Starting phenix.real_space_refine on Thu Jan 16 16:49:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wrf_21882/01_2025/6wrf_21882_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wrf_21882/01_2025/6wrf_21882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wrf_21882/01_2025/6wrf_21882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wrf_21882/01_2025/6wrf_21882.map" model { file = "/net/cci-nas-00/data/ceres_data/6wrf_21882/01_2025/6wrf_21882_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wrf_21882/01_2025/6wrf_21882_neut_trim.cif" } resolution = 3.14 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 119 5.16 5 C 16882 2.51 5 N 4581 2.21 5 O 5231 1.98 5 H 27016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 53851 Number of models: 1 Model: "" Number of chains: 27 Chain: "B" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5438 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "C" Number of atoms: 5448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5448 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "D" Number of atoms: 5448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5448 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "E" Number of atoms: 5361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5361 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "F" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5246 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain breaks: 1 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: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3105 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "N" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "S" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 100 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 5429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5429 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 20.31, per 1000 atoms: 0.38 Number of scatterers: 53851 At special positions: 0 Unit cell: (147.03, 134.85, 138.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 119 16.00 P 17 15.00 Mg 5 11.99 O 5231 8.00 N 4581 7.00 C 16882 6.00 H 27016 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.67 Conformation dependent library (CDL) restraints added in 4.2 seconds 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6330 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 39 sheets defined 52.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'B' and resid 66 through 78 removed outlier: 4.175A 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 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.655A pdb=" N LYS B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.888A pdb=" N ARG B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.691A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 190 " --> pdb=" O ASP B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 190' Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.637A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 282 through 288 removed outlier: 3.638A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.517A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.920A pdb=" N ARG B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.873A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.534A pdb=" N ARG B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 380 removed outlier: 3.740A 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: 3.869A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.552A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 124 through 136 Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.815A pdb=" N ILE C 189 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.564A pdb=" N GLN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.521A pdb=" N ILE C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 308 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.883A 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: 3.622A pdb=" N LYS C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 4.326A pdb=" N ARG C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.940A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.965A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.563A pdb=" N ASN D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 135 removed outlier: 3.649A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 159 through 169 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.588A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 217 removed outlier: 4.672A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.510A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.618A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.857A 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 removed outlier: 3.565A pdb=" N LYS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 4.236A pdb=" N ARG D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 387 Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.895A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.982A 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 135 Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 204 through 217 removed outlier: 3.720A pdb=" N ALA E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.030A 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 283 through 288 Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.576A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.693A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 345 Processing helix chain 'E' and resid 351 through 365 Processing helix chain 'E' and resid 370 through 380 removed outlier: 4.350A pdb=" N SER E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 399 through 405 removed outlier: 3.706A pdb=" N ILE E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.665A pdb=" N ASP F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.769A 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 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 153 through 170 removed outlier: 3.758A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.522A pdb=" N ARG F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 removed outlier: 4.210A pdb=" N ILE F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 185 through 190' Processing helix chain 'F' and resid 205 through 217 Processing helix chain 'F' and resid 231 through 235 Processing helix chain 'F' and resid 253 through 263 Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.655A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.509A pdb=" N LEU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 Processing helix chain 'F' and resid 318 through 328 removed outlier: 3.723A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 343 Processing helix chain 'F' and resid 351 through 366 Processing helix chain 'F' and resid 369 through 387 removed outlier: 4.239A pdb=" N ARG F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 removed outlier: 3.788A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.505A 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 70 through 83 removed outlier: 3.530A 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 25 removed outlier: 3.613A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 70 through 83 removed outlier: 3.556A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (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 Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.527A 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 169 Processing helix chain 'J' and resid 176 through 183 Processing helix chain 'K' and resid 19 through 25 removed outlier: 3.809A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.728A pdb=" N GLY K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 131 through 158 Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 176 through 183 Processing helix chain 'L' and resid 19 through 25 Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.800A pdb=" N GLY L 73 " --> pdb=" O VAL L 69 " (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 169 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 25 Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.831A pdb=" N GLY M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 131 through 158 Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'N' and resid 19 through 25 removed outlier: 3.728A pdb=" N LEU N 23 " --> pdb=" O ILE N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.771A pdb=" N GLY N 73 " --> pdb=" O VAL N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 105 Processing helix chain 'N' and resid 131 through 158 Processing helix chain 'N' and resid 160 through 169 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.738A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 101 Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.512A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.859A pdb=" N GLY A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.677A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.555A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.568A pdb=" N LEU A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.509A 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: 3.544A pdb=" N LYS A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 380 removed outlier: 3.962A 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: 3.899A pdb=" N ILE A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.559A pdb=" N THR B 141 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP B 184 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 143 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 181 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY B 248 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE B 183 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 115 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLY B 249 