Starting phenix.real_space_refine on Sun Sep 29 17:41:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/09_2024/8e8q_27946_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/09_2024/8e8q_27946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/09_2024/8e8q_27946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/09_2024/8e8q_27946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/09_2024/8e8q_27946_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e8q_27946/09_2024/8e8q_27946_trim.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 16 5.49 5 Mg 3 5.21 5 S 198 5.16 5 C 23457 2.51 5 N 6394 2.21 5 O 7190 1.98 5 H 37561 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74819 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5424 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 14, 'TRANS': 335} Chain: "B" Number of atoms: 5445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 351, 5433 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Conformer: "B" Number of residues, atoms: 351, 5433 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} bond proxies already assigned to first conformer: 5456 Chain: "C" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "D" Number of atoms: 5441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5441 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "E" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5442 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "F" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5244 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 13, 'TRANS': 324} 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: 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: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} 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: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3045 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} 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: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 197 " occ=0.50 ... (20 atoms not shown) pdb=" HG BSER B 197 " occ=0.50 Time building chain proxies: 31.76, per 1000 atoms: 0.42 Number of scatterers: 74819 At special positions: 0 Unit cell: (136.038, 147.098, 194.656, 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 198 16.00 P 16 15.00 Mg 3 11.99 O 7190 8.00 N 6394 7.00 C 23457 6.00 H 37561 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.97 Conformation dependent library (CDL) restraints added in 5.0 seconds 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8792 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 68 sheets defined 52.0% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.779A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 101 removed outlier: 3.503A pdb=" N ASN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.189A pdb=" N ASN A 106 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.875A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.837A pdb=" N GLN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.658A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.933A 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 286 through 290 Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.759A 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: 3.661A pdb=" N ASP A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 4.252A pdb=" N ARG A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.833A 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: 3.528A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.586A 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: 3.632A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.542A pdb=" N LYS B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.516A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.691A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.054A pdb=" N PHE B 235 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.772A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.630A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.552A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.047A 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: 3.633A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.217A pdb=" N ARG B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.566A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.879A 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 135 removed outlier: 3.500A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.603A pdb=" N GLN C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.690A pdb=" N ARG C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 204 through 217 removed outlier: 4.648A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 removed outlier: 3.595A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 264 " --> pdb=" O HIS C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.697A 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 Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.790A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.705A pdb=" N LYS C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 4.214A pdb=" N ARG C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 3.782A 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: 3.883A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 4.054A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.603A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.685A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.758A pdb=" N ARG D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 204 through 217 removed outlier: 3.540A pdb=" N GLN D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.659A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 removed outlier: 3.717A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.503A pdb=" N LEU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.717A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.844A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 345 removed outlier: 4.176A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 removed outlier: 3.540A pdb=" N ALA D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 370 through 380 removed outlier: 3.918A 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: 3.612A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 405 " --> pdb=" O SER D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 399 through 405' Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.585A 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 134 removed outlier: 3.681A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.921A pdb=" N GLN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS E 168 " --> pdb=" O LYS E 164 " (cutoff:3.500A) 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: 3.564A pdb=" N GLN E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.515A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.530A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.755A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.582A pdb=" N ILE E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 307 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 308 " --> pdb=" O PHE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.752A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 345 removed outlier: 4.115A 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 370 through 380 removed outlier: 4.405A 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: 3.722A pdb=" N ILE E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 405 " --> pdb=" O SER E 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 399 through 405' Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.787A 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: 3.558A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.929A pdb=" N ASP F 157 " --> pdb=" O TYR F 153 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.671A pdb=" N ARG F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 removed outlier: 4.432A pdb=" N ILE F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 3.587A 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 removed outlier: 3.501A pdb=" N GLN F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 243 No H-bonds generated for 'chain 'F' and resid 241 through 243' Processing helix chain 'F' and resid 253 through 263 removed outlier: 3.809A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 288 removed outlier: 3.703A pdb=" N GLY F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.610A 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: 3.753A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 345 removed outlier: 3.623A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 366 removed outlier: 3.547A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 387 removed outlier: 4.269A pdb=" N ARG