Starting phenix.real_space_refine on Sun Sep 29 02:39:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/09_2024/6gy6_0088.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/09_2024/6gy6_0088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/09_2024/6gy6_0088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/09_2024/6gy6_0088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/09_2024/6gy6_0088.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/09_2024/6gy6_0088.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 45513 2.51 5 N 12272 2.21 5 O 14482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72462 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "B" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Restraints were copied for chains: C, E, D, F, I, J, M, Q, P, S, R, T, G, H, K, L, O, N, U, W, V, Y, X, Z Time building chain proxies: 13.60, per 1000 atoms: 0.19 Number of scatterers: 72462 At special positions: 0 Unit cell: (265.29, 264.18, 180.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 14482 8.00 N 12272 7.00 C 45513 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.82 Conformation dependent library (CDL) restraints added in 7.0 seconds 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17472 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 26 sheets defined 87.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU A 156 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL A 269 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 270 " --> pdb=" O GLY A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 404 Proline residue: A 381 - end of helix removed outlier: 4.092A pdb=" N ASP A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 66 Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 192 removed outlier: 3.704A pdb=" N THR B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Proline residue: B 168 - end of helix removed outlier: 4.114A pdb=" N ALA B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS B 219 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 220' Processing helix chain 'B' and resid 221 through 222 No H-bonds generated for 'chain 'B' and resid 221 through 222' Processing helix chain 'B' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 306 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN G 33 " --> pdb=" O TRP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 66 Processing helix chain 'G' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE G 122 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS G 131 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER G 164 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Proline residue: G 168 - end of helix removed outlier: 4.114A pdb=" N ALA G 178 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 183 " --> pdb=" O ASP G 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 203 removed outlier: 3.616A pdb=" N MET G 198 " --> pdb=" O ASN G 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 214 Processing helix chain 'G' and resid 216 through 220 removed outlier: 3.634A pdb=" N LYS G 219 " --> pdb=" O GLN G 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU G 220 " --> pdb=" O PRO G 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 216 through 220' Processing helix chain 'G' and resid 221 through 222 No H-bonds generated for 'chain 'G' and resid 221 through 222' Processing helix chain 'G' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 240 " --> pdb=" O ILE G 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 275 " --> pdb=" O LYS G 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP G 291 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR G 292 " --> pdb=" O MET G 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS G 303 " --> pdb=" O THR G 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE G 304 " --> pdb=" O GLU G 300 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN G 306 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL G 307 " --> pdb=" O LYS G 303 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN G 345 " --> pdb=" O ASN G 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR G 346 " --> pdb=" O LEU G 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN H 23 " --> pdb=" O LYS H 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN H 33 " --> pdb=" O TRP H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 66 Processing helix chain 'H' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA H 91 " --> pdb=" O ASP H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE H 122 " --> pdb=" O ILE H 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS H 131 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP H 165 " --> pdb=" O GLU H 161 " (cutoff:3.500A) Proline residue: H 168 - end of helix removed outlier: 4.114A pdb=" N ALA H 178 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE H 183 " --> pdb=" O ASP H 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET H 198 " --> pdb=" O ASN H 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 214 Processing helix chain 'H' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS H 219 " --> pdb=" O GLN H 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU H 220 " --> pdb=" O PRO H 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 216 through 220' Processing helix chain 'H' and resid 221 through 222 No H-bonds generated for 'chain 'H' and resid 221 through 222' Processing helix chain 'H' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE H 232 " --> pdb=" O GLN H 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 240 " --> pdb=" O ILE H 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE H 260 " --> pdb=" O LEU H 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG H 275 " --> pdb=" O LYS H 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP H 291 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR H 292 " --> pdb=" O MET H 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU H 300 " --> pdb=" O THR H 296 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS H 303 " --> pdb=" O THR H 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 304 " --> pdb=" O GLU H 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN H 306 " --> pdb=" O VAL H 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE H 311 " --> pdb=" O VAL H 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN H 335 " --> pdb=" O LEU H 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN H 345 " --> pdb=" O ASN H 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR H 346 " --> pdb=" O LEU H 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN K 23 " --> pdb=" O LYS K 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN K 33 " --> pdb=" O TRP K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 66 Processing helix chain 'K' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE K 122 " --> pdb=" O ILE K 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG K 128 " --> pdb=" O SER K 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS K 131 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS K 135 " --> pdb=" O LYS K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER K 164 " --> pdb=" O THR K 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP K 165 " --> pdb=" O GLU K 161 " (cutoff:3.500A) Proline residue: K 168 - end of helix removed outlier: 4.114A pdb=" N ALA K 178 " --> pdb=" O ASN K 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE K 183 " --> pdb=" O ASP K 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE K 190 " --> pdb=" O SER K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE K 203 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 214 Processing helix chain 'K' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS K 219 " --> pdb=" O GLN K 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU K 220 " --> pdb=" O PRO K 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 216 through 220' Processing helix chain 'K' and resid 221 through 222 No H-bonds generated for 'chain 'K' and resid 221 through 222' Processing helix chain 'K' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU K 231 " --> pdb=" O LYS K 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE K 232 " --> pdb=" O GLN K 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU K 237 " --> pdb=" O ALA K 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 240 " --> pdb=" O ILE K 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE K 260 " --> pdb=" O LEU K 256 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG K 275 " --> pdb=" O LYS K 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP K 291 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR K 292 " --> pdb=" O MET K 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU K 300 " --> pdb=" O THR K 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS K 303 " --> pdb=" O THR K 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE K 304 " --> pdb=" O GLU K 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN K 306 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL K 307 " --> pdb=" O LYS K 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE K 311 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN K 335 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN K 345 " --> pdb=" O ASN K 341 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR K 346 " --> pdb=" O LEU K 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN L 23 " --> pdb=" O LYS L 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN L 33 " --> pdb=" O TRP L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 66 Processing helix chain 'L' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU L 74 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS L 131 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS L 135 " --> pdb=" O LYS L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 192 removed outlier: 3.704A pdb=" N THR L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP L 165 " --> pdb=" O GLU L 161 " (cutoff:3.500A) Proline residue: L 168 - end of helix removed outlier: 4.115A pdb=" N ALA L 178 " --> pdb=" O ASN L 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE L 183 " --> pdb=" O ASP L 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE L 190 " --> pdb=" O SER L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET L 198 " --> pdb=" O ASN L 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE L 203 " --> pdb=" O PHE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 214 Processing helix chain 'L' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS L 219 " --> pdb=" O GLN L 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU L 220 " --> pdb=" O PRO L 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 216 through 220' Processing helix chain 'L' and resid 221 through 222 No H-bonds generated for 'chain 'L' and resid 221 through 222' Processing helix chain 'L' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU L 231 " --> pdb=" O LYS L 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE L 232 " --> pdb=" O GLN L 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU L 237 " --> pdb=" O ALA L 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL L 240 " --> pdb=" O ILE L 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE L 260 " --> pdb=" O LEU L 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP L 291 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR L 292 " --> pdb=" O MET L 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU L 300 " --> pdb=" O THR L 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS L 303 " --> pdb=" O THR L 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 304 " --> pdb=" O GLU L 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN L 306 " --> pdb=" O VAL L 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL L 307 " --> pdb=" O LYS L 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE L 311 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN L 335 " --> pdb=" O LEU L 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN L 345 " --> pdb=" O ASN L 341 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR L 346 " --> pdb=" O LEU L 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN N 33 " --> pdb=" O TRP N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 66 Processing helix chain 'N' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS N 72 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU N 74 " --> pdb=" O VAL N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR N 82 " --> pdb=" O ALA N 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA N 91 " --> pdb=" O ASP N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 138 removed outlier: 3.540A pdb=" N ILE N 122 " --> pdb=" O ILE N 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG N 128 " --> pdb=" O SER N 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS N 135 " --> pdb=" O LYS N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR N 155 " --> pdb=" O LEU N 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER N 164 " --> pdb=" O THR N 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP N 165 " --> pdb=" O GLU N 161 " (cutoff:3.500A) Proline residue: N 168 - end of helix removed outlier: 4.114A pdb=" N ALA N 178 " --> pdb=" O ASN N 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE N 183 " --> pdb=" O ASP N 179 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL N 189 " --> pdb=" O GLU N 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE N 190 " --> pdb=" O SER N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET N 198 " --> pdb=" O ASN N 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE N 203 " --> pdb=" O PHE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 207 through 214 Processing helix chain 'N' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS N 219 " --> pdb=" O GLN N 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU N 220 " --> pdb=" O PRO N 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 216 through 220' Processing helix chain 'N' and resid 221 through 222 No H-bonds generated for 'chain 'N' and resid 221 through 222' Processing helix chain 'N' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU N 231 " --> pdb=" O LYS N 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE N 232 " --> pdb=" O GLN N 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU N 237 " --> pdb=" O ALA N 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL N 240 " --> pdb=" O ILE N 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE N 260 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG N 275 " --> pdb=" O LYS N 271 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP N 291 " --> pdb=" O VAL N 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR N 292 " --> pdb=" O MET N 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU N 300 " --> pdb=" O THR N 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS N 303 " --> pdb=" O THR N 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE N 304 " --> pdb=" O GLU N 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN N 306 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL N 307 " --> pdb=" O LYS N 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE N 311 " --> pdb=" O VAL N 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP N 321 " --> pdb=" O LYS N 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN N 335 " --> pdb=" O LEU N 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN N 345 " --> pdb=" O ASN N 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR N 346 " --> pdb=" O LEU N 342 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN O 23 " --> pdb=" O LYS O 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA O 24 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN O 33 " --> pdb=" O TRP O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 66 Processing helix chain 'O' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU O 74 " --> pdb=" O VAL O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA O 91 " --> pdb=" O ASP O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE O 122 " --> pdb=" O ILE O 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG O 128 " --> pdb=" O SER O 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS O 131 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS O 135 " --> pdb=" O LYS O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR O 155 " --> pdb=" O LEU O 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER O 164 " --> pdb=" O THR O 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP O 165 " --> pdb=" O GLU O 161 " (cutoff:3.500A) Proline residue: O 168 - end of helix removed outlier: 4.115A pdb=" N ALA O 178 " --> pdb=" O ASN O 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE O 183 " --> pdb=" O ASP O 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL O 189 " --> pdb=" O GLU O 185 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE O 190 " --> pdb=" O SER O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET O 198 " --> pdb=" O ASN O 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE O 203 " --> pdb=" O PHE O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 214 Processing helix chain 'O' and resid 216 through 220 removed outlier: 3.636A pdb=" N LYS O 219 " --> pdb=" O GLN O 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU O 220 " --> pdb=" O PRO O 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 216 through 220' Processing helix chain 'O' and resid 221 through 222 No H-bonds generated for 'chain 'O' and resid 221 through 222' Processing helix chain 'O' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU O 231 " --> pdb=" O LYS O 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL O 240 " --> pdb=" O ILE O 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE O 260 " --> pdb=" O LEU O 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP O 291 " --> pdb=" O VAL O 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR O 292 " --> pdb=" O MET O 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU O 300 " --> pdb=" O THR O 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS O 303 " --> pdb=" O THR O 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE O 304 " --> pdb=" O GLU O 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN O 306 " --> pdb=" O VAL O 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL O 307 " --> pdb=" O LYS O 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE O 311 " --> pdb=" O VAL O 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP O 321 " --> pdb=" O LYS O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN O 335 " --> pdb=" O LEU O 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN O 345 " --> pdb=" O ASN O 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR O 346 " --> pdb=" O LEU O 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN U 23 " --> pdb=" O LYS U 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA U 24 " --> pdb=" O ALA U 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN U 33 " --> pdb=" O TRP U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 66 Processing helix chain 'U' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS U 72 " --> pdb=" O ALA U 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU U 74 " --> pdb=" O VAL U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR U 82 " --> pdb=" O ALA U 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA U 91 " --> pdb=" O ASP U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE U 122 " --> pdb=" O ILE U 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG U 128 " --> pdb=" O SER U 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS U 131 " --> pdb=" O GLY U 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS U 135 " --> pdb=" O LYS U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR U 155 " --> pdb=" O LEU U 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER U 164 " --> pdb=" O THR U 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP U 165 " --> pdb=" O GLU U 161 " (cutoff:3.500A) Proline