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 117 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 219 through 222 Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 350 removed outlier: 6.295A pdb=" N ASP B 347 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE B 398 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU B 349 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.656A pdb=" N VAL C 181 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N GLY C 248 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 183 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 219 through 222 Processing sheet with id=AA6, first strand: chain 'C' and resid 347 through 350 removed outlier: 6.285A pdb=" N ASP C 347 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE C 398 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLU C 349 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 140 through 144 removed outlier: 6.556A pdb=" N THR D 141 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP D 184 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA D 143 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 181 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY D 248 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE D 183 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU D 116 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 219 through 222 Processing sheet with id=AA9, first strand: chain 'D' and resid 347 through 350 removed outlier: 6.230A pdb=" N ASP D 347 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE D 398 " --> pdb=" O ASP D 347 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU D 349 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 140 through 144 removed outlier: 6.557A pdb=" N THR E 141 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASP E 184 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA E 143 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE E 115 " --> pdb=" O CYS E 247 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N GLY E 249 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 117 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU E 116 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.550A pdb=" N LEU E 236 " --> pdb=" O VAL E 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 347 through 350 removed outlier: 6.453A pdb=" N ASP E 347 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE E 398 " --> pdb=" O ASP E 347 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU E 349 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.218A pdb=" N VAL F 181 " --> pdb=" O ILE F 246 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU F 116 " --> pdb=" O ALA F 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 219 through 222 Processing sheet with id=AB6, first strand: chain 'F' and resid 347 through 350 removed outlier: 6.449A pdb=" N ASP F 347 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE F 398 " --> pdb=" O ASP F 347 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU F 349 " --> pdb=" O ILE F 398 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS F 395 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 5 through 8 Processing sheet with id=AB8, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.403A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER H 65 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG H 118 " --> pdb=" O CYS H 91 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY H 93 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N MET H 120 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA H 95 " --> pdb=" O MET H 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.403A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER H 65 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AC2, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.298A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.298A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG I 111 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AC5, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.652A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.652A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 5 through 10 Processing sheet with id=AC8, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.636A pdb=" N ILE K 29 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASN K 64 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU K 31 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER K 65 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN K 94 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG K 118 " --> pdb=" O CYS K 91 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLY K 93 " --> pdb=" O ARG K 118 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N MET K 120 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.636A pdb=" N ILE K 29 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASN K 64 