F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 removed outlier: 3.524A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 26 removed outlier: 3.744A 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: 3.807A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 132 through 158 Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.626A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.762A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.514A pdb=" N GLY I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.598A 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 132 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 26 removed outlier: 3.821A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.511A pdb=" N GLY J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 3.598A 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 132 through 158 removed outlier: 3.509A pdb=" N GLU J 141 " --> pdb=" O ILE J 137 " (cutoff:3.500A) 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 26 removed outlier: 3.729A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.568A 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 132 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 26 removed outlier: 3.746A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 removed outlier: 3.630A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.625A pdb=" N GLY L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 105 Processing helix chain 'L' and resid 132 through 158 Processing helix chain 'L' and resid 160 through 168 Processing helix chain 'L' and resid 176 through 183 Processing helix chain 'M' and resid 18 through 26 removed outlier: 3.868A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.598A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 132 through 158 Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'N' and resid 19 through 25 removed outlier: 3.514A pdb=" N LYS N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.533A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 105 Processing helix chain 'N' and resid 132 through 158 Processing helix chain 'N' and resid 160 through 168 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.807A 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: 3.704A pdb=" N GLY h 73 " --> pdb=" O VAL h 69 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE h 76 " --> pdb=" O ALA h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 105 Processing helix chain 'h' and resid 132 through 158 Processing helix chain 'h' and resid 160 through 169 Processing helix chain 'h' and resid 176 through 182 Processing helix chain 'i' and resid 19 through 26 removed outlier: 3.948A pdb=" N GLU i 26 " --> pdb=" O ARG i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 54 Processing helix chain 'i' and resid 69 through 83 removed outlier: 3.785A pdb=" N GLY i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.572A 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 132 through 158 Processing helix chain 'i' and resid 160 through 169 Processing helix chain 'i' and resid 176 through 182 Processing helix chain 'j' and resid 19 through 26 removed outlier: 3.834A pdb=" N GLU j 26 " --> pdb=" O ARG j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 54 Processing helix chain 'j' and resid 69 through 83 removed outlier: 3.640A pdb=" N GLY j 73 " --> pdb=" O VAL j 69 " (cutoff:3.500A) removed outlier: 3.622A 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 132 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 26 removed outlier: 3.503A pdb=" N LYS k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU k 26 " --> pdb=" O ARG k 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 36 through 54 Processing helix chain 'k' and resid 69 through 83 removed outlier: 3.594A pdb=" N GLY k 73 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 3.673A 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 132 through 158 Processing helix chain 'k' and resid 160 through 169 Processing helix chain 'k' and resid 176 through 182 Processing helix chain 'l' and resid 19 through 26 removed outlier: 3.841A pdb=" N GLU l 26 " --> pdb=" O ARG l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 54 Processing helix chain 'l' and resid 69 through 83 removed outlier: 3.729A pdb=" N GLY l 73 " --> pdb=" O VAL l 69 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 96 through 105 Processing helix chain 'l' and resid 132 through 158 Processing helix chain 'l' and resid 160 through 169 Processing helix chain 'l' and resid 176 through 183 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: 3.687A pdb=" N GLY m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE m 76 " --> pdb=" O ALA m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 105 Processing helix chain 'm' and resid 132 through 158 Processing helix chain 'm' and resid 160 through 169 Processing helix chain 'm' and resid 176 through 183 Processing helix chain 'n' and resid 19 through 26 removed outlier: 3.566A pdb=" N LEU n 23 " --> pdb=" O ILE n 19 " (cutoff:3.500A) removed outlier: 3.693A 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: 3.674A pdb=" N GLY n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) Processing helix chain 'n' and resid 96 through 105 Processing helix chain 'n' and resid 132 through 158 Processing helix chain 'n' and resid 160 through 169 Processing helix chain 'n' and resid 176 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 144 removed outlier: 6.707A pdb=" N ILE A 115 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY A 249 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU A 117 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.328A pdb=" N ASP A 347 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE A 398 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU A 349 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 395 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 144 removed outlier: 3.823A pdb=" N THR B 141 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 115 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY B 249 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU B 117 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.614A pdb=" N VAL B 238 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.744A 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 350 removed outlier: 6.181A pdb=" N ASP B 347 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE B 398 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU B 349 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.992A pdb=" N THR C 141 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASP C 184 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 143 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 181 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLY C 248 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE C 183 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 115 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 219 through 220 removed outlier: 3.578A pdb=" N VAL C 238 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.764A pdb=" N GLU C 349 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS C 395 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 140 through 144 removed outlier: 3.667A pdb=" N THR D 141 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL D 181 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY D 248 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 183 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU D 116 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 219 through 222 Processing sheet with id=AB3, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.761A pdb=" N LYS D 395 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 144 removed outlier: 6.579A pdb=" N THR E 141 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASP E 184 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA E 143 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL E 181 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLY E 248 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE E 183 " --> pdb=" O GLY E 248 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE E 115 " --> pdb=" O CYS E 247 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLY E 249 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU E 117 " --> pdb=" O GLY E 249 " (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: 3.591A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 115 through 118 Processing sheet with id=AB8, first strand: chain 'F' and resid 140 through 144 removed outlier: 3.693A pdb=" N THR F 141 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 219 through 222 Processing sheet with id=AC1, first strand: chain 'F' and resid 347 through 350 removed outlier: 6.337A pdb=" N ASP F 347 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE F 398 " --> pdb=" O ASP F 347 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU F 349 " --> pdb=" O ILE F 398 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 6 through 9 Processing sheet with id=AC3, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.237A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER H 65 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.237A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER H 65 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC6, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AC7, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.560A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 65 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.560A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 65 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 125 through 131 Processing sheet with id=AD1, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AD2, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.587A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER J 65 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.587A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER J 65 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 125 through 131 Processing sheet with id=AD5, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AD6, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.547A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER K 65 " --> pdb=" O GLN K 94 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 118 through 121 Processing sheet with id=AD8, first strand: chain 'K' and resid 125 through 131 removed outlier: 3.502A pdb=" N TYR j 128 " --> pdb=" O TYR K 128 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.702A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.386A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 94 through 95 removed outlier: 6.428A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 125 through 131 removed outlier: 3.509A pdb=" N TYR L 128 " --> pdb=" O TYR k 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR k 128 " --> pdb=" O TYR L 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 6 through 8 Processing sheet with id=AE5, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.481A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG M 118 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY M 93 " --> pdb=" O ARG M 118 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N MET M 120 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA M 95 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.481A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER M 65 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 125 through 131 removed outlier: 3.570A pdb=" N TYR M 128 " --> pdb=" O TYR l 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR l 128 " --> pdb=" O TYR M 128 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 5 through 9 Processing sheet with id=AE9, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.431A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER N 65 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG N 118 " --> pdb=" O CYS N 91 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY N 93 " --> pdb=" O ARG N 118 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N MET N 120 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA N 95 " --> pdb=" O MET N 120 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE N 121 " --> pdb=" O ARG N 172 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.431A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER N 65 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS N 113 " --> pdb=" O SER N 187 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 125 through 131 removed outlier: 3.504A pdb=" N TYR m 128 " --> pdb=" O TYR N 128 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'h' and resid 5 through 9 Processing sheet with id=AF4, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.331A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER h 65 " --> pdb=" O GLN h 94 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG h 118 " --> pdb=" O CYS h 91 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY h 93 " --> pdb=" O ARG h 118 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N MET h 120 " --> pdb=" O GLY h 93 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA h 95 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.331A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER h 65 " --> pdb=" O GLN h 94 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE h 112 " --> pdb=" O VAL h 87 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR h 89 " --> pdb=" O PHE h 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS h 113 " --> pdb=" O SER h 187 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'i' and resid 5 through 9 Processing sheet with id=AF7, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.568A pdb=" N ILE i 29 " --> pdb=" O TYR i 62 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN i 64 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU i 31 " --> pdb=" O ASN i 64 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG i 118 " --> pdb=" O CYS i 91 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY i 93 " --> pdb=" O ARG i 118 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N MET i 120 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA i 95 " --> pdb=" O MET i 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.568A pdb=" N ILE i 29 " --> pdb=" O TYR i 62 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN i 64 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU i 31 " --> pdb=" O ASN i 64 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE i 112 " --> pdb=" O VAL i 87 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR i 89 " --> pdb=" O PHE i 112 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'j' and resid 5 through 9 Processing sheet with id=AG1, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.319A pdb=" N ILE j 59 " --> pdb=" O SER j 88 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE j 90 " --> pdb=" O ILE j 59 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU j 61 " --> pdb=" O ILE j 90 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET j 92 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE j 63 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN j 94 " --> pdb=" O ILE j 63 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER j 65 " --> pdb=" O GLN j 94 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE j 112 " --> pdb=" O VAL j 87 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR j 89 " --> pdb=" O PHE j 112 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 118 through 121 Processing sheet with id=AG3, first strand: chain 'k' and resid 5 through 9 Processing sheet with id=AG4, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.370A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER k 65 " --> pdb=" O GLN k 94 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG k 118 " --> pdb=" O CYS k 91 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY k 93 " --> pdb=" O ARG k 118 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N MET k 120 " --> pdb=" O GLY k 93 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA k 95 " --> pdb=" O MET k 120 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.370A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER k 65 " --> pdb=" O GLN k 94 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE k 112 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR k 89 " --> pdb=" O PHE k 112 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER k 187 " --> pdb=" O ARG k 111 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'l' and resid 5 through 9 Processing sheet with id=AG7, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.572A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER l 65 " --> pdb=" O GLN l 94 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG l 118 " --> pdb=" O CYS l 91 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY l 93 " --> pdb=" O ARG l 118 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N MET l 120 " --> pdb=" O GLY l 93 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA l 95 " --> pdb=" O MET l 120 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.572A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N MET l 92 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE l 63 " --> pdb=" O MET l 92 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN l 94 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER l 65 " --> pdb=" O GLN l 94 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE l 112 " --> pdb=" O VAL l 87 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR l 89 " --> pdb=" O PHE l 112 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 