residue: U 168 - end of helix removed outlier: 4.115A pdb=" N ALA U 178 " --> pdb=" O ASN U 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE U 183 " --> pdb=" O ASP U 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL U 189 " --> pdb=" O GLU U 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE U 190 " --> pdb=" O SER U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 203 removed outlier: 3.614A pdb=" N MET U 198 " --> pdb=" O ASN U 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE U 203 " --> pdb=" O PHE U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 214 Processing helix chain 'U' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS U 219 " --> pdb=" O GLN U 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU U 220 " --> pdb=" O PRO U 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 216 through 220' Processing helix chain 'U' and resid 221 through 222 No H-bonds generated for 'chain 'U' and resid 221 through 222' Processing helix chain 'U' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU U 231 " --> pdb=" O LYS U 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE U 232 " --> pdb=" O GLN U 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU U 237 " --> pdb=" O ALA U 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL U 240 " --> pdb=" O ILE U 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE U 260 " --> pdb=" O LEU U 256 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG U 275 " --> pdb=" O LYS U 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP U 291 " --> pdb=" O VAL U 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR U 292 " --> pdb=" O MET U 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU U 300 " --> pdb=" O THR U 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS U 303 " --> pdb=" O THR U 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE U 304 " --> pdb=" O GLU U 300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN U 306 " --> pdb=" O VAL U 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL U 307 " --> pdb=" O LYS U 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE U 311 " --> pdb=" O VAL U 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP U 321 " --> pdb=" O LYS U 317 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 348 removed outlier: 3.581A pdb=" N GLN U 335 " --> pdb=" O LEU U 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN U 345 " --> pdb=" O ASN U 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN V 23 " --> pdb=" O LYS V 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA V 24 " --> pdb=" O ALA V 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN V 33 " --> pdb=" O TRP V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 66 Processing helix chain 'V' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS V 72 " --> pdb=" O ALA V 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU V 74 " --> pdb=" O VAL V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR V 82 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA V 91 " --> pdb=" O ASP V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 138 removed outlier: 3.540A pdb=" N ILE V 122 " --> pdb=" O ILE V 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG V 128 " --> pdb=" O SER V 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS V 131 " --> pdb=" O GLY V 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS V 135 " --> pdb=" O LYS V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR V 155 " --> pdb=" O LEU V 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER V 164 " --> pdb=" O THR V 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP V 165 " --> pdb=" O GLU V 161 " (cutoff:3.500A) Proline residue: V 168 - end of helix removed outlier: 4.114A pdb=" N ALA V 178 " --> pdb=" O ASN V 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE V 183 " --> pdb=" O ASP V 179 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL V 189 " --> pdb=" O GLU V 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE V 190 " --> pdb=" O SER V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 203 removed outlier: 3.616A pdb=" N MET V 198 " --> pdb=" O ASN V 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE V 203 " --> pdb=" O PHE V 199 " (cutoff:3.500A) Processing helix chain 'V' and resid 207 through 214 Processing helix chain 'V' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS V 219 " --> pdb=" O GLN V 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU V 220 " --> pdb=" O PRO V 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 216 through 220' Processing helix chain 'V' and resid 221 through 222 No H-bonds generated for 'chain 'V' and resid 221 through 222' Processing helix chain 'V' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU V 231 " --> pdb=" O LYS V 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE V 232 " --> pdb=" O GLN V 228 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU V 237 " --> pdb=" O ALA V 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL V 240 " --> pdb=" O ILE V 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE V 260 " --> pdb=" O LEU V 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG V 275 " --> pdb=" O LYS V 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP V 291 " --> pdb=" O VAL V 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR V 292 " --> pdb=" O MET V 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU V 300 " --> pdb=" O THR V 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS V 303 " --> pdb=" O THR V 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE V 304 " --> pdb=" O GLU V 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN V 306 " --> pdb=" O VAL V 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL V 307 " --> pdb=" O LYS V 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE V 311 " --> pdb=" O VAL V 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP V 321 " --> pdb=" O LYS V 317 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN V 335 " --> pdb=" O LEU V 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN V 345 " --> pdb=" O ASN V 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR V 346 " --> pdb=" O LEU V 342 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN W 23 " --> pdb=" O LYS W 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA W 24 " --> pdb=" O ALA W 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN W 33 " --> pdb=" O TRP W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 66 Processing helix chain 'W' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS W 72 " --> pdb=" O ALA W 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU W 74 " --> pdb=" O VAL W 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR W 82 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA W 91 " --> pdb=" O ASP W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 138 removed outlier: 3.540A pdb=" N ILE W 122 " --> pdb=" O ILE W 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG W 128 " --> pdb=" O SER W 124 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS W 131 " --> pdb=" O GLY W 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS W 135 " --> pdb=" O LYS W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR W 155 " --> pdb=" O LEU W 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER W 164 " --> pdb=" O THR W 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP W 165 " --> pdb=" O GLU W 161 " (cutoff:3.500A) Proline residue: W 168 - end of helix removed outlier: 4.115A pdb=" N ALA W 178 " --> pdb=" O ASN W 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE W 183 " --> pdb=" O ASP W 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL W 189 " --> pdb=" O GLU W 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE W 190 " --> pdb=" O SER W 186 " (cutoff:3.500A) Processing helix chain 'W' and resid 194 through 203 removed outlier: 3.616A pdb=" N MET W 198 " --> pdb=" O ASN W 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE W 203 " --> pdb=" O PHE W 199 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 214 Processing helix chain 'W' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS W 219 " --> pdb=" O GLN W 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU W 220 " --> pdb=" O PRO W 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 216 through 220' Processing helix chain 'W' and resid 221 through 222 No H-bonds generated for 'chain 'W' and resid 221 through 222' Processing helix chain 'W' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU W 231 " --> pdb=" O LYS W 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE W 232 " --> pdb=" O GLN W 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU W 237 " --> pdb=" O ALA W 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL W 240 " --> pdb=" O ILE W 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE W 260 " --> pdb=" O LEU W 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG W 275 " --> pdb=" O LYS W 271 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP W 291 " --> pdb=" O VAL W 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR W 292 " --> pdb=" O MET W 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU W 300 " --> pdb=" O THR W 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS W 303 " --> pdb=" O THR W 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE W 304 " --> pdb=" O GLU W 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN W 306 " --> pdb=" O VAL W 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL W 307 " --> pdb=" O LYS W 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE W 311 " --> pdb=" O VAL W 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP W 321 " --> pdb=" O LYS W 317 " (cutoff:3.500A) Processing helix chain 'W' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN W 335 " --> pdb=" O LEU W 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN W 345 " --> pdb=" O ASN W 341 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR W 346 " --> pdb=" O LEU W 342 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN X 23 " --> pdb=" O LYS X 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN X 33 " --> pdb=" O TRP X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 66 Processing helix chain 'X' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS X 72 " --> pdb=" O ALA X 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU X 74 " --> pdb=" O VAL X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR X 82 " --> pdb=" O ALA X 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA X 91 " --> pdb=" O ASP X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE X 122 " --> pdb=" O ILE X 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG X 128 " --> pdb=" O SER X 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS X 131 " --> pdb=" O GLY X 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS X 135 " --> pdb=" O LYS X 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 148 through 192 removed outlier: 3.706A pdb=" N THR X 155 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER X 164 " --> pdb=" O THR X 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP X 165 " --> pdb=" O GLU X 161 " (cutoff:3.500A) Proline residue: X 168 - end of helix removed outlier: 4.114A pdb=" N ALA X 178 " --> pdb=" O ASN X 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE X 183 " --> pdb=" O ASP X 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL X 189 " --> pdb=" O GLU X 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE X 190 " --> pdb=" O SER X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET X 198 " --> pdb=" O ASN X 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE X 203 " --> pdb=" O PHE X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 214 Processing helix chain 'X' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS X 219 " --> pdb=" O GLN X 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU X 220 " --> pdb=" O PRO X 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 216 through 220' Processing helix chain 'X' and resid 221 through 222 No H-bonds generated for 'chain 'X' and resid 221 through 222' Processing helix chain 'X' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU X 231 " --> pdb=" O LYS X 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE X 232 " --> pdb=" O GLN X 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU X 237 " --> pdb=" O ALA X 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL X 240 " --> pdb=" O ILE X 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE X 260 " --> pdb=" O LEU X 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG X 275 " --> pdb=" O LYS X 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP X 291 " --> pdb=" O VAL X 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR X 292 " --> pdb=" O MET X 288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU X 300 " --> pdb=" O THR X 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS X 303 " --> pdb=" O THR X 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE X 304 " --> pdb=" O GLU X 300 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN X 306 " --> pdb=" O VAL X 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL X 307 " --> pdb=" O LYS X 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE X 311 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP X 321 " --> pdb=" O LYS X 317 " (cutoff:3.500A) Processing helix chain 'X' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN X 335 " --> pdb=" O LEU X 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN X 345 " --> pdb=" O ASN X 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR X 346 " --> pdb=" O LEU X 342 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN Y 23 " --> pdb=" O LYS Y 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN Y 33 " --> pdb=" O TRP Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 66 Processing helix chain 'Y' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS Y 72 " --> pdb=" O ALA Y 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU Y 74 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR Y 82 " --> pdb=" O ALA Y 78 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA Y 91 " --> pdb=" O ASP Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE Y 122 " --> pdb=" O ILE Y 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG Y 128 " --> pdb=" O SER Y 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS Y 131 " --> pdb=" O GLY Y 127 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS Y 135 " --> pdb=" O LYS Y 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR Y 155 " --> pdb=" O LEU Y 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER Y 164 " --> pdb=" O THR Y 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP Y 165 " --> pdb=" O GLU Y 161 " (cutoff:3.500A) Proline residue: Y 168 - end of helix removed outlier: 4.114A pdb=" N ALA Y 178 " --> pdb=" O ASN Y 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE Y 183 " --> pdb=" O ASP Y 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Y 189 " --> pdb=" O GLU Y 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE Y 190 " --> pdb=" O SER Y 186 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET Y 198 " --> pdb=" O ASN Y 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Y 203 " --> pdb=" O PHE Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 214 Processing helix chain 'Y' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS Y 219 " --> pdb=" O GLN Y 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU Y 220 " --> pdb=" O PRO Y 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 216 through 220' Processing helix chain 'Y' and resid 221 through 222 No H-bonds generated for 'chain 'Y' and resid 221 through 222' Processing helix chain 'Y' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU Y 231 " --> pdb=" O LYS Y 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE Y 232 " --> pdb=" O GLN Y 228 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU Y 237 " --> pdb=" O ALA Y 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Y 240 " --> pdb=" O ILE Y 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE Y 260 " --> pdb=" O LEU Y 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Y 275 " --> pdb=" O LYS Y 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP Y 291 " --> pdb=" O VAL Y 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR Y 292 " --> pdb=" O MET Y 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU Y 300 " --> pdb=" O THR Y 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Y 303 " --> pdb=" O THR Y 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE Y 304 " --> pdb=" O GLU Y 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN Y 306 " --> pdb=" O VAL Y 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL Y 307 " --> pdb=" O LYS Y 303 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE Y 311 " --> pdb=" O VAL Y 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP Y 321 " --> pdb=" O LYS Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN Y 335 " --> pdb=" O LEU Y 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN Y 345 " --> pdb=" O ASN Y 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR Y 346 " --> pdb=" O LEU Y 342 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA Z 24 " --> pdb=" O ALA Z 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN Z 33 " --> pdb=" O TRP Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 66 Processing helix chain 'Z' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS Z 72 " --> pdb=" O ALA Z 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU Z 74 " --> pdb=" O VAL Z 70 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA Z 91 " --> pdb=" O ASP Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 138 removed outlier: 3.540A pdb=" N ILE Z 122 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG Z 128 " --> pdb=" O SER Z 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS Z 131 " --> pdb=" O GLY Z 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS Z 135 " --> pdb=" O LYS Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR Z 155 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER Z 164 " --> pdb=" O THR Z 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP Z 165 " --> pdb=" O GLU Z 161 " (cutoff:3.500A) Proline residue: Z 168 - end of helix removed outlier: 4.115A pdb=" N ALA Z 178 " --> pdb=" O ASN Z 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE Z 183 " --> pdb=" O ASP Z 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Z 189 " --> pdb=" O GLU Z 185 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE Z 190 " --> pdb=" O SER Z 186 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET Z 198 " --> pdb=" O ASN Z 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Z 203 " --> pdb=" O PHE Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 214 Processing helix chain 'Z' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS Z 219 " --> pdb=" O GLN Z 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU Z 220 " --> pdb=" O PRO Z 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 216 through 220' Processing helix chain 'Z' and resid 221 through 222 No H-bonds generated for 'chain 'Z' and resid 221 through 222' Processing helix chain 'Z' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU Z 231 " --> pdb=" O LYS Z 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE Z 232 " --> pdb=" O GLN Z 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU Z 237 " --> pdb=" O ALA Z 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Z 240 " --> pdb=" O ILE Z 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE Z 260 " --> pdb=" O LEU Z 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Z 275 " --> pdb=" O LYS Z 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP Z 291 " --> pdb=" O VAL Z 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR Z 292 " --> pdb=" O MET Z 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU Z 300 " --> pdb=" O THR Z 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Z 303 " --> pdb=" O THR Z 