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU K 31 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER K 65 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN K 94 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 5 through 10 Processing sheet with id=AD2, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.530A pdb=" N ILE L 29 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASN L 64 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU L 31 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER L 65 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN L 94 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 118 through 121 Processing sheet with id=AD4, first strand: chain 'M' and resid 5 through 9 Processing sheet with id=AD5, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.188A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG M 118 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY M 93 " --> pdb=" O ARG M 118 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N MET M 120 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA M 95 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.188A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AD8, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.758A pdb=" N ILE N 29 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASN N 64 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU N 31 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG N 118 " --> pdb=" O CYS N 91 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY N 93 " --> pdb=" O ARG N 118 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N MET N 120 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA N 95 " --> pdb=" O MET N 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.758A pdb=" N ILE N 29 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASN N 64 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU N 31 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 140 through 144 removed outlier: 3.842A pdb=" N THR A 141 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 181 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLY A 248 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 183 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 219 through 222 Processing sheet with id=AE3, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.367A pdb=" N ASP A 347 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 398 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU A 349 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) 1289 hydrogen bonds defined for protein. 3750 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: 20.47 Time building geometry restraints manager: 13.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 26996 1.05 - 1.27: 4715 1.27 - 1.50: 11823 1.50 - 1.72: 10487 1.72 - 1.95: 213 Bond restraints: 54234 Sorted by residual: bond pdb=" CG1 ILE D 215 " pdb=" CD1 ILE D 215 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.64e+00 bond pdb=" CG1 ILE C 215 " pdb=" CD1 ILE C 215 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.70e+00 bond pdb=" CG1 ILE I 63 " pdb=" CD1 ILE I 63 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.65e+00 bond pdb=" CG1 ILE E 215 " pdb=" CD1 ILE E 215 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.47e+00 bond pdb=" CG LEU B 314 " pdb=" CD2 LEU B 314 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.91e+00 ... (remaining 54229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 96790 2.27 - 4.54: 1484 4.54 - 6.81: 153 6.81 - 9.08: 11 9.08 - 11.35: 2 Bond angle restraints: 98440 Sorted by residual: angle pdb=" C PRO E 196 " pdb=" N SER E 197 " pdb=" CA SER E 197 " ideal model delta sigma weight residual 122.66 134.01 -11.35 1.63e+00 3.76e-01 4.85e+01 angle pdb=" N GLU B 328 " pdb=" CA GLU B 328 " pdb=" C GLU B 328 " ideal model delta sigma weight residual 109.81 118.91 -9.10 2.21e+00 2.05e-01 1.69e+01 angle pdb=" CA PRO E 196 " pdb=" C PRO E 196 " pdb=" N SER E 197 " ideal model delta sigma weight residual 116.70 108.57 8.13 2.07e+00 2.33e-01 1.54e+01 angle pdb=" C ILE M 83 " pdb=" N LYS M 84 " pdb=" CA LYS M 84 " ideal model delta sigma weight residual 119.78 124.60 -4.82 1.24e+00 6.50e-01 1.51e+01 angle pdb=" N ASP J 18 " pdb=" CA ASP J 18 " pdb=" C ASP J 18 " ideal model delta sigma weight residual 110.55 105.66 4.89 1.35e+00 5.49e-01 1.31e+01 ... (remaining 98435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 24316 31.61 - 63.22: 872 63.22 - 94.83: 37 94.83 - 126.43: 0 126.43 - 158.04: 3 Dihedral angle restraints: 25228 sinusoidal: 14258 harmonic: 10970 Sorted by residual: dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 98.05 -158.04 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 72.42 -132.42 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" O1B ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PB ADP F 600 " pdb=" PA ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 66.48 -126.48 