5 through 9 removed outlier: 3.503A pdb=" N ARG m 15 " --> pdb=" O GLU m 8 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.527A pdb=" N ILE m 59 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE m 90 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU m 61 " --> pdb=" O ILE m 90 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET m 92 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE m 63 " --> pdb=" O MET m 92 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLN m 94 " --> pdb=" O ILE m 63 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER m 65 " --> pdb=" O GLN m 94 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE m 112 " --> pdb=" O VAL m 87 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR m 89 " --> pdb=" O PHE m 112 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'm' and resid 118 through 121 Processing sheet with id=AH3, first strand: chain 'n' and resid 5 through 9 Processing sheet with id=AH4, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.222A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER n 65 " --> pdb=" O GLN n 94 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG n 118 " --> pdb=" O CYS n 91 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY n 93 " --> pdb=" O ARG n 118 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N MET n 120 " --> pdb=" O GLY n 93 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA n 95 " --> pdb=" O MET n 120 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'n' and resid 28 through 32 removed outlier: 6.222A pdb=" N ILE n 59 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE n 90 " --> pdb=" O ILE n 59 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU n 61 " --> pdb=" O ILE n 90 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET n 92 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE n 63 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLN n 94 " --> pdb=" O ILE n 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER n 65 " --> pdb=" O GLN n 94 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N PHE n 112 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR n 89 " --> pdb=" O PHE n 112 " (cutoff:3.500A) 1853 hydrogen bonds defined for protein. 5400 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: 33.00 Time building geometry restraints manager: 18.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37527 1.03 - 1.23: 42 1.23 - 1.42: 15084 1.42 - 1.62: 22364 1.62 - 1.81: 362 Bond restraints: 75379 Sorted by residual: bond pdb=" C4 ADP F 600 " pdb=" C5 ADP F 600 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C5 ADP F 600 " pdb=" C6 ADP F 600 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C5 ADP E 601 " pdb=" C6 ADP E 601 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O5' ATP B 501 " pdb=" PA ATP B 501 " ideal model delta sigma weight residual 1.579 1.605 -0.026 1.10e-02 8.26e+03 5.56e+00 ... (remaining 75374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 135940 2.44 - 4.89: 714 4.89 - 7.33: 55 7.33 - 9.78: 9 9.78 - 12.22: 9 Bond angle restraints: 136727 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 129.03 10.84 1.00e+00 1.00e+00 1.18e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 126.65 10.18 1.00e+00 1.00e+00 1.04e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 129.80 10.07 1.00e+00 1.00e+00 1.01e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 130.22 9.65 1.00e+00 1.00e+00 9.31e+01 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 127.51 9.32 1.00e+00 1.00e+00 8.68e+01 ... (remaining 136722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.54: 33420 25.54 - 51.08: 1393 51.08 - 76.61: 285 76.61 - 102.15: 28 102.15 - 127.69: 5 Dihedral angle restraints: 35131 sinusoidal: 19826 harmonic: 15305 Sorted by residual: 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 300.00 172.31 127.69 1 2.00e+01 2.50e-03 3.87e+01 dihedral pdb=" O1B ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PB ADP E 601 " pdb=" PA ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 64.02 -124.02 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 57.07 -117.07 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 35128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4393 0.043 - 0.086: 1098 0.086 - 0.130: 341 0.130 - 0.173: 39 0.173 - 0.216: 2 Chirality restraints: 5873 Sorted by residual: chirality pdb=" C3' ADP E 601 " pdb=" C2' ADP E 601 " pdb=" C4' ADP E 601 " pdb=" O3' ADP E 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASP A 392 " pdb=" N ASP A 392 " pdb=" C ASP A 392 " pdb=" CB ASP A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA VAL F 222 " pdb=" N VAL F 222 " pdb=" C VAL F 222 " pdb=" CB VAL F 222 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 5870 not shown) Planarity restraints: 11209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 230 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO B 231 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 231 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 231 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 230 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO E 231 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 231 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 231 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 195 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO D 196 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " -0.029 5.00e-02 4.00e+02 ... (remaining 11206 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 10244 2.27 - 2.85: 174362 2.85 - 3.43: 193977 3.43 - 4.02: 274377 4.02 - 4.60: 423652 Nonbonded interactions: 1076612 Sorted by model distance: nonbonded pdb=" OG1 THR E 149 " pdb=" H GLU E 156 " model vdw 1.685 2.450 nonbonded pdb="HH12 ARG B 307 " pdb=" O2G ATP A 501 " model vdw 1.694 2.450 nonbonded pdb=" OE1 GLU m 14 " pdb=" H GLU m 14 " model vdw 1.703 2.450 nonbonded pdb=" O ALA M 72 " pdb=" HG SER M 75 " model vdw 1.710 2.450 nonbonded pdb=" OD1 ASP h 18 " pdb=" H SER h 21 " model vdw 1.712 2.450 ... (remaining 1076607 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 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 127 through 191 or (resid 204 \ and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 2 \ 05 through 413)) 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 413)) 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 413)) 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 413)) 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 125 or (resid 126 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG2 \ 1 or name HG22 or name HG23)) or resid 127 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 4 \ 13)) selection = (chain 'F' 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 125 or (resid 126 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG2 \ 1 or name HG22 or name HG23)) or resid 127 through 413)) } ncs_group { reference = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = (chain 'M' and resid 2 through 191) selection = (chain 'N' and resid 2 through 191) selection = (chain 'h' and resid 2 through 191) selection = (chain 'i' and resid 2 through 191) selection = (chain 'j' and resid 2 through 191) selection = (chain 'k' and resid 2 through 191) selection = (chain 'l' and resid 2 through 191) selection = (chain 'm' and resid 2 through 191) 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=0.50 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.170 Extract box with map and model: 2.160 Check model and map are aligned: 0.450 Set scattering table: 0.570 Process input model: 136.900 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.240 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 37818 Z= 0.257 Angle : 0.655 12.221 51085 Z= 0.365 Chirality : 0.043 0.216 5873 Planarity : 0.004 0.061 6627 Dihedral : 13.072 127.688 14451 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -0.37 (0.11), residues: 4743 helix: 0.45 (0.10), residues: 2278 sheet: -0.73 (0.16), residues: 779 loop : -0.78 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS N 122 PHE 0.016 0.001 PHE L 17 TYR 0.011 0.001 TYR C 153 ARG 0.006 0.000 ARG D 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 855 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 855 time to evaluate : 4.