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE Z 304 " --> pdb=" O GLU Z 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN Z 306 " --> pdb=" O VAL Z 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL Z 307 " --> pdb=" O LYS Z 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE Z 311 " --> pdb=" O VAL Z 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN Z 335 " --> pdb=" O LEU Z 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN Z 345 " --> pdb=" O ASN Z 341 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR Z 346 " --> pdb=" O LEU Z 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 removed outlier: 3.593A pdb=" N GLU C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 73 Processing helix chain 'C' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU C 156 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 229 Processing helix chain 'C' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 4.023A pdb=" N VAL C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 270 " --> pdb=" O GLY C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 270' Processing helix chain 'C' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA C 276 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 358 " --> pdb=" O THR C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 404 Proline residue: C 381 - end of helix removed outlier: 4.093A pdb=" N ASP C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 395 " --> pdb=" O GLN C 391 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 83 through 134 removed outlier: 3.518A pdb=" N SER D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP D 101 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS D 143 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU D 156 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 186 " --> pdb=" O LYS D 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL D 269 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 270 " --> pdb=" O GLY D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 270' Processing helix chain 'D' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA D 276 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 322 " --> pdb=" O GLN D 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 358 " --> pdb=" O THR D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 404 Proline residue: D 381 - end of helix removed outlier: 4.093A pdb=" N ASP D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR D 395 " --> pdb=" O GLN D 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA D 399 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU E 60 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 83 through 134 removed outlier: 3.518A pdb=" N SER E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS E 143 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.752A pdb=" N THR E 150 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU E 156 " --> pdb=" O GLN E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E 186 " --> pdb=" O LYS E 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 202 " --> pdb=" O PHE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 229 Processing helix chain 'E' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL E 269 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 270 " --> pdb=" O GLY E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 270' Processing helix chain 'E' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA E 276 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 322 " --> pdb=" O GLN E 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 358 " --> pdb=" O THR E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 404 Proline residue: E 381 - end of helix removed outlier: 4.093A pdb=" N ASP E 384 " --> pdb=" O GLU E 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR E 395 " --> pdb=" O GLN E 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU E 398 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 404 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 83 through 134 removed outlier: 3.518A pdb=" N SER F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL F 142 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS F 143 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR F 150 " --> pdb=" O GLY F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU F 156 " --> pdb=" O GLN F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 203 removed outlier: 4.281A pdb=" N GLU F 175 " --> pdb=" O GLY F 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU F 186 " --> pdb=" O LYS F 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 202 " --> pdb=" O PHE F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 229 Processing helix chain 'F' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS F 248 " --> pdb=" O ASP F 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS F 255 " --> pdb=" O ASP F 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY F 262 " --> pdb=" O ASN F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL F 269 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY F 270 " --> pdb=" O GLY F 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 266 through 270' Processing helix chain 'F' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA F 276 " --> pdb=" O ILE F 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS F 285 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 322 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 404 Proline residue: F 381 - end of helix removed outlier: 4.092A pdb=" N ASP F 384 " --> pdb=" O GLU F 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR F 395 " --> pdb=" O GLN F 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 398 " --> pdb=" O GLN F 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA F 399 " --> pdb=" O THR F 395 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU I 60 " --> pdb=" O LYS I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 73 Processing helix chain 'I' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER I 100 " --> pdb=" O ASP I 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP I 101 " --> pdb=" O HIS I 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY I 103 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR I 123 " --> pdb=" O GLY I 119 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL I 142 " --> pdb=" O ILE I 138 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS I 143 " --> pdb=" O ILE I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 removed outlier: 3.752A pdb=" N THR I 150 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU I 156 " --> pdb=" O GLN I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU I 175 " --> pdb=" O GLY I 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU I 186 " --> pdb=" O LYS I 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU I 202 " --> pdb=" O PHE I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 229 Processing helix chain 'I' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 248 " --> pdb=" O ASP I 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS I 255 " --> pdb=" O ASP I 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY I 262 " --> pdb=" O ASN I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL I 269 " --> pdb=" O SER I 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY I 270 " --> pdb=" O GLY I 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 266 through 270' Processing helix chain 'I' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA I 276 " --> pdb=" O ILE I 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE I 277 " --> pdb=" O ILE I 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE I 297 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU I 322 " --> pdb=" O GLN I 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 358 " --> pdb=" O THR I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 404 Proline residue: I 381 - end of helix removed outlier: 4.092A pdb=" N ASP I 384 " --> pdb=" O GLU I 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR I 395 " --> pdb=" O GLN I 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU I 398 " --> pdb=" O GLN I 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA I 399 " --> pdb=" O THR I 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU I 402 " --> pdb=" O GLU I 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS I 404 " --> pdb=" O LEU I 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU J 60 " --> pdb=" O LYS J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 73 Processing helix chain 'J' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER J 100 " --> pdb=" O ASP J 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP J 101 " --> pdb=" O HIS J 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER J 102 " --> pdb=" O ALA J 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR J 123 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP J 134 " --> pdb=" O ILE J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL J 142 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS J 143 " --> pdb=" O ILE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR J 150 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU J 156 " --> pdb=" O GLN J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU J 175 " --> pdb=" O GLY J 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU J 186 " --> pdb=" O LYS J 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 202 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 229 Processing helix chain 'J' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS J 237 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS J 248 " --> pdb=" O ASP J 244 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY J 262 " --> pdb=" O ASN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL J 269 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY J 270 " --> pdb=" O GLY J 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 266 through 270' Processing helix chain 'J' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA J 276 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE J 277 " --> pdb=" O ILE J 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP J 284 " --> pdb=" O GLY J 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS J 285 " --> pdb=" O ILE J 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE J 297 " --> pdb=" O LYS J 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP J 298 " --> pdb=" O ASN J 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU J 322 " --> pdb=" O GLN J 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS J 358 " --> pdb=" O THR J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 404 Proline residue: J 381 - end of helix removed outlier: 4.092A pdb=" N ASP J 384 " --> pdb=" O GLU J 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR J 395 " --> pdb=" O GLN J 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU J 398 " --> pdb=" O GLN J 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA J 399 " --> pdb=" O THR J 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU J 402 " --> pdb=" O GLU J 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS J 404 " --> pdb=" O LEU J 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 73 Processing helix chain 'M' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER M 100 " --> pdb=" O ASP M 96 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP M 101 " --> pdb=" O HIS M 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR M 123 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP M 134 " --> pdb=" O ILE M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL M 142 " --> pdb=" O ILE M 138 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS M 143 " --> pdb=" O ILE M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR M 150 " --> pdb=" O GLY M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU M 156 " --> pdb=" O GLN M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU M 186 " --> pdb=" O LYS M 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU M 202 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 229 Processing helix chain 'M' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS M 237 " --> pdb=" O SER M 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS M 248 " --> pdb=" O ASP M 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS M 255 " --> pdb=" O ASP M 251 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY M 262 " --> pdb=" O ASN M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL M 269 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY M 270 " --> pdb=" O GLY M 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 266 through 270' Processing helix chain 'M' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA M 276 " --> pdb=" O ILE M 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE M 277 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP M 284 " --> pdb=" O GLY M 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS M 285 " --> pdb=" O ILE M 281 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE M 297 " --> pdb=" O LYS M 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP M 298 " --> pdb=" O ASN M 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU M 322 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS M 358 " --> pdb=" O THR M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 404 Proline residue: M 381 - end of helix removed outlier: 4.093A pdb=" N ASP M 384 " --> pdb=" O GLU M 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR M 395 " --> pdb=" O GLN M 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU M 398 " --> pdb=" O GLN M 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA M 399 " --> pdb=" O THR M 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU M 402 " --> pdb=" O GLU M 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS M 404 " --> pdb=" O LEU M 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU P 60 " --> pdb=" O LYS P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 73 Processing helix chain 'P' and resid 83 through 134 removed outlier: 3.518A pdb=" N SER P 100 " --> pdb=" O ASP P 96 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP P 101 " --> pdb=" O HIS P 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR P 123 " --> pdb=" O GLY P 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP P 134 " --> pdb=" O ILE P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL P 142 " --> pdb=" O ILE P 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS P 143 " --> pdb=" O ILE P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 150 removed outlier: 3.750A pdb=" N THR P 150 " --> pdb=" O GLY P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU P 156 " --> pdb=" O GLN P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU P 175 " --> pdb=" O GLY P 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU P 186 " --> pdb=" O LYS P 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU P 202 " --> pdb=" O PHE P 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 229 Processing helix chain 'P' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE P 236 " --> pdb=" O LEU P 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS P 237 " --> pdb=" O SER P 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS P 248 " --> pdb=" O ASP P 244 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS P 255 " --> pdb=" O ASP P 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY P 262 " --> pdb=" O ASN P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL P 269 " --> pdb=" O SER P 266 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY P 270 " --> pdb=" O GLY P 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 266 through 270' Processing helix chain 'P' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA P 276 " --> pdb=" O ILE P 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE P 277 " --> pdb=" O ILE P 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP P 284 " --> pdb=" O GLY P 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS P 285 " --> pdb=" O ILE P 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE P 297 " --> pdb=" O LYS P 293 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP P 298 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU P 322 " --> pdb=" O GLN P 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS P 358 " --> pdb=" O THR P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 404 Proline residue: P 381 - end of helix removed outlier: 4.092A pdb=" N ASP P 384 " --> pdb=" O GLU P 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR P 395 " --> pdb=" O GLN P 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU P 398 " --> pdb=" O GLN P 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA P 399 " --> pdb=" O THR P 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU P 402 " --> pdb=" O GLU P 398 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS P 404 " --> pdb=" O LEU P 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU Q 60 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 73 Processing helix chain 'Q' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP Q 101 " --> pdb=" O HIS Q 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER Q 102 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY Q 103 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR Q 123 " --> pdb=" O GLY Q 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP Q 134 " --> pdb=" O ILE Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL Q 142 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS Q 143 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR Q 150 " --> pdb=" O GLY Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU Q 156 " --> pdb=" O GLN Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU Q 175 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU Q 186 " --> pdb=" O LYS Q 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU Q 202 " --> pdb=" O PHE Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 229 Processing helix chain 'Q' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE Q 236 " --> pdb=" O LEU Q 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS Q 237 " --> pdb=" O SER Q 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS Q 248 " --> pdb=" O ASP Q 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS Q 255 " --> pdb=" O ASP Q 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY Q 262 " --> pdb=" O ASN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL Q 269 " --> pdb=" O SER Q 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY Q 270 " --> pdb=" O GLY Q 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 266 through 270' Processing helix chain 'Q' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE Q 277 " --> pdb=" O ILE Q 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP Q 284 " --> pdb=" O GLY Q 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS Q 285 " --> pdb=" O ILE Q 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE Q 297 " --> pdb=" O LYS Q 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP Q 298 " --> pdb=" O ASN Q 294 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU Q 322 " --> pdb=" O GLN Q 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS Q 358 " --> pdb=" O THR Q 354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 367 through 404 Proline residue: Q 381 - end of helix removed outlier: 4.093A pdb=" N ASP Q 384 " --> pdb=" O GLU Q 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU Q 398 " --> pdb=" O GLN Q 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA Q 399 " --> pdb=" O THR Q 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU Q 402 " --> pdb=" O GLU Q 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Q 404 " --> pdb=" O LEU Q 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU R 60 " --> pdb=" O LYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 73 Processing helix chain 'R' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER R 100 " --> pdb=" O ASP R 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP R 101 " --> pdb=" O