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 25225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2615 0.044 - 0.088: 1157 0.088 - 0.132: 422 0.132 - 0.175: 65 0.175 - 0.219: 3 Chirality restraints: 4262 Sorted by residual: chirality pdb=" CA PRO E 196 " pdb=" N PRO E 196 " pdb=" C PRO E 196 " pdb=" CB PRO E 196 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 268 " pdb=" CA ILE B 268 " pdb=" CG1 ILE B 268 " pdb=" CG2 ILE B 268 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA GLU B 328 " pdb=" N GLU B 328 " pdb=" C GLU B 328 " pdb=" CB GLU B 328 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 4259 not shown) Planarity restraints: 8068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 194 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ASP E 194 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP E 194 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN E 195 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 328 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO E 329 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 329 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 329 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 54 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO M 55 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO M 55 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 55 " -0.030 5.00e-02 4.00e+02 ... (remaining 8065 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 1791 2.16 - 2.77: 108104 2.77 - 3.38: 149051 3.38 - 3.99: 199801 3.99 - 4.60: 320736 Nonbonded interactions: 779483 Sorted by model distance: nonbonded pdb=" HG1 THR D 149 " pdb=" O GLU D 156 " model vdw 1.545 2.450 nonbonded pdb=" HG1 THR D 126 " pdb="MG MG D 502 " model vdw 1.619 1.700 nonbonded pdb=" HG1 THR C 126 " pdb="MG MG C 502 " model vdw 1.627 1.700 nonbonded pdb=" HG1 THR B 126 " pdb="MG MG B 502 " model vdw 1.637 1.700 nonbonded pdb=" O LYS D 192 " pdb=" HG SER D 193 " model vdw 1.662 2.450 ... (remaining 779478 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 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 94 or (resid 95 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resi \ d 96 through 191 or (resid 204 and (name N or name CA or name C or name O or nam \ e HA2 or name HA3)) or resid 205 through 275 or resid 282 through 414)) selection = (chain 'B' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 275 or resid 282 through 414)) selection = (chain 'C' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 275 or resid 282 through 414)) selection = (chain 'D' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 275 or resid 282 through 414)) selection = (chain 'E' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 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 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 414)) selection = (chain 'F' and (resid 64 through 275 or resid 282 through 414)) } ncs_group { reference = (chain 'H' and resid 2 through 192) selection = (chain 'I' and resid 2 through 192) selection = (chain 'J' and resid 2 through 192) selection = (chain 'K' and resid 2 through 192) selection = (chain 'L' and resid 2 through 192) selection = (chain 'M' and resid 2 through 192) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.720 Extract box with map and model: 1.560 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 92.200 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 0.011 0.108 27218 Z= 0.711 Angle : 0.864 11.354 36798 Z= 0.464 Chirality : 0.054 0.219 4262 Planarity : 0.005 0.057 4766 Dihedral : 13.564 158.043 10361 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.07 % Allowed : 1.18 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 3418 helix: 0.36 (0.12), residues: 1655 sheet: -0.69 (0.20), residues: 541 loop : -1.85 (0.15), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 230 PHE 0.031 0.003 PHE K 17 TYR 0.021 0.002 TYR B 153 ARG 0.007 0.001 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 486 time to evaluate : 3.108 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: D 235 PHE cc_start: 0.8104 (m-10) cc_final: 0.7902 (m-10) REVERT: D 342 ASN cc_start: 0.7812 (m-40) cc_final: 0.7456 (m110) REVERT: E 342 ASN cc_start: 0.8055 (m-40) cc_final: 0.7767 (m-40) REVERT: F 331 ASN cc_start: 0.8540 (p0) cc_final: 0.8323 (p0) REVERT: I 39 MET cc_start: 0.3912 (ppp) cc_final: 0.2875 (ppp) REVERT: K 153 MET cc_start: 0.2081 (mmm) cc_final: 0.1435 (mmm) REVERT: L 7 ILE cc_start: 0.8717 (tt) cc_final: 0.8477 (tt) REVERT: L 60 TYR cc_start: 0.7602 (m-80) cc_final: 0.7387 (m-80) REVERT: L 78 ASP cc_start: 0.6856 (m-30) cc_final: 0.6574 (m-30) REVERT: M 41 ASN cc_start: 0.7813 (t0) cc_final: 0.7580 (m110) REVERT: N 153 MET cc_start: 0.0765 (mmm) cc_final: 0.0376 (mmm) outliers start: 2 outliers final: 1 residues processed: 488 average time/residue: 0.8253 time to fit residues: 605.5112 Evaluate side-chains 332 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 