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8584 (tt0) cc_final: 0.8255 (tm-30) REVERT: A 205 GLU cc_start: 0.8204 (pm20) cc_final: 0.7902 (pt0) REVERT: A 237 GLN cc_start: 0.8828 (mp10) cc_final: 0.8616 (mp10) REVERT: A 393 VAL cc_start: 0.7942 (p) cc_final: 0.7219 (p) REVERT: A 404 ASP cc_start: 0.8253 (m-30) cc_final: 0.7464 (m-30) REVERT: C 101 ASN cc_start: 0.7522 (t0) cc_final: 0.7085 (t0) REVERT: C 144 ASP cc_start: 0.7533 (p0) cc_final: 0.7206 (p0) REVERT: C 182 TYR cc_start: 0.8857 (t80) cc_final: 0.8585 (t80) REVERT: D 171 TYR cc_start: 0.8784 (m-80) cc_final: 0.8339 (m-80) REVERT: E 187 ASP cc_start: 0.8170 (p0) cc_final: 0.7920 (p0) REVERT: F 96 TYR cc_start: 0.7684 (m-80) cc_final: 0.7467 (m-80) REVERT: F 160 ASN cc_start: 0.9045 (t0) cc_final: 0.8705 (t0) REVERT: F 185 GLU cc_start: 0.7446 (mp0) cc_final: 0.7034 (mp0) REVERT: F 297 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9137 (mtpt) REVERT: F 323 ILE cc_start: 0.9659 (mt) cc_final: 0.9436 (mm) REVERT: H 70 ILE cc_start: 0.8746 (mp) cc_final: 0.8533 (mm) REVERT: I 18 ASP cc_start: 0.7417 (p0) cc_final: 0.7138 (p0) REVERT: I 34 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7787 (mm-40) REVERT: J 129 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7880 (mm-40) REVERT: K 10 THR cc_start: 0.8857 (p) cc_final: 0.8620 (p) REVERT: K 129 GLN cc_start: 0.8608 (mm-40) cc_final: 0.7628 (mm110) REVERT: K 143 LEU cc_start: 0.9316 (mm) cc_final: 0.8978 (tt) REVERT: L 9 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6975 (mm-40) REVERT: L 125 LEU cc_start: 0.8834 (pp) cc_final: 0.8545 (pp) REVERT: M 26 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7855 (tm-30) REVERT: M 129 GLN cc_start: 0.8591 (mm110) cc_final: 0.7991 (mm110) REVERT: h 86 ASP cc_start: 0.8039 (m-30) cc_final: 0.7659 (m-30) REVERT: h 116 ASN cc_start: 0.9451 (m-40) cc_final: 0.9232 (m110) REVERT: h 163 GLN cc_start: 0.8404 (tp40) cc_final: 0.7909 (tp-100) REVERT: h 182 TYR cc_start: 0.8229 (t80) cc_final: 0.7731 (t80) REVERT: i 34 GLN cc_start: 0.8346 (tp40) cc_final: 0.7720 (tp40) REVERT: i 49 PHE cc_start: 0.7762 (t80) cc_final: 0.7527 (t80) REVERT: i 77 TYR cc_start: 0.8306 (t80) cc_final: 0.8105 (t80) REVERT: i 86 ASP cc_start: 0.7787 (m-30) cc_final: 0.7331 (m-30) REVERT: i 150 ASN cc_start: 0.8850 (m-40) cc_final: 0.8476 (m-40) REVERT: j 77 TYR cc_start: 0.7823 (t80) cc_final: 0.7030 (t80) REVERT: k 58 ASP cc_start: 0.7917 (m-30) cc_final: 0.7694 (m-30) REVERT: l 110 LYS cc_start: 0.9004 (mttt) cc_final: 0.8746 (mttt) REVERT: m 77 TYR cc_start: 0.8774 (t80) cc_final: 0.8511 (t80) REVERT: m 101 PHE cc_start: 0.8143 (t80) cc_final: 0.7553 (t80) REVERT: n 34 GLN cc_start: 0.8232 (pp30) cc_final: 0.7780 (pp30) REVERT: n 86 ASP cc_start: 0.8928 (m-30) cc_final: 0.8662 (m-30) REVERT: n 163 GLN cc_start: 0.8929 (tp40) cc_final: 0.8352 (tp-100) REVERT: n 166 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8465 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 855 average time/residue: 1.1605 time to fit residues: 1549.1613 Evaluate side-chains 557 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 242 optimal weight: 0.6980 chunk 191 optimal weight: 5.9990 chunk 371 optimal weight: 10.0000 chunk 143 optimal weight: 0.2980 chunk 225 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 430 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN E 260 HIS E 406 GLN F 101 ASN H 41 ASN ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 94 GLN h 123 GLN j 41 ASN j 150 ASN l 41 ASN m 41 ASN m 191 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37818 Z= 0.213 Angle : 0.539 6.895 51085 Z= 0.289 Chirality : 0.041 0.178 5873 Planarity : 0.004 0.046 6627 Dihedral : 7.191 119.167 5309 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.07 % Favored : 97.91 % Rotamer: Outliers : 0.52 % Allowed : 6.30 % Favored : 93.18 % 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: 0.50 (0.12), residues: 4743 helix: 1.39 (0.10), residues: 2321 sheet: -0.41 (0.16), residues: 819 loop : -0.72 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 73 PHE 0.015 0.001 PHE h 173 TYR 0.022 0.001 TYR j 128 ARG 0.005 0.000 ARG M 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 596 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 575 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8525 (tt0) cc_final: 0.8204 (tm-30) REVERT: A 404 ASP cc_start: 0.7963 (m-30) cc_final: 0.7577 (m-30) REVERT: C 101 ASN cc_start: 0.7465 (t0) cc_final: 0.6963 (t0) REVERT: F 96 TYR cc_start: 0.7623 (m-80) cc_final: 0.7305 (m-80) REVERT: F 184 ASP cc_start: 0.7082 (p0) cc_final: 0.6120 (p0) REVERT: F 185 GLU cc_start: 0.7235 (mp0) cc_final: 0.6719 (mp0) REVERT: F 298 PHE cc_start: 0.8730 (t80) cc_final: 0.8207 (t80) REVERT: H 5 MET cc_start: 0.7785 (mmm) cc_final: 0.7514 (mmm) REVERT: I 18 ASP cc_start: 0.7988 (p0) cc_final: 0.7545 (p0) REVERT: J 18 ASP cc_start: 0.7822 (p0) cc_final: 0.7582 (p0) REVERT: J 129 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7665 (mm-40) REVERT: K 143 LEU cc_start: 0.9373 (mm) cc_final: 0.9037 (tt) REVERT: L 9 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7433 (mm110) REVERT: L 125 LEU cc_start: 0.8931 (pp) cc_final: 0.8633 (pp) REVERT: M 26 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7964 (tm-30) REVERT: h 5 MET cc_start: 0.2365 (mmt) cc_final: 0.2108 (mmp) REVERT: h 84 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8088 (mmtt) REVERT: h 86 ASP cc_start: 0.8212 (m-30) cc_final: 0.7010 (p0) REVERT: h 116 ASN cc_start: 0.9469 (m-40) cc_final: 0.9256 (m110) REVERT: i 34 GLN cc_start: 0.8216 (tp40) cc_final: 0.7593 (tp40) REVERT: i 49 PHE cc_start: 0.7767 (t80) cc_final: 0.7550 (t80) REVERT: i 150 ASN cc_start: 0.9039 (m-40) cc_final: 0.8631 (m110) REVERT: j 120 MET cc_start: 0.8911 (ttt) cc_final: 0.8598 (tmm) REVERT: j 171 ASP cc_start: 0.8644 (m-30) cc_final: 0.8411 (m-30) REVERT: j 190 THR cc_start: 0.8691 (p) cc_final: 0.8459 (p) REVERT: k 97 SER cc_start: 0.7406 (p) cc_final: 0.7094 (t) REVERT: m 101 PHE cc_start: 0.7950 (t80) cc_final: 0.7470 (t80) REVERT: n 41 ASN cc_start: 0.7794 (t0) cc_final: 0.7503 (t0) REVERT: n 84 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8555 (tppt) REVERT: n 113 CYS cc_start: 0.8352 (p) cc_final: 0.7753 (t) REVERT: n 163 GLN cc_start: 0.9145 (tp40) cc_final: 0.8774 (tp-100) outliers start: 21 outliers final: 11 residues processed: 583 average time/residue: 1.0321 time to fit residues: 956.7600 Evaluate side-chains 516 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 505 time to evaluate : 5.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 91 CYS Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain l residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 358 optimal weight: 7.9990 chunk 293 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 431 optimal weight: 9.9990 chunk 465 optimal weight: 9.9990 chunk 384 optimal weight: 4.9990 chunk 427 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN D 174 GLN E 195 ASN H 131 GLN L 41 ASN h 123 GLN i 41 ASN m 41 ASN m 191 HIS n 41 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 37818 Z= 0.390 Angle : 0.570 7.041 51085 Z= 0.306 Chirality : 0.043 0.216 5873 Planarity : 0.004 0.053 6627 Dihedral : 7.316 128.844 5309 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.70 % Allowed : 7.82 % Favored : 91.48 % 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: 0.65 (0.12), residues: 4743 helix: 1.52 (0.11), residues: 2349 sheet: -0.37 (0.16), residues: 817 loop : -0.70 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 73 PHE 0.020 0.002 PHE j 173 TYR 0.017 0.002 TYR A 96 ARG 0.004 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 524 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 496 time to evaluate : 4.604 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: A 130 GLU cc_start: 0.8626 (tt0) cc_final: 0.8277 (tm-30) REVERT: A 205 GLU cc_start: 0.8106 (pm20) cc_final: 0.7587 (pt0) REVERT: D 101 ASN cc_start: 0.7994 (t0) cc_final: 0.7772 (t0) REVERT: F 182 TYR cc_start: 0.7945 (t80) cc_final: 0.7615 (t80) REVERT: H 41 ASN cc_start: 0.8406 (m110) cc_final: 0.7937 (m110) REVERT: I 18 ASP cc_start: 0.8594 (p0) cc_final: 0.7963 (p0) REVERT: J 129 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7564 (mm-40) REVERT: K 17 PHE cc_start: 0.8884 (m-80) cc_final: 0.8581 (m-80) REVERT: K 18 ASP cc_start: 0.8790 (p0) cc_final: 0.8389 (p0) REVERT: K 129 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8225 (mm110) REVERT: K 143 LEU cc_start: 0.9415 (mm) cc_final: 0.9026 (tt) REVERT: L 9 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7465 (mm-40) REVERT: L 41 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8228 (m110) REVERT: L 125 LEU cc_start: 0.9035 (pp) cc_final: 0.8757 (pp) REVERT: M 26 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8124 (tm-30) REVERT: h 62 TYR cc_start: 0.8401 (m-80) cc_final: 0.8013 (m-10) REVERT: h 86 ASP cc_start: 0.8214 (m-30) cc_final: 0.7158 (p0) REVERT: h 116 ASN cc_start: 0.9354 (m-40) cc_final: 0.9037 (m110) REVERT: h 153 MET cc_start: 0.9145 (mmm) cc_final: 0.8855 (tpp) REVERT: i 34 GLN cc_start: 0.8176 (tp40) cc_final: 0.7793 (tp-100) REVERT: i 49 PHE cc_start: 0.7850 (t80) cc_final: 0.7537 (t80) REVERT: i 150 ASN cc_start: 0.8993 (m-40) cc_final: 0.8610 (m110) REVERT: j 108 LYS cc_start: 0.9126 (tptt) cc_final: 0.8906 (tptp) REVERT: j 129 GLN cc_start: 0.7922 (mp10) cc_final: 0.7637 (mp10) REVERT: k 25 