HIS R 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR R 123 " --> pdb=" O GLY R 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP R 134 " --> pdb=" O ILE R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL R 142 " --> pdb=" O ILE R 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS R 143 " --> pdb=" O ILE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR R 150 " --> pdb=" O GLY R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU R 156 " --> pdb=" O GLN R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU R 175 " --> pdb=" O GLY R 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU R 186 " --> pdb=" O LYS R 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 202 " --> pdb=" O PHE R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 229 Processing helix chain 'R' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE R 236 " --> pdb=" O LEU R 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS R 237 " --> pdb=" O SER R 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS R 248 " --> pdb=" O ASP R 244 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS R 255 " --> pdb=" O ASP R 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY R 262 " --> pdb=" O ASN R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL R 269 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY R 270 " --> pdb=" O GLY R 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 266 through 270' Processing helix chain 'R' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE R 277 " --> pdb=" O ILE R 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS R 285 " --> pdb=" O ILE R 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE R 297 " --> pdb=" O LYS R 293 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU R 322 " --> pdb=" O GLN R 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS R 358 " --> pdb=" O THR R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 404 Proline residue: R 381 - end of helix removed outlier: 4.092A pdb=" N ASP R 384 " --> pdb=" O GLU R 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR R 395 " --> pdb=" O GLN R 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU R 398 " --> pdb=" O GLN R 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA R 399 " --> pdb=" O THR R 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS R 404 " --> pdb=" O LEU R 400 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU S 60 " --> pdb=" O LYS S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 73 Processing helix chain 'S' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER S 100 " --> pdb=" O ASP S 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP S 101 " --> pdb=" O HIS S 97 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER S 102 " --> pdb=" O ALA S 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY S 103 " --> pdb=" O LEU S 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR S 123 " --> pdb=" O GLY S 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP S 134 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL S 142 " --> pdb=" O ILE S 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS S 143 " --> pdb=" O ILE S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 150 removed outlier: 3.752A pdb=" N THR S 150 " --> pdb=" O GLY S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU S 156 " --> pdb=" O GLN S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 203 removed outlier: 4.279A pdb=" N GLU S 175 " --> pdb=" O GLY S 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU S 186 " --> pdb=" O LYS S 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU S 202 " --> pdb=" O PHE S 198 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 229 Processing helix chain 'S' and resid 231 through 265 removed outlier: 3.706A pdb=" N ILE S 236 " --> pdb=" O LEU S 232 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS S 237 " --> pdb=" O SER S 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS S 248 " --> pdb=" O ASP S 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS S 255 " --> pdb=" O ASP S 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY S 262 " --> pdb=" O ASN S 258 " (cutoff:3.500A) Processing helix chain 'S' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL S 269 " --> pdb=" O SER S 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY S 270 " --> pdb=" O GLY S 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 266 through 270' Processing helix chain 'S' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA S 276 " --> pdb=" O ILE S 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE S 277 " --> pdb=" O ILE S 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP S 284 " --> pdb=" O GLY S 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS S 285 " --> pdb=" O ILE S 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE S 297 " --> pdb=" O LYS S 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP S 298 " --> pdb=" O ASN S 294 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU S 322 " --> pdb=" O GLN S 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS S 358 " --> pdb=" O THR S 354 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 404 Proline residue: S 381 - end of helix removed outlier: 4.093A pdb=" N ASP S 384 " --> pdb=" O GLU S 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR S 395 " --> pdb=" O GLN S 391 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU S 398 " --> pdb=" O GLN S 394 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA S 399 " --> pdb=" O THR S 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU S 402 " --> pdb=" O GLU S 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS S 404 " --> pdb=" O LEU S 400 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU T 60 " --> pdb=" O LYS T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 73 Processing helix chain 'T' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER T 100 " --> pdb=" O ASP T 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP T 101 " --> pdb=" O HIS T 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY T 103 " --> pdb=" O LEU T 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR T 123 " --> pdb=" O GLY T 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP T 134 " --> pdb=" O ILE T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL T 142 " --> pdb=" O ILE T 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS T 143 " --> pdb=" O ILE T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR T 150 " --> pdb=" O GLY T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU T 156 " --> pdb=" O GLN T 153 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU T 175 " --> pdb=" O GLY T 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU T 186 " --> pdb=" O LYS T 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU T 202 " --> pdb=" O PHE T 198 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 229 Processing helix chain 'T' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE T 236 " --> pdb=" O LEU T 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS T 237 " --> pdb=" O SER T 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS T 248 " --> pdb=" O ASP T 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS T 255 " --> pdb=" O ASP T 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY T 262 " --> pdb=" O ASN T 258 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL T 269 " --> pdb=" O SER T 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY T 270 " --> pdb=" O GLY T 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 266 through 270' Processing helix chain 'T' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA T 276 " --> pdb=" O ILE T 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE T 277 " --> pdb=" O ILE T 273 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP T 284 " --> pdb=" O GLY T 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS T 285 " --> pdb=" O ILE T 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE T 297 " --> pdb=" O LYS T 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP T 298 " --> pdb=" O ASN T 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU T 322 " --> pdb=" O GLN T 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS T 358 " --> pdb=" O THR T 354 " (cutoff:3.500A) Processing helix chain 'T' and resid 367 through 404 Proline residue: T 381 - end of helix removed outlier: 4.092A pdb=" N ASP T 384 " --> pdb=" O GLU T 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR T 395 " --> pdb=" O GLN T 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU T 398 " --> pdb=" O GLN T 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA T 399 " --> pdb=" O THR T 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU T 402 " --> pdb=" O GLU T 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS T 404 " --> pdb=" O LEU T 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 206 Processing sheet with id=AA3, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AA4, first strand: chain 'C' and resid 205 through 206 Processing sheet with id=AA5, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA6, first strand: chain 'D' and resid 205 through 206 Processing sheet with id=AA7, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'E' and resid 205 through 206 Processing sheet with id=AA9, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 205 through 206 Processing sheet with id=AB2, first strand: chain 'I' and resid 159 through 160 Processing sheet with id=AB3, first strand: chain 'I' and resid 205 through 206 Processing sheet with id=AB4, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'J' and resid 205 through 206 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 160 Processing sheet with id=AB7, first strand: chain 'M' and resid 205 through 206 Processing sheet with id=AB8, first strand: chain 'P' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'P' and resid 205 through 206 Processing sheet with id=AC1, first strand: chain 'Q' and resid 159 through 160 Processing sheet with id=AC2, first strand: chain 'Q' and resid 205 through 206 Processing sheet with id=AC3, first strand: chain 'R' and resid 159 through 160 Processing sheet with id=AC4, first strand: chain 'R' and resid 205 through 206 Processing sheet with id=AC5, first strand: chain 'S' and resid 159 through 160 Processing sheet with id=AC6, first strand: chain 'S' and resid 205 through 206 Processing sheet with id=AC7, first strand: chain 'T' and resid 159 through 160 Processing sheet with id=AC8, first strand: chain 'T' and resid 205 through 206 5837 hydrogen bonds defined for protein. 17355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.19 Time building geometry restraints manager: 15.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 24200 1.34 - 1.46: 9919 1.46 - 1.57: 38733 1.57 - 1.69: 0 1.69 - 1.81: 390 Bond restraints: 73242 Sorted by residual: bond pdb=" CB GLU U 300 " pdb=" CG GLU U 300 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CB GLU O 300 " pdb=" CG GLU O 300 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB GLU Y 300 " pdb=" CG GLU Y 300 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" CB GLU H 300 " pdb=" CG GLU H 300 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 bond pdb=" CB GLU K 300 " pdb=" CG GLU K 300 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 73237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 95021 1.96 - 3.92: 2735 3.92 - 5.88: 559 5.88 - 7.84: 194 7.84 - 9.80: 57 Bond angle restraints: 98566 Sorted by residual: angle pdb=" C SER W 205 " pdb=" N ALA W 206 " pdb=" CA ALA W 206 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C SER G 205 " pdb=" N ALA G 206 " pdb=" CA ALA G 206 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C SER V 205 " pdb=" N ALA V 206 " pdb=" CA ALA V 206 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C SER K 205 " pdb=" N ALA K 206 " pdb=" CA ALA K 206 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C SER L 205 " pdb=" N ALA L 206 " pdb=" CA ALA L 206 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 ... (remaining 98561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 43118 14.94 - 29.89: 1810 29.89 - 44.83: 728 44.83 - 59.78: 52 59.78 - 74.72: 39 Dihedral angle restraints: 45747 sinusoidal: 19019 harmonic: 26728 Sorted by residual: dihedral pdb=" CA LYS Q 367 " pdb=" C LYS Q 367 " pdb=" N LEU Q 368 " pdb=" CA LEU Q 368 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LYS J 367 " pdb=" C LYS J 367 " pdb=" N LEU J 368 " pdb=" CA LEU J 368 " ideal model delta harmonic sigma weight residual -180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LYS E 367 " pdb=" C LYS E 367 " pdb=" N LEU E 368 " pdb=" CA LEU E 368 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 45744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7233 0.043 - 0.086: 3573 0.086 - 0.129: 572 0.129 - 0.172: 141 0.172 - 0.215: 25 Chirality restraints: 11544 Sorted by residual: chirality pdb=" CB ILE J 139 " pdb=" CA ILE J 139 " pdb=" CG1 ILE J 139 " pdb=" CG2 ILE J 139 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE Q 139 " pdb=" CA ILE Q 139 " pdb=" CG1 ILE Q 139 " pdb=" CG2 ILE Q 139 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE D 139 " pdb=" CA ILE D 139 " pdb=" CG1 ILE D 139 " pdb=" CG2 ILE D 139 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 11541 not shown) Planarity restraints: 12701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 92 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO L 93 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO L 93 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 93 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 92 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO G 93 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 93 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 93 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 92 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO O 93 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO O 93 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO O 93 " 0.034 5.00e-02 4.00e+02 ... (remaining 12698 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 14970 2.77 - 3.30: 73755 3.30 - 3.83: 119723 3.83 - 4.37: 147124 4.37 - 4.90: 235675 Nonbonded interactions: 591247 Sorted by model distance: nonbonded pdb=" OH TYR V 246 " pdb=" OD1 ASP P 256 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR U 246 " pdb=" OD1 ASP M 256 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR K 246 " pdb=" OD1 ASP E 256 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR O 246 " pdb=" OD1 ASP J 256 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR X 246 " pdb=" OD1 ASP R 256 " model vdw 2.243 3.040 ... (remaining 591242 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 2.290 Check model and map are aligned: 0.420 Set scattering table: 0.540 Process input model: 97.380 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.006 0.063 73242 Z= 0.364 Angle : 0.879 9.799 98566 Z= 0.451 Chirality : 0.049 0.215 11544 Planarity : 0.005 0.060 12701 Dihedral : 10.549 74.723 28275 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.08 % Allowed : 4.68 % Favored : 94.24 % 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: -4.40 (0.06), residues: 9087 helix: -2.76 (0.04), residues: 7462 sheet: None (None), residues: 0 loop : -2.27 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 101 HIS 0.011 0.003 HIS R 340 PHE 0.033 0.003 PHE Y 202 TYR 0.019 0.003 TYR I 260 ARG 0.012 0.001 ARG H 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1798 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1710 time to evaluate : 7.373 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: A 226 LEU cc_start: 0.9459 (mt) cc_final: 0.9254 (mp) REVERT: A 275 TRP cc_start: 0.8595 (t-100) cc_final: 0.8241 (t-100) REVERT: B 19 LYS cc_start: 0.9378 (tmtt) cc_final: 0.9113 (tptt) REVERT: B 167 ASP cc_start: 0.9262 (t0) cc_final: 0.9049 (t0) REVERT: B 185 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8894 (pt0) REVERT: B 188 ASP cc_start: 0.8887 (m-30) cc_final: 0.8548 (m-30) REVERT: B 232 ILE cc_start: 0.8505 (tp) cc_final: 0.8236 (tp) REVERT: B 242 GLU cc_start: 0.8777 (tt0) cc_final: 0.8427 (tt0) REVERT: G 124 SER cc_start: 0.9387 (m) cc_final: 0.9165 (p) REVERT: G 167 ASP cc_start: 0.9205 (t0) cc_final: 0.8908 (t0) REVERT: G 190 ILE cc_start: 0.9115 (mt) cc_final: 0.8736 (mm) REVERT: G 232 ILE cc_start: 0.8792 (tp) cc_final: 0.8579 (tp) REVERT: G 242 GLU cc_start: 0.9056 (tt0) cc_final: 0.8646 (tm-30) REVERT: H 184 ILE cc_start: 0.9237 (mt) cc_final: 0.8858 (mm) REVERT: H 188 ASP cc_start: 0.8909 (m-30) cc_final: 0.8435 (m-30) REVERT: H 190 ILE cc_start: 0.9305 (mt) cc_final: 0.8884 (mm) REVERT: H 242 GLU cc_start: 0.8993 (tt0) cc_final: 0.8570 (tm-30) REVERT: H 288 MET cc_start: 0.8938 (mmm) cc_final: 0.8600 (tpp) REVERT: K 19 LYS cc_start: 0.9257 (tmtt) cc_final: 0.8952 (tptt) REVERT: K 167 ASP cc_start: 0.9168 (t0) cc_final: 0.8965 (t0) REVERT: K 182 LYS cc_start: 0.9337 (mttm) cc_final: 0.9105 (mmmm) REVERT: K 184 ILE cc_start: 0.9263 (mt) cc_final: 0.8855 (mm) REVERT: K 185 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8938 (pt0) REVERT: K 188 ASP cc_start: 0.8825 (m-30) cc_final: 0.8331 (m-30) REVERT: K 190 ILE cc_start: 0.9305 (mt) cc_final: 0.8901 (mm) REVERT: K 232 ILE cc_start: 0.8733 (tp) cc_final: 0.8515 (tp) REVERT: K 242 GLU cc_start: 0.8832 (tt0) cc_final: 0.8518 (tm-30) REVERT: K 288 MET cc_start: 0.8910 (mmm) cc_final: 0.8468 (tpp) REVERT: L 19 LYS cc_start: 0.9285 (tmtt) cc_final: 0.9027 (tptt) REVERT: L 184 ILE cc_start: 0.9196 (mt) cc_final: 0.8890 (mm) REVERT: L 185 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9058 (pt0) REVERT: L 188 ASP cc_start: 0.9034 (m-30) cc_final: 0.8690 (m-30) REVERT: L 232 ILE cc_start: 0.8736 (tp) cc_final: 0.8519 (tp) REVERT: L 242 GLU cc_start: 0.9002 (tt0) cc_final: 0.8523 (tt0) REVERT: L 262 GLN cc_start: 0.9152 (mt0) cc_final: 0.8927 (mm-40) REVERT: L 269 GLU cc_start: 0.9342 (tt0) cc_final: 0.9060 (tm-30) REVERT: N 124 SER cc_start: 0.9407 (m) cc_final: 0.9158 (p) REVERT: N 167 ASP cc_start: 0.9185 (t0) cc_final: 0.8970 (t0) REVERT: N 184 ILE cc_start: 0.9230 (mt) cc_final: 0.8878 (mm) REVERT: N 188 ASP cc_start: 0.8869 (m-30) cc_final: 0.8406 (m-30) REVERT: N 190 ILE cc_start: 0.9346 (mt) cc_final: 0.8904 (mm) REVERT: N 198 MET cc_start: 0.8999 (ttt) cc_final: 0.8786 (ttp) REVERT: N 202 PHE cc_start: 0.8762 (m-80) cc_final: 0.8426 (m-10) REVERT: N 223 LYS cc_start: 0.9020 (mttt) cc_final: 0.8790 (mtmp) REVERT: N 232 ILE cc_start: 0.8544 (tp) cc_final: 0.8267 (tp) REVERT: N 242 GLU cc_start: 0.8800 (tt0) cc_final: 0.8429 (tm-30) REVERT: N 269 GLU cc_start: 0.9225 (tt0) cc_final: 0.9003 (tm-30) REVERT: N 288 MET cc_start: 0.9032 (mmm) cc_final: 0.8590 (tpp) REVERT: O 188 ASP cc_start: 0.8852 (m-30) cc_final: 0.8441 (m-30) REVERT: O 190 ILE cc_start: 0.9275 (mt) cc_final: 0.8985 (mm) REVERT: O 232 ILE cc_start: 0.8882 (tp) cc_final: 0.8570 (tp) REVERT: O 242 GLU cc_start: 0.8933 (tt0) cc_final: 0.8551 (tm-30) REVERT: O 304 ILE cc_start: 0.9272 (mt) cc_final: 0.8970 (mt) REVERT: U 124 SER cc_start: 0.9352 (m) cc_final: 0.9118 (p) REVERT: U 182 LYS cc_start: 0.9436 (mttm) cc_final: 0.9194 (mmmm) REVERT: U 185 GLU cc_start: 0.9279 (mt-10) cc_final: 0.9071 (pt0) REVERT: U 188 ASP cc_start: 0.9034 (m-30) cc_final: 0.8709 (m-30) REVERT: U 190 ILE cc_start: 0.9118 (mt) cc_final: 0.8616 (mm) REVERT: U 198 MET cc_start: 0.8979 (ttt) cc_final: 0.8707 (ttp) REVERT: U 202 PHE cc_start: 0.8833 (m-80) cc_final: 0.8615 (m-10) REVERT: U 223 LYS cc_start: 0.9025 (mttt) cc_final: 0.8794 (mtmt) REVERT: U 242 GLU cc_start: 0.9057 (tt0) cc_final: 0.8539 (tm-30) REVERT: V 21 MET cc_start: 0.8629 (ttt) cc_final: 0.8130 (ttt) REVERT: V 124 SER cc_start: 0.9370 (m) cc_final: 0.9104 (p) REVERT: V 182 LYS cc_start: 0.9417 (mttm) cc_final: 0.9182 (mmmm) REVERT: V 188 ASP cc_start: 0.8927 (m-30) cc_final: 0.8717 (m-30) REVERT: V 198 MET cc_start: 0.9046 (ttt) cc_final: 0.8825 (ttt) REVERT: V 202 PHE cc_start: 0.8865 (m-80) cc_final: 0.8605 (m-10) REVERT: V 232 ILE cc_start: 0.8639 (tp) cc_final: 0.8416 (tp) REVERT: V 242 GLU cc_start: 0.8998 (tt0) cc_final: 0.8611 (tt0) REVERT: V 308 TRP cc_start: 0.8920 (m100) cc_final: 0.8606 (m100) REVERT: W 19 LYS cc_start: 0.9244 (tmtt) cc_final: 0.9011 (tptt) REVERT: W 188 ASP cc_start: 0.8939 (m-30) cc_final: 0.8544 (m-30) REVERT: W 190 ILE cc_start: 0.9320 (mt) cc_final: 0.9058 (mm) REVERT: W 232 ILE cc_start: 0.8564 (tp) cc_final: 0.8332 (tp) REVERT: W 242 GLU cc_start: 0.8807 (tt0) cc_final: 0.8447 (tm-30) REVERT: X 19 LYS cc_start: 0.9334 (tmtt) cc_final: 0.9031 (tptt) REVERT: X 184 ILE cc_start: 0.9302 (mt) cc_final: 0.8974 (mm) REVERT: X 185 GLU cc_start: 0.9234 (mt-10) cc_final: 0.9019 (pt0) REVERT: X 188 ASP cc_start: 0.8925 (m-30) cc_final: 0.8435 (m-30) REVERT: X 232 ILE cc_start: 0.8761 (tp) cc_final: 0.8526 (tp) REVERT: X 242 GLU cc_start: 0.8937 (tt0) cc_final: 0.8601 (tt0) REVERT: X 269 GLU cc_start: 0.9180 (tt0) cc_final: 0.8966 (tm-30) REVERT: X 288 MET cc_start: 0.8867 (mmm) cc_final: 0.8655 (mmm) REVERT: Y 184 ILE cc_start: 0.9384 (mt) cc_final: 0.9142 (mm) REVERT: Y 188 ASP cc_start: 0.8863 (m-30) cc_final: 0.8332 (m-30) REVERT: Y 198 MET cc_start: 0.9138 (ttt) cc_final: 0.8908 (ttt) REVERT: Y 202 PHE cc_start: 0.8931 (m-80) cc_final: 0.8658 (m-10) REVERT: Y 232 ILE cc_start: 0.8698 (tp) cc_final: 0.8456 (tp) REVERT: Y 242 GLU cc_start: 0.9059 (tt0) cc_final: 0.8705 (tt0) REVERT: Z 18 ILE cc_start: 0.8728 (pp) cc_final: 0.8519 (pp) REVERT: Z 19 LYS cc_start: 0.9236 (tmtt) cc_final: 0.9005 (tptt) REVERT: Z 144 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8702 (pt) REVERT: Z 185 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9048 (pt0) REVERT: Z 188 ASP cc_start: 0.8899 (m-30) cc_final: 0.8627 (m-30) REVERT: Z 190 ILE cc_start: 0.9267 (mt) cc_final: 0.8793 (mm) REVERT: Z 232 ILE cc_start: 0.8673 (tp) cc_final: 0.8446 (tp) REVERT: Z 242 GLU cc_start: 0.8994 (tt0) cc_final: 0.8555 (tm-30) REVERT: Z 261 ASP cc_start: 0.8392 (m-30) cc_final: 0.8147 (m-30) REVERT: Z 269 GLU cc_start: 0.9153 (tt0) cc_final: 0.8945 (tm-30) REVERT: C 49 ILE cc_start: 0.9500 (mt) cc_final: 0.9259 (mm) REVERT: C 275 TRP cc_start: 0.8642 (t-100) cc_final: 0.8237 (t-100) REVERT: D 226 LEU cc_start: 0.9373 (mt) cc_final: 0.9151 (mp) REVERT: D 257 TYR cc_start: 0.9231 (t80) cc_final: 0.9021 (t80) REVERT: D 275 TRP cc_start: 0.8687 (t-100) cc_final: 0.8380 (t-100) REVERT: E 49 ILE cc_start: 0.9513 (mt) cc_final: 0.9310 (mm) REVERT: E 93 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8133 (tp30) REVERT: E 226 LEU cc_start: 0.9413 (mt) cc_final: 0.9173 (mp) REVERT: E 257 TYR cc_start: 0.9181 (t80) cc_final: 0.8953 (t80) REVERT: E 258 ASN cc_start: 0.9082 (m-40) cc_final: 0.8718 (t0) REVERT: E 275 TRP cc_start: 0.8708 (t-100) cc_final: 0.8319 (t-100) REVERT: F 275 TRP cc_start: 0.8649 (t-100) cc_final: 0.8330 (t-100) REVERT: I 49 ILE cc_start: 0.9528 (mt) cc_final: 0.9315 (mm) REVERT: I 237 LYS cc_start: 0.9457 (ttmt) cc_final: 0.9248 (tppt) REVERT: J 49 ILE cc_start: 0.9515 (mt) cc_final: 0.9204 (mm) REVERT: J 93 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8134 (tp30) REVERT: J 226 LEU cc_start: 0.9368 (mt) cc_final: 0.9019 (mt) REVERT: J 275 TRP cc_start: 0.8587 (t-100) cc_final: 0.8324 (t-100) REVERT: M 93 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8101 (tp30) REVERT: M 275 TRP cc_start: 0.8671 (t-100) cc_final: 0.8377 (t-100) REVERT: M 333 ASP cc_start: 0.8610 (m-30) cc_final: 0.8398 (m-30) REVERT: P 226 LEU cc_start: 0.9442 (mt) cc_final: 0.9226 (mp) REVERT: P 275 TRP cc_start: 0.8581 (t-100) cc_final: 0.8365 (t-100) REVERT: Q 54 TYR cc_start: 0.9024 (t80) cc_final: 0.8811 (t80) REVERT: Q 226 LEU cc_start: 0.9379 (mt) cc_final: 0.9122 (mp) REVERT: Q 275 TRP cc_start: 0.8660 (t-100) cc_final: 0.8310 (t-100) REVERT: R 226 LEU cc_start: 0.9386 (mt) cc_final: 0.9046 (mt) REVERT: R 275 TRP cc_start: 0.8640 (t-100) cc_final: 0.8109 (t-100) REVERT: S 87 MET cc_start: 0.9106 (mmm) cc_final: 0.8896 (mmp) REVERT: S 93 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8041 (tp30) REVERT: S 226 LEU cc_start: 0.9440 (mt) cc_final: 0.9166 (mp) REVERT: S 275 TRP cc_start: 0.8600 (t-100) cc_final: 0.8309 (t-100) REVERT: S 342 ASP cc_start: 0.8459 (t0) cc_final: 0.8253 (t0) REVERT: T 342 ASP cc_start: 0.8472 (t0) cc_final: 0.8267 (t0) outliers start: 88 outliers final: 7 residues processed: 1774 average time/residue: 0.7038 time to fit residues: 2094.9440 Evaluate side-chains 731 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 723 time to evaluate : 7.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 256 LEU Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain Y residue 256 LEU Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain S residue 183 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 757 optimal weight: 3.9990 chunk 679 optimal weight: 0.8980 chunk 377 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 458 optimal weight: 0.9980 chunk 363 optimal weight: 4.9990 chunk 703 optimal weight: 0.6980 chunk 272 optimal weight: 6.9990 chunk 427 optimal weight: 4.9990 chunk 523 optimal weight: 6.9990 chunk 814 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 318 GLN A 377 GLN B 120 ASN B 192 GLN G 26 ASN G 120 ASN H 26 ASN H 120 ASN K 26 ASN K 120 ASN L 26 ASN L 120 ASN N 26 ASN N 120 ASN N 192 GLN O 26 ASN O 120 ASN U 26 ASN U 120 ASN V 120 ASN W 26 ASN W 120 ASN X 26 ASN X 120 ASN X 192 GLN Y 26 ASN Y 120 ASN Y 340 ASN Z 26 ASN Z 120 ASN C 95 HIS C 318 GLN C 377 GLN D 95 HIS D 318 GLN D 377 GLN E 95 HIS E 318 GLN E 377 GLN F 95 HIS F 318 GLN F 377 GLN I 95 HIS I 318 GLN I 377 GLN J 95 HIS J 318 GLN J 377 GLN M 95 HIS M 318 GLN M 377 GLN P 95 HIS P 318 GLN P 377 GLN Q 95 HIS Q 318 GLN Q 377 GLN R 95 HIS R 318 GLN R 377 GLN S 95 HIS S 318 GLN S 377 GLN T 95 HIS T 318 GLN T 377 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 73242 Z= 0.198 Angle : 0.625 9.397 98566 Z= 0.341 Chirality : 0.039 0.162 11544 Planarity : 0.004 0.036 12701 Dihedral : 5.201 57.428 9547 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.44 % Allowed : 8.81 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.08), residues: 9087 helix: 0.04 (0.06), residues: 7358 sheet: None (None), residues: 0 loop : -1.40 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 101 HIS 0.004 0.001 HIS J 95 PHE 0.020 0.001 PHE T 375 TYR 0.028 0.002 TYR F 257 ARG 0.007 0.001 ARG U 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 985 time to evaluate : 6.789 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: A 54 TYR cc_start: 0.9087 (t80) cc_final: 0.8810 (t80) REVERT: A 74 TYR cc_start: 0.8385 (p90) cc_final: 0.8163 (p90) REVERT: A 257 TYR cc_start: 0.9306 (t80) cc_final: 0.8985 (t80) REVERT: A 275 TRP cc_start: 0.8668 (t-100) cc_final: 0.8381 (t-100) REVERT: A 335 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 19 LYS cc_start: 0.9479 (tmtt) cc_final: 0.9158 (tptt) REVERT: B 21 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8752 (ttt) REVERT: B 181 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8841 (pp20) REVERT: B 184 ILE cc_start: 0.9370 (mt) cc_final: 0.9111 (mm) REVERT: B 185 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8784 (tp30) REVERT: B 188 ASP cc_start: 0.8736 (m-30) cc_final: 0.8228 (m-30) REVERT: B 198 MET cc_start: 0.8889 (ttt) cc_final: 0.8447 (ttm) REVERT: B 242 GLU cc_start: 0.8853 (tt0) cc_final: 0.8454 (tm-30) REVERT: G 181 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8469 (tm-30) REVERT: G 191 ARG cc_start: 0.8741 (tmm160) cc_final: 0.8210 (ttp80) REVERT: G 242 GLU cc_start: 0.9076 (tt0) cc_final: 0.8780 (tp30) REVERT: H 181 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8618 (tm-30) REVERT: H 188 ASP cc_start: 0.8941 (m-30) cc_final: 0.8573 (m-30) REVERT: H 197 ASP cc_start: 0.8615 (m-30) cc_final: 0.8410 (m-30) REVERT: H 242 GLU cc_start: 0.8956 (tt0) cc_final: 0.8719 (tp30) REVERT: H 288 MET cc_start: 0.8665 (mmm) cc_final: 0.8292 (mmm) REVERT: K 19 LYS cc_start: 0.9478 (tmtt) cc_final: 0.9244 (tptt) REVERT: K 184 ILE cc_start: 0.9348 (mt) cc_final: 0.8991 (mm) REVERT: K 185 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8963 (mt-10) REVERT: K 188 ASP cc_start: 0.8827 (m-30) cc_final: 0.8462 (m-30) REVERT: K 223 LYS cc_start: 0.8891 (mttt) cc_final: 0.8684 (mtmt) REVERT: K 242 GLU cc_start: 0.8895 (tt0) cc_final: 0.8687 (tp30) REVERT: L 19 LYS cc_start: 0.9422 (tmtt) cc_final: 0.9145 (tptt) REVERT: L 181 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8331 (pp20) REVERT: L 184 ILE cc_start: 0.9378 (mt) cc_final: 0.9177 (mm) REVERT: L 185 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8767 (mt-10) REVERT: L 188 ASP cc_start: 0.8959 (m-30) cc_final: 0.8693 (m-30) REVERT: L 198 MET cc_start: 0.9273 (ttt) cc_final: 0.8482 (ttm) REVERT: L 202 PHE cc_start: 0.9073 (m-10) cc_final: 0.8764 (m-80) REVERT: L 242 GLU cc_start: 0.9112 (tt0) cc_final: 0.8626 (tm-30) REVERT: N 181 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8602 (tp30) REVERT: N 184 ILE cc_start: 0.9407 (mt) cc_final: 0.9193 (mm) REVERT: N 188 ASP cc_start: 0.8886 (m-30) cc_final: 0.8416 (m-30) REVERT: N 192 GLN cc_start: 0.9226 (tp-100) cc_final: 0.9017 (mm-40) REVERT: N 223 LYS cc_start: 0.9003 (mttt) cc_final: 0.8781 (mtmp) REVERT: N 242 GLU cc_start: 0.8842 (tt0) cc_final: 0.8618 (tp30) REVERT: O 21 MET cc_start: 0.9029 (ttt) cc_final: 0.8706 (ttt) REVERT: O 181 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8547 (tm-30) REVERT: O 184 ILE cc_start: 0.9429 (mt) cc_final: 0.9126 (mm) REVERT: O 188 ASP cc_start: 0.8908 (m-30) cc_final: 0.8604 (m-30) REVERT: O 197 ASP cc_start: 0.8786 (m-30) cc_final: 0.8470 (m-30) REVERT: O 242 GLU cc_start: 0.8951 (tt0) cc_final: 0.8678 (tp30) REVERT: U 184 ILE cc_start: 0.9423 (mt) cc_final: 0.9145 (mm) REVERT: U 185 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9090 (mt-10) REVERT: U 188 ASP cc_start: 0.8979 (m-30) cc_final: 0.8608 (m-30) REVERT: U 190 ILE cc_start: 0.9021 (mt) cc_final: 0.8741 (mp) REVERT: U 223 LYS cc_start: 0.8942 (mttt) cc_final: 0.8722 (mtmt) REVERT: U 242 GLU cc_start: 0.9158 (tt0) cc_final: 0.8715 (tt0) REVERT: V 181 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8395 (tm-30) REVERT: V 188 ASP cc_start: 0.8893 (m-30) cc_final: 0.8547 (m-30) REVERT: V 242 GLU cc_start: 0.9135 (tt0) cc_final: 0.8779 (tt0) REVERT: W 19 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9092 (tptt) REVERT: W 181 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8349 (tm-30) REVERT: W 184 ILE cc_start: 0.9263 (mt) cc_final: 0.8957 (mm) REVERT: W 188 ASP cc_start: 0.8980 (m-30) cc_final: 0.8651 (m-30) REVERT: W 223 LYS cc_start: 0.8939 (mttt) cc_final: 0.8686 (mtmm) REVERT: W 242 GLU cc_start: 0.8950 (tt0) cc_final: 0.8536 (tm-30) REVERT: X 19 LYS cc_start: 0.9438 (tmtt) cc_final: 0.9103 (tptt) REVERT: X 184 ILE cc_start: 0.9386 (mt) cc_final: 0.9101 (mm) REVERT: X 185 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8960 (mt-10) REVERT: X 188 ASP cc_start: 0.8851 (m-30) cc_final: 0.8320 (m-30) REVERT: X 190 ILE cc_start: 0.9105 (mm) cc_final: 0.8822 (mp) REVERT: X 242 GLU cc_start: 0.9069 (tt0) cc_final: 0.8806 (tp30) REVERT: X 288 MET cc_start: 0.8945 (mmm) cc_final: 0.8713 (mmm) REVERT: Y 181 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8592 (tm-30) REVERT: Y 184 ILE cc_start: 0.9419 (mt) cc_final: 0.9204 (mm) REVERT: Y 188 ASP cc_start: 0.8913 (m-30) cc_final: 0.8484 (m-30) REVERT: Y 223 LYS cc_start: 0.8889 (mttt) cc_final: 0.8597 (mtmp) REVERT: Y 242 GLU cc_start: 0.9069 (tt0) cc_final: 0.8652 (tt0) REVERT: Z 19 LYS cc_start: 0.9461 (tmtt) cc_final: 0.9169 (tptt) REVERT: Z 181 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8754 (tm-30) REVERT: Z 185 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8796 (tp30) REVERT: Z 188 ASP cc_start: 0.8877 (m-30) cc_final: 0.8647 (m-30) REVERT: Z 190 ILE cc_start: 0.9060 (mt) cc_final: 0.8729 (mp) REVERT: Z 223 LYS cc_start: 0.8954 (mttt) cc_final: 0.8731 (mtmt) REVERT: Z 242 GLU cc_start: 0.9013 (tt0) cc_final: 0.8523 (tp30) REVERT: Z 256 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9112 (mm) REVERT: C 260 TYR cc_start: 0.9319 (m-10) cc_final: 0.8921 (m-10) REVERT: C 275 TRP cc_start: 0.8652 (t-100) cc_final: 0.8424 (t-100) REVERT: D 260 TYR cc_start: 0.9377 (m-10) cc_final: 0.9121 (m-10) REVERT: D 342 ASP cc_start: 0.8656 (t0) cc_final: 0.8439 (t0) REVERT: E 87 MET cc_start: 0.9096 (mmm) cc_final: 0.8813 (mmp) REVERT: E 275 TRP cc_start: 0.8742 (t-100) cc_final: 0.8433 (t-100) REVERT: E 320 LEU cc_start: 0.9408 (tp) cc_final: 0.9191 (tp) REVERT: E 335 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7644 (tm-30) REVERT: F 260 TYR cc_start: 0.9355 (m-10) cc_final: 0.9008 (m-10) REVERT: F 275 TRP cc_start: 0.8714 (t-100) cc_final: 0.8182 (t-100) REVERT: F 333 ASP cc_start: 0.8479 (m-30) cc_final: 0.8251 (m-30) REVERT: I 260 TYR cc_start: 0.9423 (m-10) cc_final: 0.9209 (m-10) REVERT: I 275 TRP cc_start: 0.8490 (t-100) cc_final: 0.8272 (t-100) REVERT: J 96 ASP cc_start: 0.8527 (p0) cc_final: 0.8216 (p0) REVERT: J 275 TRP cc_start: 0.8633 (t-100) cc_final: 0.8423 (t-100) REVERT: M 96 ASP cc_start: 0.8531 (p0) cc_final: 0.8186 (p0) REVERT: M 275 TRP cc_start: 0.8752 (t-100) cc_final: 0.8423 (t-100) REVERT: M 331 MET cc_start: 0.8978 (mtt) cc_final: 0.8687 (mtt) REVERT: P 54 TYR cc_start: 0.9012 (t80) cc_final: 0.8564 (t80) REVERT: P 275 TRP cc_start: 0.8709 (t-100) cc_final: 0.8415 (t-100) REVERT: Q 54 TYR cc_start: 0.9061 (t80) cc_final: 0.8713 (t80) REVERT: Q 257 TYR cc_start: 0.9353 (t80) cc_final: 0.8986 (t80) REVERT: Q 260 TYR cc_start: 0.9391 (m-10) cc_final: 0.9040 (m-10) REVERT: Q 275 TRP cc_start: 0.8732 (t-100) cc_final: 0.8434 (t-100) REVERT: Q 335 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7333 (tm-30) REVERT: R 275 TRP cc_start: 0.8707 (t-100) cc_final: 0.8122 (t-100) REVERT: S 105 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: S 275 TRP cc_start: 0.8754 (t-100) cc_final: 0.8400 (t-100) REVERT: S 342 ASP cc_start: 0.8587 (t0) cc_final: 0.8376 (t0) REVERT: S 345 TRP cc_start: 0.9156 (m100) cc_final: 0.8945 (m100) REVERT: T 260 TYR cc_start: 0.9346 (m-10) cc_final: 0.9077 (m-10) REVERT: T 275 TRP cc_start: 0.8697 (t-100) cc_final: 0.8439 (t-100) REVERT: T 342 ASP cc_start: 0.8650 (t0) cc_final: 0.8342 (t0) REVERT: T 349 LEU cc_start: 0.9547 (tp) cc_final: 0.9191 (tt) outliers start: 198 outliers final: 52 residues processed: 1153 average time/residue: 0.6514 time to fit residues: 1321.0091 Evaluate side-chains 674 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 619 time to evaluate : 6.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 195 ILE Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 195 ILE Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain Y residue 28 ILE Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 256 LEU Chi-restraints excluded: chain Z residue 342 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain M residue 156 GLU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain P residue 269 VAL Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 269 VAL Chi-restraints excluded: chain T residue 322 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 452 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 677 optimal weight: 10.0000 chunk 554 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 816 optimal weight: 0.6980 chunk 881 optimal weight: 2.9990 chunk 726 optimal weight: 1.9990 chunk 809 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 654 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 73242 Z= 0.212 Angle : 0.584 9.607 98566 Z= 0.311 Chirality : 0.039 0.186 11544 Planarity : 0.003 0.034 12701 Dihedral : 4.760 59.111 9535 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.25 % Allowed : 11.37 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.09), residues: 9087 helix: 1.05 (0.06), residues: 7371 sheet: None (None), residues: 0 loop : -1.18 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 101 HIS 0.005 0.001 HIS D 97 PHE 0.019 0.001 PHE C 375 TYR 0.028 0.002 TYR D 257 ARG 0.008 0.001 ARG O 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 704 time to evaluate : 6.796 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: A 54 TYR cc_start: 0.9215 (t80) cc_final: 0.8866 (t80) REVERT: A 74 TYR cc_start: 0.8478 (p90) cc_final: 0.8123 (p90) REVERT: A 275 TRP cc_start: 0.8762 (t-100) cc_final: 0.8470 (t-100) REVERT: B 19 LYS cc_start: 0.9572 (tmtt) cc_final: 0.9219 (tptt) REVERT: B 59 MET cc_start: 0.8702 (ttt) cc_final: 0.8396 (ppp) REVERT: B 184 ILE cc_start: 0.9354 (mt) cc_final: 0.9114 (mm) REVERT: B 188 ASP cc_start: 0.8705 (m-30) cc_final: 0.8332 (m-30) REVERT: B 242 GLU cc_start: 0.8959 (tt0) cc_final: 0.8562 (tm-30) REVERT: G 59 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8306 (ppp) REVERT: G 181 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8473 (tm-30) REVERT: G 242 GLU cc_start: 0.9111 (tt0) cc_final: 0.8786 (tt0) REVERT: H 181 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8554 (tm-30) REVERT: H 188 ASP cc_start: 0.8983 (m-30) cc_final: 0.8547 (m-30) REVERT: H 197 ASP cc_start: 0.8623 (m-30) cc_final: 0.8405 (m-30) REVERT: H 242 GLU cc_start: 0.9020 (tt0) cc_final: 0.8605 (tt0) REVERT: H 288 MET cc_start: 0.8708 (mmm) cc_final: 0.8323 (mmm) REVERT: K 184 ILE cc_start: 0.9326 (mt) cc_final: 0.8947 (mm) REVERT: K 185 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8827 (tp30) REVERT: K 188 ASP cc_start: 0.8898 (m-30) cc_final: 0.8394 (m-30) REVERT: K 242 GLU cc_start: 0.8908 (tt0) cc_final: 0.8588 (tt0) REVERT: K 308 TRP cc_start: 0.8920 (m100) cc_final: 0.8308 (m100) REVERT: L 19 LYS cc_start: 0.9510 (tmtt) cc_final: 0.9179 (tptt) REVERT: L 184 ILE cc_start: 0.9366 (mt) cc_final: 0.9163 (mm) REVERT: L 185 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8894 (mt-10) REVERT: L 188 ASP cc_start: 0.8964 (m-30) cc_final: 0.8720 (m-30) REVERT: L 242 GLU cc_start: 0.9116 (tt0) cc_final: 0.8654 (tm-30) REVERT: N 181 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8605 (tp30) REVERT: N 184 ILE cc_start: 0.9402 (mt) cc_final: 0.9005 (mt) REVERT: N 188 ASP cc_start: 0.8814 (m-30) cc_final: 0.8364 (m-30) REVERT: N 223 LYS cc_start: 0.8988 (mttt) cc_final: 0.8751 (mtmp) REVERT: N 242 GLU cc_start: 0.8896 (tt0) cc_final: 0.8643 (tt0) REVERT: O 181 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8488 (tm-30) REVERT: O 184 ILE cc_start: 0.9421 (mt) cc_final: 0.9121 (mm) REVERT: O 188 ASP cc_start: 0.8964 (m-30) cc_final: 0.8544 (m-30) REVERT: O 197 ASP cc_start: 0.8826 (m-30) cc_final: 0.8568 (m-30) REVERT: O 242 GLU cc_start: 0.9025 (tt0) cc_final: 0.8669 (tt0) REVERT: U 177 ASP cc_start: 0.8846 (m-30) cc_final: 0.8628 (m-30) REVERT: U 184 ILE cc_start: 0.9420 (mt) cc_final: 0.9140 (mm) REVERT: U 185 GLU cc_start: 0.9248 (mt-10) cc_final: 0.9022 (mt-10) REVERT: U 188 ASP cc_start: 0.9026 (m-30) cc_final: 0.8662 (m-30) REVERT: U 190 ILE cc_start: 0.9030 (mt) cc_final: 0.8723 (mm) REVERT: U 223 LYS cc_start: 0.8921 (mttt) cc_final: 0.8685 (mtmt) REVERT: U 242 GLU cc_start: 0.9195 (tt0) cc_final: 0.8766 (tt0) REVERT: V 59 MET cc_start: 0.8920 (ptm) cc_final: 0.8293 (ppp) REVERT: V 181 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8356 (tp30) REVERT: V 188 ASP cc_start: 0.8882 (m-30) cc_final: 0.8566 (m-30) REVERT: V 197 ASP cc_start: 0.9068 (m-30) cc_final: 0.8708 (m-30) REVERT: V 242 GLU cc_start: 0.9211 (tt0) cc_final: 0.8913 (tt0) REVERT: V 308 TRP cc_start: 0.9005 (m100) cc_final: 0.8541 (m100) REVERT: W 19 LYS cc_start: 0.9426 (tmtt) cc_final: 0.9054 (tptt) REVERT: W 59 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7986 (ppp) REVERT: W 181 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8318 (tp30) REVERT: W 184 ILE cc_start: 0.9247 (mt) cc_final: 0.8957 (mm) REVERT: W 188 ASP cc_start: 0.9036 (m-30) cc_final: 0.8594 (m-30) REVERT: W 223 LYS cc_start: 0.8948 (mttt) cc_final: 0.8744 (mtmm) REVERT: W 242 GLU cc_start: 