REVERT: H 120 MET cc_start: 0.8756 (ttp) cc_final: 0.8167 (tpp) REVERT: H 162 GLU cc_start: 0.9501 (mp0) cc_final: 0.9103 (pm20) REVERT: I 120 MET cc_start: 0.8839 (ttp) cc_final: 0.8140 (ttt) REVERT: I 171 ASP cc_start: 0.8849 (m-30) cc_final: 0.8024 (t0) REVERT: J 34 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8284 (mm-40) REVERT: K 118 ARG cc_start: 0.8547 (ptp-170) cc_final: 0.8148 (ptp-170) REVERT: K 120 MET cc_start: 0.8110 (ttt) cc_final: 0.7228 (tmm) REVERT: L 113 CYS cc_start: 0.8472 (t) cc_final: 0.8115 (t) REVERT: M 60 TYR cc_start: 0.8917 (m-80) cc_final: 0.8053 (m-80) REVERT: N 34 GLN cc_start: 0.9026 (mm110) cc_final: 0.8748 (mm-40) REVERT: Y 25 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7734 (tm-30) REVERT: Y 43 MET cc_start: 0.8004 (mpp) cc_final: 0.7592 (mmt) outliers start: 20 outliers final: 20 residues processed: 200 average time/residue: 0.8469 time to fit residues: 259.5341 Evaluate side-chains 209 residues out of total 3034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 113 CYS Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 113 CYS Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Z residue 19 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 286 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 293 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.053852 restraints weight = 366475.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056357 restraints weight = 169043.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056326 restraints weight = 105946.563| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 28740 Z= 0.292 Angle : 0.640 59.197 38873 Z= 0.356 Chirality : 0.040 0.154 4496 Planarity : 0.003 0.037 5041 Dihedral : 6.538 117.381 4011 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.66 % Allowed : 7.94 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.14), residues: 3597 helix: 1.86 (0.12), residues: 1744 sheet: 0.39 (0.23), residues: 489 loop : -0.38 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 20 HIS 0.005 0.001 HIS K 156 PHE 0.013 0.001 PHE L 101 TYR 0.010 0.001 TYR A 337 ARG 0.005 0.000 ARG L 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7358.35 seconds wall clock time: 129 minutes 2.13 seconds (7742.13 seconds total)