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8746 (mmmt) REVERT: k 97 SER cc_start: 0.7448 (p) cc_final: 0.7222 (t) REVERT: l 98 MET cc_start: 0.7888 (tpt) cc_final: 0.7579 (tpt) REVERT: l 120 MET cc_start: 0.9246 (ttp) cc_final: 0.8901 (tmm) REVERT: m 47 MET cc_start: 0.7801 (mtt) cc_final: 0.7488 (mtp) REVERT: m 101 PHE cc_start: 0.8111 (t80) cc_final: 0.7470 (t80) REVERT: n 74 MET cc_start: 0.6695 (mmp) cc_final: 0.6404 (mmp) outliers start: 28 outliers final: 13 residues processed: 512 average time/residue: 1.0346 time to fit residues: 841.0689 Evaluate side-chains 483 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 469 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 91 CYS Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain l residue 92 MET Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 91 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 9.9990 chunk 324 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 432 optimal weight: 9.9990 chunk 458 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 chunk 410 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 41 ASN j 191 HIS m 191 HIS n 41 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 37818 Z= 0.250 Angle : 0.492 6.265 51085 Z= 0.259 Chirality : 0.041 0.149 5873 Planarity : 0.003 0.049 6627 Dihedral : 7.022 126.553 5309 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.55 % Allowed : 8.29 % Favored : 91.16 % 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: 0.84 (0.12), residues: 4743 helix: 1.68 (0.11), residues: 2350 sheet: -0.34 (0.16), residues: 807 loop : -0.58 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 260 PHE 0.015 0.001 PHE I 101 TYR 0.012 0.001 TYR A 96 ARG 0.004 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 521 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 499 time to evaluate : 4.565 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: A 130 GLU cc_start: 0.8585 (tt0) cc_final: 0.8197 (tm-30) REVERT: A 144 ASP cc_start: 0.7590 (p0) cc_final: 0.7343 (p0) REVERT: A 205 GLU cc_start: 0.8236 (pm20) cc_final: 0.7798 (pt0) REVERT: C 101 ASN cc_start: 0.7560 (t0) cc_final: 0.7060 (t0) REVERT: D 101 ASN cc_start: 0.8039 (t0) cc_final: 0.7815 (t0) REVERT: F 363 MET cc_start: 0.8685 (mtp) cc_final: 0.8240 (mtp) REVERT: H 41 ASN cc_start: 0.8359 (m110) cc_final: 0.7947 (m110) REVERT: I 18 ASP cc_start: 0.8589 (p0) cc_final: 0.7969 (p0) REVERT: J 18 ASP cc_start: 0.8587 (p0) cc_final: 0.8286 (p0) REVERT: J 129 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7628 (mm-40) REVERT: K 17 PHE cc_start: 0.8871 (m-80) cc_final: 0.8634 (m-80) REVERT: K 18 ASP cc_start: 0.8700 (p0) cc_final: 0.8247 (p0) REVERT: K 129 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7894 (mm-40) REVERT: K 143 LEU cc_start: 0.9412 (mm) cc_final: 0.9043 (tt) REVERT: L 9 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7459 (mm-40) REVERT: L 125 LEU cc_start: 0.9042 (pp) cc_final: 0.8780 (pp) REVERT: M 26 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8107 (tm-30) REVERT: h 62 TYR cc_start: 0.8385 (m-80) cc_final: 0.8012 (m-10) REVERT: h 86 ASP cc_start: 0.8208 (m-30) cc_final: 0.7177 (p0) REVERT: h 113 CYS cc_start: 0.8742 (p) cc_final: 0.8493 (p) REVERT: h 116 ASN cc_start: 0.9362 (m-40) cc_final: 0.9081 (m110) REVERT: h 153 MET cc_start: 0.9142 (mmm) cc_final: 0.8877 (tpp) REVERT: i 49 PHE cc_start: 0.7815 (t80) cc_final: 0.7514 (t80) REVERT: i 141 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: i 150 ASN cc_start: 0.8961 (m-40) cc_final: 0.8603 (m110) REVERT: j 108 LYS cc_start: 0.9121 (tptt) cc_final: 0.8911 (tptp) REVERT: j 173 PHE cc_start: 0.8509 (m-80) cc_final: 0.8035 (m-80) REVERT: k 25 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8742 (mmmt) REVERT: k 97 SER cc_start: 0.7438 (p) cc_final: 0.7195 (t) REVERT: l 98 MET cc_start: 0.7859 (tpt) cc_final: 0.7594 (tpt) REVERT: m 47 MET cc_start: 0.7887 (mtt) cc_final: 0.7596 (mtp) REVERT: m 101 PHE cc_start: 0.8069 (t80) cc_final: 0.7285 (t80) outliers start: 22 outliers final: 15 residues processed: 511 average time/residue: 1.0417 time to fit residues: 847.8933 Evaluate side-chains 491 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 475 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain j residue 191 HIS Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 187 SER Chi-restraints excluded: chain m residue 41 ASN Chi-restraints excluded: chain m residue 92 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 341 optimal weight: 20.0000 chunk 189 optimal weight: 0.0370 chunk 390 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 0.0370 chunk 411 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN j 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 37818 Z= 0.262 Angle : 0.490 6.137 51085 Z= 0.258 Chirality : 0.041 0.147 5873 Planarity : 0.003 0.054 6627 Dihedral : 6.935 126.237 5309 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.55 % Allowed : 8.69 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.12), residues: 4743 helix: 1.81 (0.11), residues: 2353 sheet: -0.40 (0.16), residues: 819 loop : -0.55 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 260 PHE 0.016 0.001 PHE J 17 TYR 0.014 0.001 TYR A 96 ARG 0.005 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 514 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 492 time to evaluate : 4.486 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: A 130 GLU cc_start: 0.8614 (tt0) cc_final: 0.8216 (tm-30) REVERT: A 144 ASP cc_start: 0.7598 (p0) cc_final: 0.7351 (p0) REVERT: A 205 GLU cc_start: 0.8239 (pm20) cc_final: 0.7867 (pt0) REVERT: C 101 ASN cc_start: 0.7582 (t0) cc_final: 0.7085 (t0) REVERT: C 263 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: D 101 ASN cc_start: 0.8000 (t0) cc_final: 0.7737 (t0) REVERT: D 230 HIS cc_start: 0.6733 (m-70) cc_final: 0.6527 (m170) REVERT: F 363 MET cc_start: 0.8700 (mtp) cc_final: 0.8235 (mtp) REVERT: H 41 ASN cc_start: 0.8400 (m110) cc_final: 0.8128 (m110) REVERT: I 18 ASP cc_start: 0.8649 (p0) cc_final: 0.8010 (p0) REVERT: I 74 MET cc_start: 0.8750 (mmp) cc_final: 0.8345 (mmp) REVERT: J 18 ASP cc_start: 0.8663 (p0) cc_final: 0.8349 (p0) REVERT: K 17 PHE cc_start: 0.8927 (m-80) cc_final: 0.8662 (m-80) REVERT: K 18 ASP cc_start: 0.8712 (p0) cc_final: 0.8289 (p0) REVERT: K 129 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7763 (mm110) REVERT: K 143 LEU cc_start: 0.9417 (mm) cc_final: 0.9036 (tt) REVERT: L 9 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7472 (mm-40) REVERT: L 125 LEU cc_start: 0.9091 (pp) cc_final: 0.8835 (pp) REVERT: M 25 LYS cc_start: 0.9209 (mtpp) cc_final: 0.8904 (ttmm) REVERT: M 26 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8058 (tm-30) REVERT: h 62 TYR cc_start: 0.8388 (m-80) cc_final: 0.8062 (m-10) REVERT: h 84 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7908 (mmtt) REVERT: h 113 CYS cc_start: 0.8824 (p) cc_final: 0.8590 (p) REVERT: h 116 ASN cc_start: 0.9359 (m-40) cc_final: 0.9071 (m110) REVERT: h 182 TYR cc_start: 0.8575 (t80) cc_final: 0.8268 (t80) REVERT: i 49 PHE cc_start: 0.7799 (t80) cc_final: 0.7489 (t80) REVERT: i 141 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: i 150 ASN cc_start: 0.8946 (m-40) cc_final: 0.8399 (m110) REVERT: j 108 LYS cc_start: 0.9140 (tptt) cc_final: 0.8927 (tptp) REVERT: j 173 PHE cc_start: 0.8532 (m-80) cc_final: 0.8017 (m-80) REVERT: k 25 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8772 (mmmt) REVERT: k 74 MET cc_start: 0.7604 (mmp) cc_final: 0.7390 (mmp) REVERT: k 97 SER cc_start: 0.7497 (p) cc_final: 0.7269 (t) REVERT: l 98 MET cc_start: 0.7954 (tpt) cc_final: 0.7740 (tpt) REVERT: l 110 LYS cc_start: 0.9243 (mtpp) cc_final: 0.9015 (mtpt) REVERT: m 47 MET cc_start: 0.7904 (mtt) cc_final: 0.7613 (mtp) REVERT: m 77 TYR cc_start: 0.8443 (t80) cc_final: 0.8105 (t80) REVERT: m 101 PHE cc_start: 0.8191 (t80) cc_final: 0.7560 (t80) outliers start: 22 outliers final: 18 residues processed: 504 average time/residue: 1.0536 time to fit residues: 845.6573 Evaluate side-chains 492 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 472 time to evaluate : 4.