0.8983 (tt0) cc_final: 0.8682 (tm-30) REVERT: X 19 LYS cc_start: 0.9493 (tmtt) cc_final: 0.9184 (tptt) REVERT: X 31 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9161 (mp) REVERT: X 59 MET cc_start: 0.8796 (ttt) cc_final: 0.8224 (ppp) REVERT: X 184 ILE cc_start: 0.9369 (mt) cc_final: 0.9064 (mm) REVERT: X 185 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8948 (mt-10) REVERT: X 188 ASP cc_start: 0.8878 (m-30) cc_final: 0.8322 (m-30) REVERT: X 242 GLU cc_start: 0.9029 (tt0) cc_final: 0.8746 (tt0) REVERT: Y 184 ILE cc_start: 0.9404 (mt) cc_final: 0.9185 (mm) REVERT: Y 188 ASP cc_start: 0.8877 (m-30) cc_final: 0.8441 (m-30) REVERT: Y 198 MET cc_start: 0.9268 (ttt) cc_final: 0.8898 (ttm) REVERT: Y 223 LYS cc_start: 0.8927 (mttt) cc_final: 0.8586 (mtmp) REVERT: Y 242 GLU cc_start: 0.9215 (tt0) cc_final: 0.8771 (tt0) REVERT: Z 19 LYS cc_start: 0.9498 (tmtt) cc_final: 0.9081 (tptt) REVERT: Z 59 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8130 (ppp) REVERT: Z 188 ASP cc_start: 0.8954 (m-30) cc_final: 0.8674 (m-30) REVERT: Z 242 GLU cc_start: 0.9047 (tt0) cc_final: 0.8655 (tt0) REVERT: C 275 TRP cc_start: 0.8686 (t-100) cc_final: 0.8378 (t-100) REVERT: C 351 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8865 (mp10) REVERT: D 268 MET cc_start: 0.7360 (mtt) cc_final: 0.6670 (mtt) REVERT: D 275 TRP cc_start: 0.8384 (t-100) cc_final: 0.7976 (t-100) REVERT: D 342 ASP cc_start: 0.8740 (t0) cc_final: 0.8503 (t0) REVERT: E 87 MET cc_start: 0.9089 (mmm) cc_final: 0.8746 (mmp) REVERT: E 275 TRP cc_start: 0.8708 (t-100) cc_final: 0.8330 (t-100) REVERT: I 351 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8672 (mp10) REVERT: J 275 TRP cc_start: 0.8624 (t-100) cc_final: 0.8352 (t-100) REVERT: M 275 TRP cc_start: 0.8579 (t-100) cc_final: 0.8288 (t-100) REVERT: M 331 MET cc_start: 0.9018 (mtt) cc_final: 0.8676 (mtm) REVERT: M 351 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8954 (mt0) REVERT: P 54 TYR cc_start: 0.9131 (t80) cc_final: 0.8822 (t80) REVERT: P 96 ASP cc_start: 0.8714 (p0) cc_final: 0.8454 (p0) REVERT: P 268 MET cc_start: 0.7304 (mtt) cc_final: 0.7096 (mtt) REVERT: P 275 TRP cc_start: 0.8714 (t-100) cc_final: 0.8029 (t-100) REVERT: P 351 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8737 (mp10) REVERT: Q 275 TRP cc_start: 0.8751 (t-100) cc_final: 0.8367 (t-100) REVERT: Q 351 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8993 (mt0) REVERT: R 87 MET cc_start: 0.9101 (mmm) cc_final: 0.8863 (mmp) REVERT: R 105 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: R 335 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: S 105 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: S 275 TRP cc_start: 0.8766 (t-100) cc_final: 0.8339 (t-100) REVERT: S 342 ASP cc_start: 0.8665 (t0) cc_final: 0.8459 (t0) REVERT: T 275 TRP cc_start: 0.8728 (t-100) cc_final: 0.8348 (t-100) REVERT: T 342 ASP cc_start: 0.8746 (t0) cc_final: 0.8392 (t0) REVERT: T 349 LEU cc_start: 0.9579 (tp) cc_final: 0.9359 (tt) outliers start: 183 outliers final: 90 residues processed: 871 average time/residue: 0.6385 time to fit residues: 974.2384 Evaluate side-chains 687 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 585 time to evaluate : 6.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 244 LEU Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 244 LEU Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 105 LEU Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 31 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 105 LEU Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 244 LEU Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 105 LEU Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain Z residue 244 LEU Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 342 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 156 GLU Chi-restraints excluded: chain M residue 269 VAL Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain M residue 384 ASP Chi-restraints excluded: chain P residue 269 VAL Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 351 GLN Chi-restraints excluded: chain R residue 105 GLU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 335 GLU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 227 MET Chi-restraints excluded: chain T residue 322 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 806 optimal weight: 9.9990 chunk 613 optimal weight: 0.0670 chunk 423 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 389 optimal weight: 5.9990 chunk 547 optimal weight: 7.9990 chunk 818 optimal weight: 3.9990 chunk 867 optimal weight: 5.9990 chunk 427 optimal weight: 0.9990 chunk 776 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 316 HIS H 316 HIS K 316 HIS K 340 ASN N 149 GLN N 340 ASN O 316 HIS U 316 HIS ** W 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 316 HIS Y 316 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 73242 Z= 0.175 Angle : 0.547 9.487 98566 Z= 0.288 Chirality : 0.038 0.190 11544 Planarity : 0.003 0.033 12701 Dihedral : 4.515 53.104 9533 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.23 % Allowed : 11.47 % Favored : 86.30 % 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: 1.63 (0.09), residues: 9087 helix: 1.56 (0.06), residues: 7423 sheet: None (None), residues: 0 loop : -1.02 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 101 HIS 0.003 0.001 HIS M 95 PHE 0.012 0.001 PHE F 324 TYR 0.019 0.001 TYR H 346 ARG 0.008 0.001 ARG U 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 704 time to evaluate : 6.754 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: A 275 TRP cc_start: 0.8753 (t-100) cc_final: 0.8375 (t-100) REVERT: B 55 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8401 (pt0) REVERT: B 181 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8528 (tp30) REVERT: B 184 ILE cc_start: 0.9323 (mt) cc_final: 0.9100 (mm) REVERT: B 188 ASP cc_start: 0.8764 (m-30) cc_final: 0.8354 (m-30) REVERT: B 242 GLU cc_start: 0.8928 (tt0) cc_final: 0.8575 (tm-30) REVERT: B 254 MET cc_start: 0.9012 (mmm) cc_final: 0.8679 (mmm) REVERT: B 308 TRP cc_start: 0.8849 (m100) cc_final: 0.8602 (m100) REVERT: G 21 MET cc_start: 0.8901 (ttt) cc_final: 0.8672 (ttt) REVERT: G 59 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8282 (ppp) REVERT: G 181 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8446 (tp30) REVERT: G 242 GLU cc_start: 0.9103 (tt0) cc_final: 0.8789 (tt0) REVERT: H 52 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: H 181 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8520 (tm-30) REVERT: H 188 ASP cc_start: 0.8939 (m-30) cc_final: 0.8533 (m-30) REVERT: H 242 GLU cc_start: 0.9023 (tt0) cc_final: 0.8615 (tt0) REVERT: H 288 MET cc_start: 0.8718 (mmm) cc_final: 0.8361 (mmm) REVERT: K 184 ILE cc_start: 0.9344 (mt) cc_final: 0.8967 (mm) REVERT: K 188 ASP cc_start: 0.8888 (m-30) cc_final: 0.8427 (m-30) REVERT: K 242 GLU cc_start: 0.8979 (tt0) cc_final: 0.8643 (tt0) REVERT: K 308 TRP cc_start: 0.8861 (m100) cc_final: 0.8390 (m100) REVERT: L 19 LYS cc_start: 0.9465 (tmtt) cc_final: 0.9116 (tptt) REVERT: L 52 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: L 185 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8882 (mt-10) REVERT: L 188 ASP cc_start: 0.9014 (m-30) cc_final: 0.8737 (m-30) REVERT: L 198 MET cc_start: 0.9275 (ttt) cc_final: 0.8951 (ttm) REVERT: L 242 GLU cc_start: 0.9120 (tt0) cc_final: 0.8687 (tt0) REVERT: N 55 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8469 (mt-10) REVERT: N 181 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8711 (tp30) REVERT: N 184 ILE cc_start: 0.9413 (mt) cc_final: 0.9040 (mt) REVERT: N 188 ASP cc_start: 0.8845 (m-30) cc_final: 0.8417 (m-30) REVERT: N 223 LYS cc_start: 0.8987 (mttt) cc_final: 0.8730 (mtmp) REVERT: O 161 GLU cc_start: 0.8986 (pt0) cc_final: 0.8610 (pt0) REVERT: O 181 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8497 (tm-30) REVERT: O 184 ILE cc_start: 0.9426 (mt) cc_final: 0.9125 (mm) REVERT: O 188 ASP cc_start: 0.8792 (m-30) cc_final: 0.8466 (m-30) REVERT: O 197 ASP cc_start: 0.8814 (m-30) cc_final: 0.8543 (m-30) REVERT: O 242 GLU cc_start: 0.9017 (tt0) cc_final: 0.8643 (tt0) REVERT: U 181 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8738 (tm-30) REVERT: U 184 ILE cc_start: 0.9422 (mt) cc_final: 0.9085 (mm) REVERT: U 185 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8602 (tp30) REVERT: U 188 ASP cc_start: 0.9019 (m-30) cc_final: 0.8495 (m-30) REVERT: U 190 ILE cc_start: 0.9088 (mt) cc_final: 0.8758 (mm) REVERT: U 223 LYS cc_start: 0.8928 (mttt) cc_final: 0.8677 (mtmt) REVERT: U 242 GLU cc_start: 0.9223 (tt0) cc_final: 0.8822 (tm-30) REVERT: U 308 TRP cc_start: 0.8906 (m100) cc_final: 0.8486 (m100) REVERT: V 19 LYS cc_start: 0.9239 (tptt) cc_final: 0.8641 (tptp) REVERT: V 55 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8305 (pt0) REVERT: V 59 MET cc_start: 0.8959 (ptm) cc_final: 0.8392 (ppp) REVERT: V 181 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8307 (tp30) REVERT: V 188 ASP cc_start: 0.8952 (m-30) cc_final: 0.8568 (m-30) REVERT: V 197 ASP cc_start: 0.9072 (m-30) cc_final: 0.8762 (m-30) REVERT: V 242 GLU cc_start: 0.9273 (tt0) cc_final: 0.8957 (tt0) REVERT: V 308 TRP cc_start: 0.8977 (m100) cc_final: 0.8515 (m100) REVERT: W 19 LYS cc_start: 0.9402 (tmtt) cc_final: 0.9032 (tptt) REVERT: W 59 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8105 (ppp) REVERT: W 181 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8270 (tp30) REVERT: W 184 ILE cc_start: 0.9276 (mt) cc_final: 0.8973 (mm) REVERT: W 188 ASP cc_start: 0.9017 (m-30) cc_final: 0.8609 (m-30) REVERT: W 242 GLU cc_start: 0.9143 (tt0) cc_final: 0.8788 (tm-30) REVERT: X 31 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9113 (mp) REVERT: X 59 MET cc_start: 0.8871 (ttt) cc_final: 0.8265 (ppp) REVERT: X 184 ILE cc_start: 0.9350 (mt) cc_final: 0.9036 (mm) REVERT: X 185 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8921 (mt-10) REVERT: X 188 ASP cc_start: 0.8898 (m-30) cc_final: 0.8326 (m-30) REVERT: X 242 GLU cc_start: 0.9020 (tt0) cc_final: 0.8724 (tt0) REVERT: X 308 TRP cc_start: 0.8891 (m100) cc_final: 0.8502 (m100) REVERT: Y 184 ILE cc_start: 0.9416 (mt) cc_final: 0.9189 (mm) REVERT: Y 188 ASP cc_start: 0.8880 (m-30) cc_final: 0.8436 (m-30) REVERT: Y 242 GLU cc_start: 0.9245 (tt0) cc_final: 0.8821 (tt0) REVERT: Z 19 LYS cc_start: 0.9515 (tmtt) cc_final: 0.9078 (tptt) REVERT: Z 59 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8205 (ppp) REVERT: Z 181 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8301 (tp30) REVERT: Z 188 ASP cc_start: 0.8908 (m-30) cc_final: 0.8665 (m-30) REVERT: Z 242 GLU cc_start: 0.9023 (tt0) cc_final: 0.8711 (tt0) REVERT: C 54 TYR cc_start: 0.9224 (t80) cc_final: 0.8945 (t80) REVERT: C 275 TRP cc_start: 0.8711 (t-100) cc_final: 0.8325 (t-100) REVERT: C 351 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.8909 (mp10) REVERT: D 268 MET cc_start: 0.7360 (mtt) cc_final: 0.6666 (mtt) REVERT: D 275 TRP cc_start: 0.8369 (t-100) cc_final: 0.7860 (t-100) REVERT: D 342 ASP cc_start: 0.8751 (t0) cc_final: 0.8545 (t0) REVERT: D 349 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9423 (tt) REVERT: E 331 MET cc_start: 0.8883 (mtt) cc_final: 0.8652 (mtt) REVERT: F 322 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8945 (pp) REVERT: F 342 ASP cc_start: 0.8708 (t0) cc_final: 0.8345 (t0) REVERT: I 351 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8666 (mp10) REVERT: J 116 GLU cc_start: 0.8209 (tp30) cc_final: 0.7945 (tp30) REVERT: J 275 TRP cc_start: 0.8615 (t-100) cc_final: 0.8321 (t-100) REVERT: M 45 LYS cc_start: 0.9087 (ptpt) cc_final: 0.8744 (pttt) REVERT: M 275 TRP cc_start: 0.8685 (t-100) cc_final: 0.7831 (t-100) REVERT: M 351 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8951 (mp10) REVERT: P 54 TYR cc_start: 0.9154 (t80) cc_final: 0.8880 (t80) REVERT: P 275 TRP cc_start: 0.8735 (t-100) cc_final: 0.8372 (t-100) REVERT: P 349 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9426 (tt) REVERT: P 351 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8745 (mp10) REVERT: Q 275 TRP cc_start: 0.8719 (t-100) cc_final: 0.8318 (t-100) REVERT: Q 299 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8176 (tm-30) REVERT: Q 351 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.9026 (mt0) REVERT: R 87 MET cc_start: 0.9086 (mmm) cc_final: 0.8812 (mmp) REVERT: R 268 MET cc_start: 0.6575 (pmm) cc_final: 0.5820 (mpp) REVERT: S 275 TRP cc_start: 0.8768 (t-100) cc_final: 0.8264 (t-100) REVERT: S 342 ASP cc_start: 0.8732 (t0) cc_final: 0.8521 (t0) REVERT: T 250 ILE cc_start: 0.9428 (mt) cc_final: 0.9147 (mt) REVERT: T 275 TRP cc_start: 0.8708 (t-100) cc_final: 0.8278 (t-100) REVERT: T 331 MET cc_start: 0.9073 (mtt) cc_final: 0.8863 (mtm) REVERT: T 342 ASP cc_start: 0.8761 (t0) cc_final: 0.8382 (t0) outliers start: 181 outliers final: 87 residues processed: 858 average time/residue: 0.6494 time to fit residues: 976.3435 Evaluate side-chains 680 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 579 time to evaluate : 6.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 198 MET Chi-restraints excluded: chain O residue 244 LEU Chi-restraints excluded: chain O residue 300 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain U residue 328 LEU Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 105 LEU Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 144 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain X residue 31 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 328 LEU Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain Z residue 342 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 351 GLN Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 322 LEU Chi-restraints excluded: chain T residue 335 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 722 optimal weight: 5.9990 chunk 492 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 645 optimal weight: 4.9990 chunk 357 optimal weight: 0.9980 chunk 739 optimal weight: 8.9990 chunk 599 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 442 optimal weight: 2.9990 chunk 778 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 316 HIS ** W 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 340 ASN X 340 ASN ** Z 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 73242 Z= 0.279 Angle : 0.606 9.223 98566 Z= 0.322 Chirality : 0.040 0.195 11544 Planarity : 0.003 0.038 12701 Dihedral : 4.472 22.446 9529 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.56 % Allowed : 11.93 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.09), residues: 9087 helix: 1.62 (0.06), residues: 7410 sheet: None (None), residues: 0 loop : -1.01 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 275 HIS 0.004 0.001 HIS A 97 PHE 0.013 0.001 PHE U 202 TYR 0.027 0.002 TYR B 346 ARG 0.010 0.001 ARG U 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 567 time to evaluate : 6.758 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: A 275 TRP cc_start: 0.8740 (t-100) cc_final: 0.7891 (t-100) REVERT: B 52 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: B 55 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8445 (pt0) REVERT: B 181 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8558 (tp30) REVERT: B 188 ASP cc_start: 0.8749 (m-30) cc_final: 0.8281 (m-30) REVERT: B 242 GLU cc_start: 0.8899 (tt0) cc_final: 0.8574 (tm-30) REVERT: B 254 MET cc_start: 0.8989 (mmm) cc_final: 0.8685 (mmm) REVERT: B 308 TRP cc_start: 0.8824 (m100) cc_final: 0.8556 (m100) REVERT: G 59 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8358 (ppp) REVERT: G 181 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8484 (tm-30) REVERT: G 191 ARG cc_start: 0.8749 (tmm160) cc_final: 0.8528 (ttp80) REVERT: G 242 GLU cc_start: 0.9113 (tt0) cc_final: 0.8789 (tt0) REVERT: H 52 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: H 181 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8564 (tm-30) REVERT: H 188 ASP cc_start: 0.8950 (m-30) cc_final: 0.8578 (m-30) REVERT: H 242 GLU cc_start: 0.9079 (tt0) cc_final: 0.8640 (tt0) REVERT: K 52 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: K 242 GLU cc_start: 0.9002 (tt0) cc_final: 0.8648 (tt0) REVERT: K 308 TRP cc_start: 0.8851 (m100) cc_final: 0.8343 (m100) REVERT: L 52 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: L 161 GLU cc_start: 0.9032 (pt0) cc_final: 0.8770 (pt0) REVERT: L 185 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8921 (mt-10) REVERT: L 188 ASP cc_start: 0.8992 (m-30) cc_final: 0.8716 (m-30) REVERT: L 242 GLU cc_start: 0.9150 (tt0) cc_final: 0.8756 (tt0) REVERT: L 270 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8845 (tt) REVERT: N 52 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8570 (m-80) REVERT: N 55 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8484 (pt0) REVERT: N 181 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8710 (tp30) REVERT: N 184 ILE cc_start: 0.9408 (mt) cc_final: 0.9025 (mt) REVERT: N 188 ASP cc_start: 0.8838 (m-30) cc_final: 0.8407 (m-30) REVERT: N 349 LEU cc_start: 0.7078 (tp) cc_final: 0.6817 (mp) REVERT: O 52 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: O 59 MET cc_start: 0.8984 (ptm) cc_final: 0.8555 (ppp) REVERT: O 161 GLU cc_start: 0.9005 (pt0) cc_final: 0.8644 (pt0) REVERT: O 181 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8633 (tm-30) REVERT: O 184 ILE cc_start: 0.9475 (mt) cc_final: 0.9203 (mm) REVERT: O 188 ASP cc_start: 0.8839 (m-30) cc_final: 0.8560 (m-30) REVERT: O 197 ASP cc_start: 0.8827 (m-30) cc_final: 0.8600 (m-30) REVERT: O 242 GLU cc_start: 0.9040 (tt0) cc_final: 0.8660 (tm-30) REVERT: U 181 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8815 (tm-30) REVERT: U 184 ILE cc_start: 0.9417 (mt) cc_final: 0.9084 (mm) REVERT: U 185 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8642 (tp30) REVERT: U 188 ASP cc_start: 0.9005 (m-30) cc_final: 0.8489 (m-30) REVERT: U 190 ILE cc_start: 0.9110 (mt) cc_final: 0.8765 (mm) REVERT: U 223 LYS cc_start: 0.8929 (mttt) cc_final: 0.8688 (mtmt) REVERT: U 242 GLU cc_start: 0.9241 (tt0) cc_final: 0.8846 (tm-30) REVERT: U 308 TRP cc_start: 0.8871 (m100) cc_final: 0.8341 (m100) REVERT: V 19 LYS cc_start: 0.9252 (tptt) cc_final: 0.8965 (tptp) REVERT: V 52 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: V 55 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8386 (pt0) REVERT: V 59 MET cc_start: 0.8997 (ptm) cc_final: 0.8492 (ppp) REVERT: V 181 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8457 (tp30) REVERT: V 188 ASP cc_start: 0.8927 (m-30) cc_final: 0.8711 (m-30) REVERT: V 197 ASP cc_start: 0.9071 (m-30) cc_final: 0.8800 (m-30) REVERT: V 242 GLU cc_start: 0.9287 (tt0) cc_final: 0.8958 (tt0) REVERT: V 308 TRP cc_start: 0.8939 (m100) cc_final: 0.8452 (m100) REVERT: W 59 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8293 (ppp) REVERT: W 181 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8500 (tp30) REVERT: W 184 ILE cc_start: 0.9281 (mt) cc_final: 0.8985 (mm) REVERT: W 188 ASP cc_start: 0.9002 (m-30) cc_final: 0.8600 (m-30) REVERT: W 242 GLU cc_start: 0.9158 (tt0) cc_final: 0.8794 (tm-30) REVERT: X 31 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9156 (mp) REVERT: X 52 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: X 59 MET cc_start: 0.9017 (ttt) cc_final: 0.8441 (ppp) REVERT: X 60 MET cc_start: 0.9251 (tpp) cc_final: 0.8954 (tpp) REVERT: X 184 ILE cc_start: 0.9343 (mt) cc_final: 0.9019 (mm) REVERT: X 185 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8969 (mt-10) REVERT: X 188 ASP cc_start: 0.8837 (m-30) cc_final: 0.8327 (m-30) REVERT: X 242 GLU cc_start: 0.8981 (tt0) cc_final: 0.8743 (tm-30) REVERT: X 288 MET cc_start: 0.8975 (mmm) cc_final: 0.8766 (mmm) REVERT: Y 52 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: Y 184 ILE cc_start: 0.9431 (mt) cc_final: 0.9192 (mm) REVERT: Y 188 ASP cc_start: 0.8883 (m-30) cc_final: 0.8445 (m-30) REVERT: Y 242 GLU cc_start: 0.9240 (tt0) cc_final: 0.8860 (tt0) REVERT: Z 52 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: Z 59 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8338 (ppp) REVERT: Z 181 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8273 (tp30) REVERT: Z 188 ASP cc_start: 0.8962 (m-30) cc_final: 0.8731 (m-30) REVERT: Z 190 ILE cc_start: 0.9211 (mt) cc_final: 0.8953 (mm) REVERT: Z 242 GLU cc_start: 0.9016 (tt0) cc_final: 0.8717 (tt0) REVERT: C 128 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 275 TRP cc_start: 0.8722 (t-100) cc_final: 0.8296 (t-100) REVERT: C 351 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8924 (mp10) REVERT: E 268 MET cc_start: 0.7392 (mtt) cc_final: 0.7111 (mtt) REVERT: F 275 TRP cc_start: 0.9034 (t60) cc_final: 0.8832 (t60) REVERT: F 342 ASP cc_start: 0.8771 (t0) cc_final: 0.8420 (t0) REVERT: I 351 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8661 (mp10) REVERT: J 54 TYR cc_start: 0.9249 (t80) cc_final: 0.8899 (t80) REVERT: J 275 TRP cc_start: 0.8595 (t-100) cc_final: 0.7896 (t-100) REVERT: M 45 LYS cc_start: 0.9117 (ptpt) cc_final: 0.8740 (pttt) REVERT: M 275 TRP cc_start: 0.8522 (t-100) cc_final: 0.7750 (t-100) REVERT: M 351 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8991 (mp10) REVERT: P 54 TYR cc_start: 0.9181 (t80) cc_final: 0.8805 (t80) REVERT: P 275 TRP cc_start: 0.8758 (t-100) cc_final: 0.8010 (t-100) REVERT: P 351 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8759 (mp10) REVERT: Q 275 TRP cc_start: 0.8702 (t-100) cc_final: 0.8202 (t-100) REVERT: Q 299 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8192 (tm-30) REVERT: Q 351 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.9049 (mt0) REVERT: R 87 MET cc_start: 0.9136 (mmm) cc_final: 0.8799 (mmp) REVERT: R 268 MET cc_start: 0.7007 (pmm) cc_final: 0.5831 (mpp) REVERT: R 275 TRP cc_start: 0.9069 (t60) cc_final: 0.8371 (t60) REVERT: S 87 MET cc_start: 0.9175 (mmm) cc_final: 0.8806 (mmp) REVERT: S 275 TRP cc_start: 0.8735 (t-100) cc_final: 0.8189 (t-100) REVERT: T 275 TRP cc_start: 0.8770 (t-100) cc_final: 0.7822 (t-100) REVERT: T 342 ASP cc_start: 0.8746 (t0) cc_final: 0.8352 (t0) outliers start: 208 outliers final: 124 residues processed: 750 average time/residue: 0.6243 time to fit residues: 825.7273 Evaluate side-chains 647 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 503 time to evaluate : 6.