407 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 308 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN C 342 ASN D 230 HIS D 233 GLN E 163 GLN E 167 GLN E 225 GLN E 289 GLN E 406 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN F 160 ASN H 46 GLN J 41 ASN J 116 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN M 41 ASN ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN A 209 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.159916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114981 restraints weight = 148660.149| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.98 r_work: 0.3077 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27218 Z= 0.216 Angle : 0.568 5.938 36798 Z= 0.296 Chirality : 0.042 0.173 4262 Planarity : 0.004 0.049 4766 Dihedral : 7.829 160.648 3812 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.21 % Allowed : 6.00 % Favored : 93.79 % 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 (0.14), residues: 3418 helix: 1.21 (0.12), residues: 1696 sheet: -0.54 (0.21), residues: 541 loop : -1.57 (0.16), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 95 PHE 0.011 0.001 PHE J 101 TYR 0.012 0.001 TYR A 96 ARG 0.005 0.000 ARG N 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 344 time to evaluate : 3.161 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: B 377 GLU cc_start: 0.8577 (tp30) cc_final: 0.8293 (tp30) REVERT: C 390 MET cc_start: 0.8228 (mtt) cc_final: 0.7935 (mtt) REVERT: E 342 ASN cc_start: 0.9134 (m-40) cc_final: 0.8796 (m-40) REVERT: E 390 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8288 (mtm) REVERT: H 25 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8841 (ttmm) REVERT: H 39 MET cc_start: 0.6350 (ppp) cc_final: 0.6015 (ppp) REVERT: H 78 ASP cc_start: 0.8286 (m-30) cc_final: 0.7979 (m-30) REVERT: H 153 MET cc_start: 0.0190 (mmm) cc_final: -0.0198 (mmm) REVERT: I 116 ASN cc_start: 0.9148 (m110) cc_final: 0.8135 (m110) REVERT: J 56 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8359 (mm-30) REVERT: J 77 TYR cc_start: 0.8981 (t80) cc_final: 0.8213 (t80) REVERT: J 78 ASP cc_start: 0.8708 (m-30) cc_final: 0.8206 (m-30) REVERT: K 58 ASP cc_start: 0.8784 (p0) cc_final: 0.8574 (p0) REVERT: K 111 ARG cc_start: 0.7528 (mtm-85) cc_final: 0.7049 (mtm-85) REVERT: L 7 ILE cc_start: 0.9098 (tt) cc_final: 0.8873 (tt) REVERT: L 9 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8484 (mm-40) REVERT: L 37 ASP cc_start: 0.8364 (m-30) cc_final: 0.8145 (m-30) REVERT: L 78 ASP cc_start: 0.8526 (m-30) cc_final: 0.7955 (m-30) REVERT: L 116 ASN cc_start: 0.9035 (m110) cc_final: 0.8579 (m110) REVERT: M 8 GLU cc_start: 0.8422 (tt0) cc_final: 0.8193 (tt0) REVERT: M 41 ASN cc_start: 0.8093 (t0) cc_final: 0.7768 (m110) REVERT: M 47 MET cc_start: 0.8572 (mtt) cc_final: 0.8362 (mtt) REVERT: N 153 MET cc_start: 0.0131 (mmm) cc_final: -0.0098 (mmm) outliers start: 6 outliers final: 4 residues processed: 345 average time/residue: 0.7349 time to fit residues: 402.3125 Evaluate side-chains 314 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 309 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain L residue 8 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 333 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 101 ASN H 41 ASN J 41 ASN ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN K 94 GLN N 41 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.160039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114300 restraints weight = 149879.746| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.98 r_work: 0.3033 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27218 Z= 0.253 Angle : 0.509 6.384 36798 Z= 0.262 Chirality : 0.041 0.156 4262 Planarity : 0.003 0.046 4766 Dihedral : 7.536 154.228 3811 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.49 % Allowed : 6.94 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3418 helix: 1.49 (0.13), residues: 1711 sheet: -0.40 (0.21), residues: 539 loop : -1.42 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 260 PHE 0.009 0.001 PHE M 101 TYR 0.014 0.001 TYR A 96 ARG 0.004 0.000 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 329 time to evaluate : 3.138 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: C 390 MET cc_start: 0.8234 (mtt) cc_final: 0.7924 (mtt) REVERT: E 390 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8336 (mtm) REVERT: I 5 MET cc_start: 0.4992 (mmt) cc_final: 0.4762 (mmt) REVERT: I 116 ASN cc_start: 0.9223 (m110) cc_final: 0.8136 (m110) REVERT: J 74 MET cc_start: 0.7796 (mmm) cc_final: 0.7351 (mmm) REVERT: J 77 TYR cc_start: 0.8948 (t80) cc_final: 0.8177 (t80) REVERT: J 78 ASP cc_start: 0.8710 (m-30) cc_final: 0.8110 (m-30) REVERT: K 58 ASP cc_start: 0.8838 (p0) cc_final: 0.8619 (p0) REVERT: K 111 ARG cc_start: 0.7363 (mtm-85) cc_final: 0.7065 (mtm-85) REVERT: L 78 ASP cc_start: 0.8474 (m-30) cc_final: 0.8217 (m-30) REVERT: M 8 GLU cc_start: 0.8439 (tt0) cc_final: 0.7961 (tt0) REVERT: M 41 ASN cc_start: 0.8161 (t0) cc_final: 0.7800 (m110) REVERT: N 8 GLU cc_start: 0.7723 (tt0) cc_final: 0.7007 (tt0) REVERT: N 54 ASN cc_start: 0.7576 (t0) cc_final: 0.7233 (t0) REVERT: N 58 ASP cc_start: 0.8495 (m-30) cc_final: 0.8250 (m-30) REVERT: N 86 ASP cc_start: 0.8616 (m-30) cc_final: 0.8345 (m-30) REVERT: N 153 MET cc_start: -0.0027 (mmm) cc_final: -0.0259 (mmm) REVERT: A 377 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8656 (mm-30) outliers start: 14 outliers final: 9 residues processed: 332 average time/residue: 0.8004 time to fit residues: 424.4114 Evaluate side-chains 317 residues out of total 2882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 307 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain F residue 260 HIS Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain K residue 94 GLN Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 149 MET Chi-restraints excluded: chain M residue 92 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6658 > 50: distance: 61 - 119: 13.272 distance: 77 - 93: 5.956 distance: 78 - 136: 11.271 distance: 93 - 94: 6.134 distance: 93 - 101: 4.322 distance: 94 - 95: 7.302 distance: 94 - 97: 3.252 distance: 94 - 102: 3.936 distance: 95 - 96: 8.519 distance: 95 - 105: 12.117 distance: 96 - 157: 11.051 distance: 97 - 98: 7.450 distance: 97 - 103: 8.162 distance: 97 - 104: 3.615 distance: 98 - 99: 5.349 distance: 98 - 100: 4.292 distance: 105 - 112: 12.103 distance: 106 - 107: 16.811 distance: 106 - 109: 7.440 distance: 106 - 113: 6.585 distance: 107 - 108: 10.970 distance: 107 - 119: 11.390 distance: 108 - 169: 23.735 distance: 109 - 110: 17.338 distance: 109 - 111: 12.138 distance: 109 - 114: 15.948 distance: 110 - 115: 15.152 distance: 111 - 116: 6.275 distance: 111 - 117: 4.147 distance: 111 - 118: 4.190 distance: 119 - 120: 6.682 distance: 119 - 127: 19.464 distance: 120 - 121: 15.147 distance: 120 - 123: 8.201 distance: 120 - 128: 12.697 distance: 121 - 122: 5.510 distance: 121 - 136: 16.359 distance: 123 - 124: 9.714 distance: 123 - 129: 22.885 distance: 123 - 130: 9.741 distance: 124 - 125: 5.696 distance: 124 - 131: 7.029 distance: 125 - 126: 6.765 distance: 126 - 135: 3.394 distance: 136 - 137: 4.904 distance: 136 - 148: 12.032 distance: 137 - 138: 15.180 distance: 137 - 140: 11.100 distance: 137 - 149: 8.821 distance: 138 - 139: 8.657 distance: 138 - 157: 6.083 distance: 140 - 141: 6.936 distance: 140 - 150: 4.576 distance: 140 - 151: 14.357 distance: 142 - 152: 3.775 distance: 143 - 145: 3.726 distance: 144 - 146: 3.105 distance: 145 - 155: 3.125 distance: 146 - 147: 4.372 distance: 147 - 156: 4.445 distance: 157 - 158: 11.023 distance: 157 - 165: 16.544 distance: 158 - 159: 19.742 distance: 158 - 161: 11.935 distance: 158 - 166: 6.743 distance: 159 - 160: 18.034 distance: 159 - 169: 9.965 distance: 161 - 162: 10.995 distance: 161 - 167: 7.520 distance: 161 - 168: 11.668 distance: 162 - 163: 10.108 distance: 162 - 164: 6.344 distance: 169 - 170: 14.630 distance: 169 - 177: 31.017 distance: 170 - 171: 12.763 distance: 170 - 173: 11.048 distance: 170 - 178: 24.326 distance: 171 - 172: 20.187 distance: 171 - 188: 4.739 distance: 173 - 174: 6.171 distance: 173 - 179: 6.000 distance: 173 - 180: 9.070 distance: 174 - 175: 4.382 distance: 174 - 176: 4.553 distance: 174 - 181: 10.055 distance: 175 - 182: 3.550 distance: 175 - 183: 4.844 distance: 175 - 184: 3.974 distance: 176 - 185: 6.978 distance: 176 - 186: 3.405 distance: 176 - 187: 4.311 distance: 188 - 189: 18.561 distance: 188 - 194: 9.281 distance: 189 - 190: 11.542 distance: 189 - 192: 9.947 distance: 189 - 195: 8.714 distance: 190 - 191: 9.174 distance: 190 - 202: 10.362 distance: 192 - 193: 6.618 distance: 192 - 196: 13.894 distance: 192 - 197: 10.287 distance: 193 - 194: 9.252 distance: 193 - 198: 7.798 distance: 193 - 199: 4.811 distance: 194 - 200: 16.461 distance: 194 - 201: 12.862 distance: 202 - 203: 4.818 distance: 202 - 208: 3.641 distance: 203 - 204: 11.375 distance: 203 - 206: 10.112 distance: 203 - 209: 4.294 distance: 204 - 205: 14.486 distance: 204 - 213: 8.210 distance: 206 - 207: 5.855 distance: 206 - 210: 5.092 distance: 206 - 211: 5.107 distance: 213 - 214: 10.020 distance: 213 - 221: 9.006 distance: 214 - 215: 20.980 distance: 214 - 217: 13.869 distance: 214 - 222: 6.339 distance: 215 - 216: 15.498 distance: 215 - 230: 44.985 distance: 217 - 218: 5.273 distance: 217 - 223: 23.842 distance: 217 - 224: 11.710 distance: 218 - 219: 6.993 distance: 218 - 225: 11.616 distance: 219 - 220: 10.781 distance: 220 - 227: 6.260 distance: 220 - 229: 3.647 distance: 230 - 231: 21.743 distance: 230 - 239: 6.588 distance: 231 - 232: 15.011 distance: 231 - 234: 21.309 distance: 231 - 240: 12.086 distance: 232 - 233: 12.457 distance: 232 - 245: 24.311 distance: 234 - 235: 5.406 distance: 234 - 241: 14.562 distance: 234 - 242: 21.228 distance: 235 - 243: 7.908 distance: 235 - 244: 10.051 distance: 236 - 238: 4.649