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 187 SER Chi-restraints excluded: chain l residue 92 MET Chi-restraints excluded: chain m residue 41 ASN Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 41 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 5.9990 chunk 412 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 458 optimal weight: 10.0000 chunk 380 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** K 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN k 34 GLN n 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 37818 Z= 0.200 Angle : 0.471 7.255 51085 Z= 0.245 Chirality : 0.040 0.164 5873 Planarity : 0.003 0.049 6627 Dihedral : 6.830 126.054 5309 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.62 % Allowed : 9.09 % Favored : 90.29 % 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: 1.13 (0.12), residues: 4743 helix: 1.99 (0.11), residues: 2355 sheet: -0.40 (0.16), residues: 832 loop : -0.46 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS j 191 PHE 0.021 0.001 PHE h 173 TYR 0.012 0.001 TYR A 96 ARG 0.005 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 515 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 490 time to evaluate : 4.570 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: A 144 ASP cc_start: 0.7472 (p0) cc_final: 0.7227 (p0) REVERT: A 205 GLU cc_start: 0.8210 (pm20) cc_final: 0.7885 (pt0) REVERT: C 101 ASN cc_start: 0.7622 (t0) cc_final: 0.7140 (t0) REVERT: C 263 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: D 101 ASN cc_start: 0.8145 (t0) cc_final: 0.7866 (t0) REVERT: D 230 HIS cc_start: 0.6835 (m-70) cc_final: 0.6607 (m170) REVERT: H 41 ASN cc_start: 0.8345 (m110) cc_final: 0.7971 (m110) REVERT: I 18 ASP cc_start: 0.8519 (p0) cc_final: 0.7882 (p0) REVERT: I 74 MET cc_start: 0.8727 (mmp) cc_final: 0.8389 (mmp) REVERT: J 18 ASP cc_start: 0.8627 (p0) cc_final: 0.8338 (p0) REVERT: K 18 ASP cc_start: 0.8656 (p0) cc_final: 0.8271 (p0) REVERT: K 129 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7695 (mm110) REVERT: K 143 LEU cc_start: 0.9433 (mm) cc_final: 0.9041 (tt) REVERT: L 125 LEU cc_start: 0.9099 (pp) cc_final: 0.8850 (pp) REVERT: M 25 LYS cc_start: 0.9195 (mtpp) cc_final: 0.8887 (ttmm) REVERT: M 26 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8074 (tm-30) REVERT: h 62 TYR cc_start: 0.8356 (m-80) cc_final: 0.8034 (m-10) REVERT: h 86 ASP cc_start: 0.8068 (m-30) cc_final: 0.6971 (p0) REVERT: h 113 CYS cc_start: 0.8826 (p) cc_final: 0.8601 (p) REVERT: i 49 PHE cc_start: 0.7798 (t80) cc_final: 0.7471 (t80) REVERT: i 141 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: i 150 ASN cc_start: 0.8921 (m-40) cc_final: 0.8346 (m110) REVERT: j 108 LYS cc_start: 0.9154 (tptt) cc_final: 0.8944 (tptp) REVERT: j 173 PHE cc_start: 0.8533 (m-80) cc_final: 0.7985 (m-80) REVERT: k 25 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8774 (mmmt) REVERT: k 74 MET cc_start: 0.7618 (mmp) cc_final: 0.7416 (mmp) REVERT: k 97 SER cc_start: 0.7475 (p) cc_final: 0.7232 (t) REVERT: m 47 MET cc_start: 0.8006 (mtt) cc_final: 0.7709 (mtp) REVERT: m 77 TYR cc_start: 0.8446 (t80) cc_final: 0.8226 (t80) REVERT: m 101 PHE cc_start: 0.8242 (t80) cc_final: 0.7957 (t80) REVERT: n 167 ASP cc_start: 0.8590 (m-30) cc_final: 0.8148 (m-30) outliers start: 25 outliers final: 19 residues processed: 504 average time/residue: 1.0273 time to fit residues: 822.0876 Evaluate side-chains 487 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 466 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 187 SER Chi-restraints excluded: chain m residue 41 ASN Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 41 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 334 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 386 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 456 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN B 163 GLN E 289 GLN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN k 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 37818 Z= 0.334 Angle : 0.517 6.093 51085 Z= 0.273 Chirality : 0.041 0.146 5873 Planarity : 0.003 0.050 6627 Dihedral : 6.956 127.525 5309 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.60 % Allowed : 9.74 % Favored : 89.67 % 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: 0.95 (0.12), residues: 4743 helix: 1.85 (0.11), residues: 2362 sheet: -0.40 (0.16), residues: 836 loop : -0.61 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS L 156 PHE 0.013 0.001 PHE h 173 TYR 0.017 0.001 TYR A 96 ARG 0.004 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 467 time to evaluate : 4.507 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: A 144 ASP cc_start: 0.7640 (p0) cc_final: 0.7378 (p0) REVERT: A 205 GLU cc_start: 0.8225 (pm20) cc_final: 0.8005 (pt0) REVERT: C 263 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: D 101 ASN cc_start: 0.8015 (t0) cc_final: 0.7708 (t0) REVERT: D 201 ASP cc_start: 0.7780 (m-30) cc_final: 0.7562 (t0) REVERT: D 230 HIS cc_start: 0.6954 (m-70) cc_final: 0.6719 (m170) REVERT: F 323 ILE cc_start: 0.9651 (mt) cc_final: 0.9425 (mm) REVERT: F 363 MET cc_start: 0.8671 (mtp) cc_final: 0.8252 (mtp) REVERT: H 41 ASN cc_start: 0.8421 (m110) cc_final: 0.7994 (m110) REVERT: H 70 ILE cc_start: 0.8714 (mp) cc_final: 0.8468 (mm) REVERT: K 18 ASP cc_start: 0.8785 (p0) cc_final: 0.8372 (p0) REVERT: K 129 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7646 (mm110) REVERT: K 143 LEU cc_start: 0.9451 (mm) cc_final: 0.9039 (tt) REVERT: M 26 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8080 (tm-30) REVERT: N 47 MET cc_start: 0.8627 (mtm) cc_final: 0.8246 (mtm) REVERT: h 62 TYR cc_start: 0.8349 (m-80) cc_final: 0.8014 (m-10) REVERT: h 86 ASP cc_start: 0.8077 (m-30) cc_final: 0.6934 (p0) REVERT: h 113 CYS cc_start: 0.8917 (p) cc_final: 0.8697 (p) REVERT: i 49 PHE cc_start: 0.7819 (t80) cc_final: 0.7495 (t80) REVERT: i 141 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: j 108 LYS cc_start: 0.9188 (tptt) cc_final: 0.8985 (tptp) REVERT: j 173 PHE cc_start: 0.8562 (m-80) cc_final: 0.8102 (m-80) REVERT: k 25 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8768 (mmmt) REVERT: m 47 MET cc_start: 0.7923 (mtt) cc_final: 0.7645 (mtp) REVERT: m 77 TYR cc_start: 0.8542 (t80) cc_final: 0.8323 (t80) REVERT: n 74 MET cc_start: 0.6729 (mmp) cc_final: 0.6497 (mmp) REVERT: n 167 ASP cc_start: 0.8591 (m-30) cc_final: 0.8156 (m-30) outliers start: 24 outliers final: 19 residues processed: 481 average time/residue: 1.0271 time to fit residues: 782.9354 Evaluate side-chains 477 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 456 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain h residue 92 MET Chi-restraints excluded: chain h residue 188 ILE Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 89 THR Chi-restraints excluded: chain k residue 187 SER Chi-restraints excluded: chain m residue 41 ASN Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 41 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 0.4980 chunk 182 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 290 optimal weight: 0.0970 chunk 311 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 359 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37818 Z= 0.127 Angle : 0.462 6.339 51085 Z= 0.237 Chirality : 0.040 0.145 5873 Planarity : 0.003 0.047 6627 Dihedral : 6.751 118.822 5309 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.62 % Allowed : 9.66 % Favored : 89.72 % 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: 1.29 (0.12), residues: 4743 helix: 2.14 (0.11), residues: 2361 sheet: -0.35 (0.17), residues: 816 loop : -0.41 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 122 PHE 0.015 0.001 PHE j 49 TYR 0.010 0.001 TYR A 96 ARG 0.008 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 509 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 484 time to evaluate : 4.574 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: A 144 ASP cc_start: 0.7450 (p0) cc_final: 0.7219 (p0) REVERT: A 344 GLU cc_start: 0.8428 (tt0) cc_final: 0.8107 (tm-30) REVERT: C 101 ASN cc_start: 0.7638 (t0) cc_final: 0.7164 (t0) REVERT: C 263 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: D 101 ASN cc_start: 0.8159 (t0) cc_final: 0.7850 (t0) REVERT: D 201 ASP cc_start: 0.7709 (m-30) cc_final: 0.7474 (t0) REVERT: D 230 HIS cc_start: 0.6936 (m-70) cc_final: 0.6686 (m170) REVERT: F 363 MET cc_start: 0.8668 (mtp) cc_final: 0.8154 (mtp) REVERT: H 41 ASN cc_start: 0.8312 (m110) cc_final: 0.7965 (m110) REVERT: I 18 ASP cc_start: 0.8518 (p0) cc_final: 0.7885 (p0) REVERT: I 74 MET cc_start: 0.8684 (mmp) cc_final: 0.8181 (mmp) REVERT: K 18 ASP cc_start: 0.8604 (p0) cc_final: 0.8207 (p0) REVERT: K 129 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7600 (mm110) REVERT: K 143 LEU cc_start: 0.9435 (mm) cc_final: 0.9040 (tt) REVERT: M 25 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8943 (ttmm) REVERT: M 26 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8107 (tm-30) REVERT: h 62 TYR cc_start: 0.8341 (m-80) cc_final: 0.8013 (m-10) REVERT: i 49 PHE cc_start: 0.7798 (t80) cc_final: 0.7474 (t80) REVERT: i 141 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: j 108 LYS cc_start: 0.9211 (tptt) cc_final: 0.8972 (tptp) REVERT: j 173 PHE cc_start: 0.8526 (m-80) cc_final: 0.8023 (m-80) REVERT: k 25 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8744 (mmmt) REVERT: m 5 MET cc_start: 0.4700 (mmm) cc_final: 0.4033 (mmt) REVERT: m 47 MET cc_start: 0.7975 (mtt) cc_final: 0.7696 (mtp) REVERT: n 74 MET cc_start: 0.6674 (mmp) cc_final: 0.6392 (mmp) REVERT: n 113 CYS cc_start: 0.8272 (p) cc_final: 0.7859 (t) REVERT: n 167 ASP cc_start: 0.8520 (m-30) cc_final: 0.8134 (m-30) outliers start: 25 outliers final: 15 residues processed: 496 average time/residue: 1.0335 time to fit residues: 811.5642 Evaluate side-chains 482 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 465 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 187 SER Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 41 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 7.9990 chunk 437 optimal weight: 8.9990 chunk 399 optimal weight: 1.9990 chunk 425 optimal weight: 10.0000 chunk 256 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 334 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 384 optimal weight: 0.6980 chunk 402 optimal weight: 10.0000 chunk 424 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37818 Z= 0.191 Angle : 0.471 6.674 51085 Z= 0.243 Chirality : 0.040 0.146 5873 Planarity : 0.003 0.048 6627 Dihedral : 6.630 115.971 5309 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.45 % Allowed : 10.06 % Favored : 89.49 % 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: 1.29 (0.12), residues: 4743 helix: 2.17 (0.11), residues: 2362 sheet: -0.35 (0.17), residues: 830 loop : -0.46 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS j 191 PHE 0.014 0.001 PHE j 49 TYR 0.015 0.001 TYR F 153 ARG 0.004 0.000 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 486 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 468 time to evaluate : 4.542 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: A 144 ASP cc_start: 0.7495 (p0) cc_final: 0.7263 (p0) REVERT: C 101 ASN cc_start: 0.7656 (t0) cc_final: 0.7179 (t0) REVERT: C 256 LYS cc_start: 0.9087 (mttp) cc_final: 0.8763 (tptt) REVERT: C 263 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: D 101 ASN cc_start: 0.8095 (t0) cc_final: 0.7767 (t0) REVERT: D 201 ASP cc_start: 0.7728 (m-30) cc_final: 0.7497 (t0) REVERT: D 230 HIS cc_start: 0.6939 (m-70) cc_final: 0.6687 (m170) REVERT: F 323 ILE cc_start: 0.9650 (mt) cc_final: 0.9393 (mm) REVERT: F 363 MET cc_start: 0.8684 (mtp) cc_final: 0.8251 (mtp) REVERT: H 41 ASN cc_start: 0.8372 (m110) cc_final: 0.7982 (m110) REVERT: K 18 ASP cc_start: 0.8642 (p0) cc_final: 0.8219 (p0) REVERT: K 129 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7591 (mm110) REVERT: K 143 LEU cc_start: 0.9449 (mm) cc_final: 0.9042 (tt) REVERT: M 25 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8972 (ttmm) REVERT: M 26 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8086 (tm-30) REVERT: M 98 MET cc_start: 0.8774 (tpp) cc_final: 0.8473 (tpp) REVERT: h 62 TYR cc_start: 0.8343 (m-80) cc_final: 0.8016 (m-10) REVERT: h 86 ASP cc_start: 0.8083 (m-30) cc_final: 0.7003 (p0) REVERT: i 49 PHE cc_start: 0.7781 (t80) cc_final: 0.7448 (t80) REVERT: i 141 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: j 25 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8632 (mmtm) REVERT: j 108 LYS cc_start: 0.9194 (tptt) cc_final: 0.8968 (tptp) REVERT: j 173 PHE cc_start: 0.8520 (m-80) cc_final: 0.8034 (m-80) REVERT: k 25 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8732 (mmmt) REVERT: m 5 MET cc_start: 0.4630 (mmm) cc_final: 0.4001 (mmt) REVERT: m 47 MET cc_start: 0.7983 (mtt) cc_final: 0.7706 (mtp) REVERT: n 74 MET cc_start: 0.6640 (mmp) cc_final: 0.6401 (mmp) REVERT: n 113 CYS cc_start: 0.8250 (p) cc_final: 0.7885 (t) REVERT: n 167 ASP cc_start: 0.8541 (m-30) cc_final: 0.8151 (m-30) outliers start: 18 outliers final: 14 residues processed: 478 average time/residue: 1.0659 time to fit residues: 809.5340 Evaluate side-chains 477 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 461 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain h residue 103 LEU Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 187 SER Chi-restraints excluded: chain m residue 41 ASN Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 41 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 0.5980 chunk 450 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 472 optimal weight: 1.9990 chunk 434 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 290 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37818 Z= 0.181 Angle : 0.470 6.893 51085 Z= 0.242 Chirality : 0.040 0.146 5873 Planarity : 0.003 0.048 6627 Dihedral : 6.544 109.677 5309 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.40 % Allowed : 10.08 % Favored : 89.52 % 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 (0.12), residues: 4743 helix: 2.21 (0.11), residues: 2362 sheet: -0.36 (0.17), residues: 830 loop : -0.45 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS j 191 PHE 0.014 0.001 PHE j 49 TYR 0.012 0.001 TYR A 96 ARG 0.004 0.000 ARG M 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9486 Ramachandran restraints generated. 4743 Oldfield, 0 Emsley, 4743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 468 time to evaluate : 4.578 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: A 144 ASP cc_start: 0.7478 (p0) cc_final: 0.7249 (p0) REVERT: C 101 ASN cc_start: 0.7664 (t0) cc_final: 0.7190 (t0) REVERT: C 256 LYS cc_start: 0.9087 (mttp) cc_final: 0.8767 (tptt) REVERT: C 263 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: D 101 ASN cc_start: 0.8033 (t0) cc_final: 0.7722 (t0) REVERT: D 201 ASP cc_start: 0.7788 (m-30) cc_final: 0.7580 (t0) REVERT: D 230 HIS cc_start: 0.6967 (m-70) cc_final: 0.6726 (m170) REVERT: D 390 MET cc_start: 0.8905 (mtt) cc_final: 0.8680 (mtt) REVERT: F 323 ILE cc_start: 0.9649 (mt) cc_final: 0.9416 (mm) REVERT: F 363 MET cc_start: 0.8689 (mtp) cc_final: 0.8252 (mtp) REVERT: H 41 ASN cc_start: 0.8367 (m110) cc_final: 0.7973 (m110) REVERT: K 18 ASP cc_start: 0.8639 (p0) cc_final: 0.8214 (p0) REVERT: K 129 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7586 (mm110) REVERT: K 143 LEU cc_start: 0.9452 (mm) cc_final: 0.9042 (tt) REVERT: M 25 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8955 (ttmm) REVERT: M 26 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8077 (tm-30) REVERT: h 62 TYR cc_start: 0.8333 (m-80) cc_final: 0.7990 (m-10) REVERT: h 86 ASP cc_start: 0.8099 (m-30) cc_final: 0.6991 (p0) REVERT: i 34 GLN cc_start: 0.7978 (tp40) cc_final: 0.7776 (tp40) REVERT: i 49 PHE cc_start: 0.7777 (t80) cc_final: 0.7466 (t80) REVERT: i 141 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: j 108 LYS cc_start: 0.9210 (tptt) cc_final: 0.8992 (tptp) REVERT: j 173 PHE cc_start: 0.8514 (m-80) cc_final: 0.8063 (m-80) REVERT: k 25 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8717 (mmmt) REVERT: k 74 MET cc_start: 0.7599 (mmp) cc_final: 0.7170 (mmp) REVERT: l 110 LYS cc_start: 0.9156 (mtpp) cc_final: 0.8720 (mtpt) REVERT: m 5 MET cc_start: 0.4594 (mmm) cc_final: 0.3993 (mmt) REVERT: m 47 MET cc_start: 0.8027 (mtt) cc_final: 0.7759 (mtp) REVERT: n 74 MET cc_start: 0.6617 (mmp) cc_final: 0.6376 (mmp) REVERT: n 113 CYS cc_start: 0.8296 (p) cc_final: 0.7978 (t) REVERT: n 116 ASN cc_start: 0.9315 (m-40) cc_final: 0.8971 (m-40) REVERT: n 167 ASP cc_start: 0.8516 (m-30) cc_final: 0.8128 (m-30) outliers start: 16 outliers final: 14 residues processed: 478 average time/residue: 1.0456 time to fit residues: 800.6697 Evaluate side-chains 478 residues out of total 4013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 462 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain h residue 103 LEU Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 98 MET Chi-restraints excluded: chain j residue 117 SER Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 187 SER Chi-restraints excluded: chain m residue 41 ASN Chi-restraints excluded: chain m residue 92 MET Chi-restraints excluded: chain n residue 41 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 4.9990 chunk 400 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 346 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 376 optimal weight: 9.9990 chunk 157 optimal weight: 0.3980 chunk 386 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 163 GLN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 41 ASN ** j 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.098575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.065792 restraints weight = 258942.752| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.24 r_work: 0.2840 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37818 Z= 0.187 Angle : 0.469 6.775 51085 Z= 0.242 Chirality : 0.040 0.145 5873 Planarity : 0.003 0.048 6627 Dihedral : 6.482 102.252 5309 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.50 % Allowed : 10.01 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.12), residues: 4743 helix: 2.24 (0.11), residues: 2362 sheet: -0.35 (0.17), residues: 828 loop : -0.45 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS h 156 PHE 0.014 0.001 PHE l 49 TYR 0.012 0.001 TYR A 96 ARG 0.008 0.000 ARG m 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16586.65 seconds wall clock time: 282 minutes 49.55 seconds (16969.55 seconds total)