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain K residue 52 TYR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 52 TYR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 244 LEU Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 139 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 MET Chi-restraints excluded: chain O residue 244 LEU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 244 LEU Chi-restraints excluded: chain U residue 328 LEU Chi-restraints excluded: chain V residue 52 TYR Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 139 ILE Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain V residue 244 LEU Chi-restraints excluded: chain V residue 328 LEU Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 105 LEU Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 139 ILE Chi-restraints excluded: chain W residue 144 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 31 LEU Chi-restraints excluded: chain X residue 45 LYS Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 328 LEU Chi-restraints excluded: chain Y residue 52 TYR Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 52 TYR Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain Z residue 139 ILE Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 244 LEU Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain Z residue 342 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain J residue 335 GLU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 335 GLU Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 335 GLU Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 351 GLN Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 335 GLU Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 322 LEU Chi-restraints excluded: chain T residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 291 optimal weight: 8.9990 chunk 780 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 509 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 867 optimal weight: 0.9990 chunk 720 optimal weight: 1.9990 chunk 401 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 287 optimal weight: 0.0030 chunk 455 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 316 HIS N 316 HIS U 316 HIS W 316 HIS Z 316 HIS M 340 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 73242 Z= 0.148 Angle : 0.537 10.580 98566 Z= 0.279 Chirality : 0.037 0.202 11544 Planarity : 0.003 0.034 12701 Dihedral : 4.299 24.664 9529 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.80 % Allowed : 12.95 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.09), residues: 9087 helix: 1.89 (0.06), residues: 7397 sheet: None (None), residues: 0 loop : -0.84 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 101 HIS 0.002 0.001 HIS Q 95 PHE 0.013 0.001 PHE P 324 TYR 0.021 0.001 TYR T 257 ARG 0.010 0.001 ARG U 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 712 time to evaluate : 6.872 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: A 45 LYS cc_start: 0.9114 (ptpt) cc_final: 0.8846 (ptmt) REVERT: A 275 TRP cc_start: 0.8406 (t-100) cc_final: 0.7992 (t-100) REVERT: B 52 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: B 55 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8300 (pt0) REVERT: B 62 ASP cc_start: 0.8584 (m-30) cc_final: 0.8279 (m-30) REVERT: B 181 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8488 (tp30) REVERT: B 188 ASP cc_start: 0.8743 (m-30) cc_final: 0.8211 (m-30) REVERT: B 242 GLU cc_start: 0.8822 (tt0) cc_final: 0.8513 (tt0) REVERT: B 254 MET cc_start: 0.9015 (mmm) cc_final: 0.8724 (mmm) REVERT: B 308 TRP cc_start: 0.8714 (m100) cc_final: 0.8508 (m100) REVERT: G 59 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8322 (ppp) REVERT: G 181 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8518 (tp30) REVERT: G 191 ARG cc_start: 0.8684 (tmm160) cc_final: 0.8475 (ttp80) REVERT: G 242 GLU cc_start: 0.9089 (tt0) cc_final: 0.8799 (tt0) REVERT: H 52 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: H 181 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8521 (tm-30) REVERT: H 188 ASP cc_start: 0.8925 (m-30) cc_final: 0.8504 (m-30) REVERT: H 242 GLU cc_start: 0.9013 (tt0) cc_final: 0.8600 (tt0) REVERT: K 52 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: K 242 GLU cc_start: 0.8993 (tt0) cc_final: 0.8723 (tm-30) REVERT: K 293 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8390 (mt-10) REVERT: K 308 TRP cc_start: 0.8808 (m100) cc_final: 0.8304 (m100) REVERT: L 19 LYS cc_start: 0.9457 (tmtt) cc_final: 0.9022 (tptt) REVERT: L 52 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: L 59 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8065 (ppp) REVERT: L 185 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8843 (mt-10) REVERT: L 188 ASP cc_start: 0.9018 (m-30) cc_final: 0.8653 (m-30) REVERT: L 242 GLU cc_start: 0.9070 (tt0) cc_final: 0.8670 (tt0) REVERT: L 293 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8148 (mt-10) REVERT: N 52 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: N 161 GLU cc_start: 0.9028 (pt0) cc_final: 0.8753 (pt0) REVERT: N 181 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8705 (tp30) REVERT: N 184 ILE cc_start: 0.9401 (mt) cc_final: 0.9045 (mt) REVERT: N 188 ASP cc_start: 0.8879 (m-30) cc_final: 0.8366 (m-30) REVERT: N 192 GLN cc_start: 0.9381 (mm-40) cc_final: 0.9159 (tp40) REVERT: N 246 TYR cc_start: 0.9154 (t80) cc_final: 0.8755 (t80) REVERT: N 349 LEU cc_start: 0.6851 (tp) cc_final: 0.6607 (mp) REVERT: O 52 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: O 59 MET cc_start: 0.8912 (ptm) cc_final: 0.8445 (ppp) REVERT: O 62 ASP cc_start: 0.8666 (m-30) cc_final: 0.8172 (m-30) REVERT: O 161 GLU cc_start: 0.8958 (pt0) cc_final: 0.8742 (pp20) REVERT: O 181 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8509 (tm-30) REVERT: O 242 GLU cc_start: 0.9036 (tt0) cc_final: 0.8640 (tt0) REVERT: U 181 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8616 (tm-30) REVERT: U 184 ILE cc_start: 0.9401 (mt) cc_final: 0.9064 (mm) REVERT: U 185 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8618 (tp30) REVERT: U 188 ASP cc_start: 0.9026 (m-30) cc_final: 0.8503 (m-30) REVERT: U 190 ILE cc_start: 0.9098 (mt) cc_final: 0.8637 (mm) REVERT: U 242 GLU cc_start: 0.9123 (tt0) cc_final: 0.8776 (tm-30) REVERT: U 308 TRP cc_start: 0.8791 (m100) cc_final: 0.8311 (m100) REVERT: V 55 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8298 (pt0) REVERT: V 59 MET cc_start: 0.8966 (ptm) cc_final: 0.8288 (ppp) REVERT: V 181 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8375 (tp30) REVERT: V 188 ASP cc_start: 0.8954 (m-30) cc_final: 0.8573 (m-30) REVERT: V 197 ASP cc_start: 0.9030 (m-30) cc_final: 0.8816 (m-30) REVERT: V 198 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9055 (ttp) REVERT: V 242 GLU cc_start: 0.9209 (tt0) cc_final: 0.8920 (tt0) REVERT: V 308 TRP cc_start: 0.8923 (m100) cc_final: 0.8390 (m100) REVERT: W 19 LYS cc_start: 0.9371 (tmtt) cc_final: 0.8993 (tptt) REVERT: W 52 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: W 59 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8056 (ppp) REVERT: W 62 ASP cc_start: 0.8593 (m-30) cc_final: 0.8137 (m-30) REVERT: W 177 ASP cc_start: 0.8754 (m-30) cc_final: 0.8526 (m-30) REVERT: W 181 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8439 (tp30) REVERT: W 184 ILE cc_start: 0.9275 (mt) cc_final: 0.8967 (mm) REVERT: W 188 ASP cc_start: 0.8982 (m-30) cc_final: 0.8608 (m-30) REVERT: W 242 GLU cc_start: 0.9116 (tt0) cc_final: 0.8776 (tm-30) REVERT: X 31 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9145 (mp) REVERT: X 52 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: X 59 MET cc_start: 0.8752 (ttt) cc_final: 0.8253 (ppp) REVERT: X 60 MET cc_start: 0.9162 (tpp) cc_final: 0.8959 (tpp) REVERT: X 177 ASP cc_start: 0.8898 (m-30) cc_final: 0.8606 (m-30) REVERT: X 181 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8632 (tm-30) REVERT: X 184 ILE cc_start: 0.9331 (mt) cc_final: 0.8979 (mm) REVERT: X 185 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8659 (tp30) REVERT: X 188 ASP cc_start: 0.8897 (m-30) cc_final: 0.8233 (m-30) REVERT: X 242 GLU cc_start: 0.8858 (tt0) cc_final: 0.8617 (tm-30) REVERT: X 254 MET cc_start: 0.8881 (mmm) cc_final: 0.8641 (mmm) REVERT: Y 52 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: Y 59 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7980 (ppp) REVERT: Y 184 ILE cc_start: 0.9435 (mt) cc_final: 0.9124 (mt) REVERT: Y 188 ASP cc_start: 0.8883 (m-30) cc_final: 0.8455 (m-30) REVERT: Y 242 GLU cc_start: 0.9191 (tt0) cc_final: 0.8829 (tt0) REVERT: Z 19 LYS cc_start: 0.9488 (tmtt) cc_final: 0.9205 (tptt) REVERT: Z 52 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: Z 59 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8308 (ppp) REVERT: Z 181 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8305 (tp30) REVERT: Z 188 ASP cc_start: 0.8894 (m-30) cc_final: 0.8612 (m-30) REVERT: Z 190 ILE cc_start: 0.9220 (mt) cc_final: 0.8959 (mm) REVERT: Z 242 GLU cc_start: 0.8952 (tt0) cc_final: 0.8592 (tt0) REVERT: C 254 GLN cc_start: 0.9084 (tp40) cc_final: 0.8817 (tp40) REVERT: C 275 TRP cc_start: 0.8713 (t-100) cc_final: 0.8343 (t-100) REVERT: C 351 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8899 (mp10) REVERT: D 268 MET cc_start: 0.7372 (mtt) cc_final: 0.6645 (mtt) REVERT: D 275 TRP cc_start: 0.8363 (t-100) cc_final: 0.7873 (t-100) REVERT: D 349 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9419 (tt) REVERT: E 54 TYR cc_start: 0.9133 (t80) cc_final: 0.8811 (t80) REVERT: E 87 MET cc_start: 0.8998 (mmm) cc_final: 0.8747 (mmm) REVERT: E 268 MET cc_start: 0.7233 (mtt) cc_final: 0.6986 (mtt) REVERT: F 45 LYS cc_start: 0.8955 (ptpt) cc_final: 0.8742 (pttp) REVERT: F 275 TRP cc_start: 0.9018 (t60) cc_final: 0.8781 (t60) REVERT: I 54 TYR cc_start: 0.9286 (t80) cc_final: 0.9045 (t80) REVERT: I 351 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8747 (mp10) REVERT: J 258 ASN cc_start: 0.9182 (m-40) cc_final: 0.8973 (m-40) REVERT: J 275 TRP cc_start: 0.8621 (t-100) cc_final: 0.8097 (t-100) REVERT: J 299 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8104 (tm-30) REVERT: M 45 LYS cc_start: 0.9120 (ptpt) cc_final: 0.8868 (pttt) REVERT: M 54 TYR cc_start: 0.9243 (t80) cc_final: 0.9013 (t80) REVERT: M 342 ASP cc_start: 0.8664 (t0) cc_final: 0.8368 (t0) REVERT: P 45 LYS cc_start: 0.9093 (ptpt) cc_final: 0.8875 (pttt) REVERT: P 349 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9421 (tt) REVERT: P 351 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8695 (mp10) REVERT: Q 275 TRP cc_start: 0.8746 (t-100) cc_final: 0.8284 (t-100) REVERT: Q 299 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8149 (tm-30) REVERT: Q 331 MET cc_start: 0.9052 (mtp) cc_final: 0.8833 (mtp) REVERT: Q 351 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8973 (mt0) REVERT: R 87 MET cc_start: 0.9067 (mmm) cc_final: 0.8795 (mmp) REVERT: R 268 MET cc_start: 0.7120 (pmm) cc_final: 0.5959 (mpp) REVERT: R 275 TRP cc_start: 0.8983 (t60) cc_final: 0.8196 (t60) REVERT: R 342 ASP cc_start: 0.8716 (t0) cc_final: 0.8444 (t0) REVERT: T 45 LYS cc_start: 0.9138 (ptpt) cc_final: 0.8897 (pttt) REVERT: T 342 ASP cc_start: 0.8712 (t0) cc_final: 0.8383 (t0) outliers start: 146 outliers final: 76 residues processed: 836 average time/residue: 0.6491 time to fit residues: 944.8228 Evaluate side-chains 640 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 541 time to evaluate : 6.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 125 PHE Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain K residue 52 TYR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 52 TYR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 139 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 198 MET Chi-restraints excluded: chain O residue 300 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 328 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 139 ILE Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain V residue 198 MET Chi-restraints excluded: chain V residue 328 LEU Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 139 ILE Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain X residue 31 LEU Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 328 LEU Chi-restraints excluded: chain Y residue 52 TYR Chi-restraints excluded: chain Y residue 59 MET Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 52 TYR Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 139 ILE Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 349 LEU Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 351 GLN Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 322 LEU Chi-restraints excluded: chain T residue 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 836 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 494 optimal weight: 0.7980 chunk 633 optimal weight: 7.9990 chunk 491 optimal weight: 0.9980 chunk 730 optimal weight: 1.9990 chunk 484 optimal weight: 6.9990 chunk 864 optimal weight: 0.8980 chunk 541 optimal weight: 0.7980 chunk 527 optimal weight: 3.9990 chunk 399 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 ASN L 192 GLN U 22 ASN U 117 HIS V 340 ASN D 258 ASN P 340 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 73242 Z= 0.158 Angle : 0.555 11.015 98566 Z= 0.286 Chirality : 0.038 0.216 11544 Planarity : 0.003 0.036 12701 Dihedral : 4.222 20.935 9529 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.81 % Allowed : 13.55 % Favored : 84.64 % 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: 2.25 (0.09), residues: 9087 helix: 2.00 (0.06), residues: 7423 sheet: None (None), residues: 0 loop : -0.82 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 275 HIS 0.002 0.001 HIS I 95 PHE 0.018 0.001 PHE I 324 TYR 0.018 0.001 TYR S 54 ARG 0.010 0.001 ARG Y 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 611 time to evaluate : 6.814 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: A 45 LYS cc_start: 0.9085 (ptpt) cc_final: 0.7961 (pttt) REVERT: A 342 ASP cc_start: 0.8628 (t0) cc_final: 0.8326 (t0) REVERT: B 52 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: B 55 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8252 (pt0) REVERT: B 62 ASP cc_start: 0.8630 (m-30) cc_final: 0.8268 (m-30) REVERT: B 181 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8459 (tp30) REVERT: B 188 ASP cc_start: 0.8757 (m-30) cc_final: 0.8209 (m-30) REVERT: B 242 GLU cc_start: 0.8753 (tt0) cc_final: 0.8431 (tt0) REVERT: G 59 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8307 (ppp) REVERT: G 181 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8567 (tm-30) REVERT: G 191 ARG cc_start: 0.8648 (tmm160) cc_final: 0.8436 (ttp80) REVERT: G 242 GLU cc_start: 0.9082 (tt0) cc_final: 0.8795 (tt0) REVERT: H 52 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: H 181 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8499 (tm-30) REVERT: H 188 ASP cc_start: 0.8849 (m-30) cc_final: 0.8472 (m-30) REVERT: H 242 GLU cc_start: 0.8999 (tt0) cc_final: 0.8620 (tt0) REVERT: K 52 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: K 142 MET cc_start: 0.8461 (ttm) cc_final: 0.8191 (mtt) REVERT: K 242 GLU cc_start: 0.9017 (tt0) cc_final: 0.8755 (tm-30) REVERT: K 308 TRP cc_start: 0.8776 (m100) cc_final: 0.8265 (m100) REVERT: L 19 LYS cc_start: 0.9485 (tmtt) cc_final: 0.9115 (tptt) REVERT: L 52 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: L 55 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8266 (pt0) REVERT: L 59 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8118 (ppp) REVERT: L 142 MET cc_start: 0.8236 (mtt) cc_final: 0.7898 (ttm) REVERT: L 181 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8613 (tm-30) REVERT: L 185 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8667 (tp30) REVERT: L 188 ASP cc_start: 0.8985 (m-30) cc_final: 0.8497 (m-30) REVERT: L 198 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8893 (ttm) REVERT: L 242 GLU cc_start: 0.9065 (tt0) cc_final: 0.8644 (tt0) REVERT: L 293 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8531 (mt-10) REVERT: N 52 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: N 88 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8598 (tm-30) REVERT: N 181 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8700 (tp30) REVERT: N 184 ILE cc_start: 0.9393 (mt) cc_final: 0.9029 (mt) REVERT: N 188 ASP cc_start: 0.8873 (m-30) cc_final: 0.8356 (m-30) REVERT: N 192 GLN cc_start: 0.9345 (mm-40) cc_final: 0.9090 (tp40) REVERT: O 48 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7352 (mpt-90) REVERT: O 52 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: O 59 MET cc_start: 0.8945 (ptm) cc_final: 0.8449 (ppp) REVERT: O 62 ASP cc_start: 0.8661 (m-30) cc_final: 0.8188 (m-30) REVERT: O 174 ASN cc_start: 0.9244 (t0) cc_final: 0.8849 (m-40) REVERT: O 181 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8594 (tp30) REVERT: O 242 GLU cc_start: 0.9083 (tt0) cc_final: 0.8640 (tt0) REVERT: U 62 ASP cc_start: 0.8421 (m-30) cc_final: 0.7998 (m-30) REVERT: U 181 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8620 (tm-30) REVERT: U 184 ILE cc_start: 0.9396 (mt) cc_final: 0.9055 (mm) REVERT: U 185 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8593 (tp30) REVERT: U 188 ASP cc_start: 0.8994 (m-30) cc_final: 0.8289 (m-30) REVERT: U 242 GLU cc_start: 0.9103 (tt0) cc_final: 0.8732 (tm-30) REVERT: U 308 TRP cc_start: 0.8789 (m100) cc_final: 0.8328 (m100) REVERT: V 55 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8285 (pt0) REVERT: V 59 MET cc_start: 0.9010 (ptm) cc_final: 0.8339 (ppp) REVERT: V 181 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8355 (tp30) REVERT: V 188 ASP cc_start: 0.8937 (m-30) cc_final: 0.8693 (m-30) REVERT: V 197 ASP cc_start: 0.9033 (m-30) cc_final: 0.8818 (m-30) REVERT: V 242 GLU cc_start: 0.9189 (tt0) cc_final: 0.8890 (tt0) REVERT: V 246 TYR cc_start: 0.9164 (t80) cc_final: 0.8819 (t80) REVERT: V 308 TRP cc_start: 0.8940 (m100) cc_final: 0.8435 (m100) REVERT: W 19 LYS cc_start: 0.9387 (tmtt) cc_final: 0.8997 (tptt) REVERT: W 52 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: W 59 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8011 (ppp) REVERT: W 62 ASP cc_start: 0.8608 (m-30) cc_final: 0.8140 (m-30) REVERT: W 177 ASP cc_start: 0.8746 (m-30) cc_final: 0.8531 (m-30) REVERT: W 181 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8477 (tp30) REVERT: W 184 ILE cc_start: 0.9283 (mt) cc_final: 0.8981 (mm) REVERT: W 188 ASP cc_start: 0.8976 (m-30) cc_final: 0.8531 (m-30) REVERT: W 242 GLU cc_start: 0.9025 (tt0) cc_final: 0.8735 (tt0) REVERT: X 52 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: X 55 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: X 177 ASP cc_start: 0.8856 (m-30) cc_final: 0.8580 (m-30) REVERT: X 181 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8584 (tm-30) REVERT: X 184 ILE cc_start: 0.9336 (mt) cc_final: 0.8986 (mm) REVERT: X 185 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8631 (tp30) REVERT: X 188 ASP cc_start: 0.8881 (m-30) cc_final: 0.8215 (m-30) REVERT: X 242 GLU cc_start: 0.8838 (tt0) cc_final: 0.8567 (tt0) REVERT: X 254 MET cc_start: 0.8880 (mmm) cc_final: 0.8649 (mmm) REVERT: X 268 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8691 (p0) REVERT: Y 52 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: Y 55 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8413 (pt0) REVERT: Y 59 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8220 (ppp) REVERT: Y 181 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8694 (tm-30) REVERT: Y 184 ILE cc_start: 0.9430 (mt) cc_final: 0.9137 (mt) REVERT: Y 188 ASP cc_start: 0.8870 (m-30) cc_final: 0.8445 (m-30) REVERT: Y 242 GLU cc_start: 0.9099 (tt0) cc_final: 0.8791 (tt0) REVERT: Z 19 LYS cc_start: 0.9520 (tmtt) cc_final: 0.9233 (tptt) REVERT: Z 59 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8282 (ppp) REVERT: Z 181 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8321 (tp30) REVERT: Z 242 GLU cc_start: 0.8942 (tt0) cc_final: 0.8633 (tt0) REVERT: C 284 ASP cc_start: 0.8312 (p0) cc_final: 0.7569 (m-30) REVERT: C 342 ASP cc_start: 0.8674 (t0) cc_final: 0.8297 (t0) REVERT: C 351 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8943 (mp10) REVERT: D 268 MET cc_start: 0.7260 (mtt) cc_final: 0.6846 (mtt) REVERT: E 87 MET cc_start: 0.9013 (mmm) cc_final: 0.8661 (mmm) REVERT: E 268 MET cc_start: 0.7232 (mtt) cc_final: 0.6868 (mtt) REVERT: F 275 TRP cc_start: 0.9069 (t60) cc_final: 0.8628 (t60) REVERT: F 284 ASP cc_start: 0.8238 (p0) cc_final: 0.7371 (m-30) REVERT: F 322 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8981 (pp) REVERT: I 284 ASP cc_start: 0.8347 (p0) cc_final: 0.7484 (m-30) REVERT: I 351 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8776 (mp10) REVERT: J 284 ASP cc_start: 0.8134 (p0) cc_final: 0.7362 (m-30) REVERT: M 54 TYR cc_start: 0.9185 (t80) cc_final: 0.8896 (t80) REVERT: M 275 TRP cc_start: 0.8988 (t60) cc_final: 0.8352 (t60) REVERT: M 342 ASP cc_start: 0.8643 (t0) cc_final: 0.8351 (t0) REVERT: P 45 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8804 (pttt) REVERT: P 351 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8676 (mp10) REVERT: Q 299 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8145 (tm-30) REVERT: Q 331 MET cc_start: 0.9150 (mtp) cc_final: 0.8932 (mtp) REVERT: Q 351 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9062 (mt0) REVERT: R 87 MET cc_start: 0.9085 (mmm) cc_final: 0.8647 (mmm) REVERT: R 268 MET cc_start: 0.7152 (pmm) cc_final: 0.6126 (mpp) REVERT: R 275 TRP cc_start: 0.9009 (t60) cc_final: 0.8173 (t60) REVERT: R 342 ASP cc_start: 0.8703 (t0) cc_final: 0.8360 (t0) REVERT: S 322 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8941 (pp) REVERT: T 45 LYS cc_start: 0.9142 (ptpt) cc_final: 0.8840 (pttt) REVERT: T 342 ASP cc_start: 0.8679 (t0) cc_final: 0.8392 (t0) outliers start: 147 outliers final: 77 residues processed: 731 average time/residue: 0.6366 time to fit residues: 812.8504 Evaluate side-chains 621 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 521 time to evaluate : 6.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 125 PHE Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain K residue 52 TYR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 198 MET Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 52 TYR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 139 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 300 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 328 LEU Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 139 ILE Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 328 LEU Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 139 ILE Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 142 MET Chi-restraints excluded: chain X residue 268 ASP Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 328 LEU Chi-restraints excluded: chain Y residue 45 LYS Chi-restraints excluded: chain Y residue 52 TYR Chi-restraints excluded: chain Y residue 59 MET Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 139 ILE Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 351 GLN Chi-restraints excluded: chain R residue 392 LEU Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 322 LEU Chi-restraints excluded: chain T residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 534 optimal weight: 2.9990 chunk 345 optimal weight: 7.9990 chunk 516 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 549 optimal weight: 9.9990 chunk 589 optimal weight: 8.9990 chunk 427 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 679 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 333 ASN ** W 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 117 HIS C 340 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 73242 Z= 0.231 Angle : 0.596 11.318 98566 Z= 0.313 Chirality : 0.040 0.280 11544 Planarity : 0.003 0.040 12701 Dihedral : 4.265 22.447 9529 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.97 % Allowed : 13.85 % Favored : 84.18 % 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: 2.21 (0.09), residues: 9087 helix: 1.97 (0.06), residues: 7384 sheet: None (None), residues: 0 loop : -0.73 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP T 275 HIS 0.003 0.001 HIS F 97 PHE 0.013 0.001 PHE I 324 TYR 0.022 0.002 TYR D 260 ARG 0.011 0.001 ARG U 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 530 time to evaluate : 6.790 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: A 342 ASP cc_start: 0.8645 (t0) cc_final: 0.8355 (t0) REVERT: B 52 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8553 (m-80) REVERT: B 55 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8321 (pt0) REVERT: B 181 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8505 (tp30) REVERT: B 188 ASP cc_start: 0.8740 (m-30) cc_final: 0.8232 (m-30) REVERT: B 242 GLU cc_start: 0.8844 (tt0) cc_final: 0.8493 (tt0) REVERT: B 308 TRP cc_start: 0.8798 (m100) cc_final: 0.8495 (m100) REVERT: G 59 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8273 (ppp) REVERT: G 181 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8560 (tp30) REVERT: G 191 ARG cc_start: 0.8584 (tmm160) cc_final: 0.8362 (ttp80) REVERT: G 242 GLU cc_start: 0.9064 (tt0) cc_final: 0.8821 (tt0) REVERT: H 52 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: H 181 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8539 (tm-30) REVERT: H 188 ASP cc_start: 0.8880 (m-30) cc_final: 0.8516 (m-30) REVERT: H 242 GLU cc_start: 0.8981 (tt0) cc_final: 0.8607 (tt0) REVERT: K 52 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: K 242 GLU cc_start: 0.9033 (tt0) cc_final: 0.8747 (tm-30) REVERT: K 308 TRP cc_start: 0.8810 (m100) cc_final: 0.8304 (m100) REVERT: L 52 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: L 55 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8325 (pt0) REVERT: L 181 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8670 (tm-30) REVERT: L 185 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8691 (tp30) REVERT: L 188 ASP cc_start: 0.8968 (m-30) cc_final: 0.8473 (m-30) REVERT: L 242 GLU cc_start: 0.9124 (tt0) cc_final: 0.8742 (tt0) REVERT: L 268 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8751 (p0) REVERT: L 293 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8193 (mm-30) REVERT: N 88 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8551 (tm-30) REVERT: N 181 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8741 (tp30) REVERT: N 184 ILE cc_start: 0.9403 (mt) cc_final: 0.9047 (mt) REVERT: N 188 ASP cc_start: 0.8814 (m-30) cc_final: 0.8349 (m-30) REVERT: N 192 GLN cc_start: 0.9351 (mm-40) cc_final: 0.9105 (tp40) REVERT: N 268 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8698 (p0) REVERT: O 48 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7241 (mmt180) REVERT: O 52 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: O 59 MET cc_start: 0.9017 (ptm) cc_final: 0.8508 (ppp) REVERT: O 142 MET cc_start: 0.7254 (mtt) cc_final: 0.6762 (ttm) REVERT: O 181 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8681 (tm-30) REVERT: O 242 GLU cc_start: 0.9076 (tt0) cc_final: 0.8666 (tt0) REVERT: U 181 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8735 (tm-30) REVERT: U 184 ILE cc_start: 0.9393 (mt) cc_final: 0.9069 (mm) REVERT: U 185 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8649 (tp30) REVERT: U 188 ASP cc_start: 0.8977 (m-30) cc_final: 0.8354 (m-30) REVERT: U 242 GLU cc_start: 0.9100 (tt0) cc_final: 0.8736 (tt0) REVERT: U 308 TRP cc_start: 0.8800 (m100) cc_final: 0.8311 (m100) REVERT: V 55 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8374 (pt0) REVERT: V 59 MET cc_start: 0.9060 (ptm) cc_final: 0.8426 (ppp) REVERT: V 181 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8320 (tp30) REVERT: V 188 ASP cc_start: 0.8933 (m-30) cc_final: 0.8705 (m-30) REVERT: V 197 ASP cc_start: 0.9100 (m-30) cc_final: 0.8840 (m-30) REVERT: V 242 GLU cc_start: 0.9190 (tt0) cc_final: 0.8866 (tt0) REVERT: V 308 TRP cc_start: 0.8932 (m100) cc_final: 0.8395 (m100) REVERT: W 59 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8260 (ppp) REVERT: W 177 ASP cc_start: 0.8769 (m-30) cc_final: 0.8535 (m-30) REVERT: W 181 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8490 (tp30) REVERT: W 184 ILE cc_start: 0.9279 (mt) cc_final: 0.8979 (mm) REVERT: W 188 ASP cc_start: 0.9023 (m-30) cc_final: 0.8544 (m-30) REVERT: W 242 GLU cc_start: 0.9053 (tt0) cc_final: 0.8756 (tt0) REVERT: X 55 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: X 177 ASP cc_start: 0.8854 (m-30) cc_final: 0.8595 (m-30) REVERT: X 181 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8723 (tm-30) REVERT: X 184 ILE cc_start: 0.9336 (mt) cc_final: 0.8990 (mm) REVERT: X 185 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8693 (tp30) REVERT: X 188 ASP cc_start: 0.8854 (m-30) cc_final: 0.8226 (m-30) REVERT: X 242 GLU cc_start: 0.8865 (tt0) cc_final: 0.8441 (tt0) REVERT: X 254 MET cc_start: 0.8856 (mmm) cc_final: 0.8620 (mmm) REVERT: Y 52 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: Y 59 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8274 (ppp) REVERT: Y 181 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8753 (tm-30) REVERT: Y 184 ILE cc_start: 0.9430 (mt) cc_final: 0.9140 (mt) REVERT: Y 188 ASP cc_start: 0.8848 (m-30) cc_final: 0.8459 (m-30) REVERT: Y 242 GLU cc_start: 0.9126 (tt0) cc_final: 0.8840 (tt0) REVERT: Y 268 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8489 (p0) REVERT: Z 59 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8322 (ppp) REVERT: Z 181 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8407 (tp30) REVERT: Z 190 ILE cc_start: 0.9226 (mt) cc_final: 0.8948 (mm) REVERT: Z 198 MET cc_start: 0.9347 (ttt) cc_final: 0.9068 (ttm) REVERT: Z 242 GLU cc_start: 0.8892 (tt0) cc_final: 0.8580 (tt0) REVERT: Z 268 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8453 (p0) REVERT: C 87 MET cc_start: 0.9117 (mmm) cc_final: 0.8899 (mmp) REVERT: C 342 ASP cc_start: 0.8730 (t0) cc_final: 0.8461 (t0) REVERT: C 351 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8923 (mp10) REVERT: D 268 MET cc_start: 0.7227 (mtt) cc_final: 0.6523 (mtt) REVERT: D 275 TRP cc_start: 0.8317 (t-100) cc_final: 0.7811 (t-100) REVERT: E 87 MET cc_start: 0.9091 (mmm) cc_final: 0.8660 (mmm) REVERT: E 268 MET cc_start: 0.7304 (mtt) cc_final: 0.6912 (mtt) REVERT: E 342 ASP cc_start: 0.8711 (t0) cc_final: 0.8428 (t0) REVERT: F 275 TRP cc_start: 0.9110 (t60) cc_final: 0.8660 (t60) REVERT: F 284 ASP cc_start: 0.8322 (p0) cc_final: 0.7400 (m-30) REVERT: I 344 MET cc_start: 0.8834 (ttp) cc_final: 0.8594 (ttm) REVERT: I 351 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8780 (mp10) REVERT: J 275 TRP cc_start: 0.9119 (t60) cc_final: 0.8848 (t60) REVERT: J 284 ASP cc_start: 0.8187 (p0) cc_final: 0.7429 (m-30) REVERT: M 275 TRP cc_start: 0.9023 (t60) cc_final: 0.8391 (t60) REVERT: M 342 ASP cc_start: 0.8661 (t0) cc_final: 0.8359 (t0) REVERT: P 45 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8827 (pttt) REVERT: P 275 TRP cc_start: 0.9059 (t60) cc_final: 0.8475 (t60) REVERT: P 284 ASP cc_start: 0.8375 (p0) cc_final: 0.7472 (m-30) REVERT: P 351 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8709 (mp10) REVERT: Q 268 MET cc_start: 0.6853 (mtt) cc_final: 0.6451 (mtt) REVERT: Q 299 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8173 (tm-30) REVERT: Q 351 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.9060 (mt0) REVERT: R 87 MET cc_start: 0.9110 (mmm) cc_final: 0.8614 (mmm) REVERT: R 268 MET cc_start: 0.7359 (pmm) cc_final: 0.6743 (mpp) REVERT: R 275 TRP cc_start: 0.9065 (t60) cc_final: 0.8300 (t60) REVERT: R 342 ASP cc_start: 0.8738 (t0) cc_final: 0.8449 (t0) REVERT: S 275 TRP cc_start: 0.8572 (t-100) cc_final: 0.8034 (t-100) REVERT: T 275 TRP cc_start: 0.9062 (t60) cc_final: 0.8398 (t60) REVERT: T 342 ASP cc_start: 0.8737 (t0) cc_final: 0.8437 (t0) outliers start: 160 outliers final: 96 residues processed: 672 average time/residue: 0.6415 time to fit residues: 766.0317 Evaluate side-chains 616 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 501 time to evaluate : 6.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 125 PHE Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain K residue 52 TYR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 268 ASP Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 268 ASP Chi-restraints excluded: chain N residue 328 LEU Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 139 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 300 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 328 LEU Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 139 ILE Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 284 LEU Chi-restraints excluded: chain V residue 328 LEU Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 139 ILE Chi-restraints excluded: chain W residue 284 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 59 MET Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 142 MET Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 198 MET Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 328 LEU Chi-restraints excluded: chain Y residue 45 LYS Chi-restraints excluded: chain Y residue 52 TYR Chi-restraints excluded: chain Y residue 59 MET Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 268 ASP Chi-restraints excluded: chain Y residue 284 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Y residue 328 LEU Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 139 ILE Chi-restraints excluded: chain Z residue 268 ASP Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 351 GLN Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 392 LEU Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 322 LEU Chi-restraints excluded: chain T residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 786 optimal weight: 0.9980 chunk 828 optimal weight: 0.9990 chunk 755 optimal weight: 1.9990 chunk 805 optimal weight: 7.9990 chunk 484 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 632 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 chunk 728 optimal weight: 5.9990 chunk 761 optimal weight: 0.9980 chunk 802 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS K 117 HIS ** N 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 73242 Z= 0.171 Angle : 0.571 12.227 98566 Z= 0.297 Chirality : 0.039 0.259 11544 Planarity : 0.003 0.045 12701 Dihedral : 4.226 21.026 9529 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.56 % Allowed : 14.28 % Favored : 84.16 % 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: 2.31 (0.09), residues: 9087 helix: 2.02 (0.06), residues: 7384 sheet: None (None), residues: 0 loop : -0.62 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 275 HIS 0.002 0.001 HIS M 95 PHE 0.013 0.001 PHE S 324 TYR 0.023 0.002 TYR S 54 ARG 0.012 0.001 ARG U 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 567 time to evaluate : 6.773 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: A 257 TYR cc_start: 0.9225 (t80) cc_final: 0.8976 (t80) REVERT: A 342 ASP cc_start: 0.8592 (t0) cc_final: 0.8272 (t0) REVERT: B 52 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8490 (m-80) REVERT: B 55 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8259 (pt0) REVERT: B 62 ASP cc_start: 0.8677 (m-30) cc_final: 0.8327 (m-30) REVERT: B 181 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8468 (tp30) REVERT: B 188 ASP cc_start: 0.8745 (m-30) cc_final: 0.8215 (m-30) REVERT: B 242 GLU cc_start: 0.8796 (tt0) cc_final: 0.8451 (tt0) REVERT: B 308 TRP cc_start: 0.8756 (m100) cc_final: 0.8418 (m100) REVERT: G 59 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8340 (ppp) REVERT: G 181 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8570 (tp30) REVERT: G 191 ARG cc_start: 0.8570 (tmm160) cc_final: 0.8338 (ttp80) REVERT: G 242 GLU cc_start: 0.9054 (tt0) cc_final: 0.8785 (tt0) REVERT: G 308 TRP cc_start: 0.8988 (m100) cc_final: 0.8284 (m100) REVERT: H 52 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: H 181 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8502 (tm-30) REVERT: H 188 ASP cc_start: 0.8836 (m-30) cc_final: 0.8457 (m-30) REVERT: H 242 GLU cc_start: 0.8950 (tt0) cc_final: 0.8608 (tt0) REVERT: H 308 TRP cc_start: 0.8766 (m100) cc_final: 0.8492 (m100) REVERT: K 52 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: K 242 GLU cc_start: 0.8981 (tt0) cc_final: 0.8718 (tm-30) REVERT: K 308 TRP cc_start: 0.8748 (m100) cc_final: 0.8302 (m100) REVERT: L 52 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: L 55 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8327 (pt0) REVERT: L 59 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8146 (ppp) REVERT: L 181 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8647 (tm-30) REVERT: L 185 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8690 (tp30) REVERT: L 188 ASP cc_start: 0.8914 (m-30) cc_final: 0.8372 (m-30) REVERT: L 242 GLU cc_start: 0.9095 (tt0) cc_final: 0.8734 (tt0) REVERT: L 268 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8738 (p0) REVERT: L 308 TRP cc_start: 0.8813 (m100) cc_final: 0.8511 (m100) REVERT: N 88 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8567 (tm-30) REVERT: N 181 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8717 (tp30) REVERT: N 184 ILE cc_start: 0.9402 (mt) cc_final: 0.9050 (mt) REVERT: N 188 ASP cc_start: 0.8850 (m-30) cc_final: 0.8393 (m-30) REVERT: N 268 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8707 (p0) REVERT: O 48 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7019 (mtt-85) REVERT: O 52 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: O 59 MET cc_start: 0.8978 (ptm) cc_final: 0.8443 (ppp) REVERT: O 62 ASP cc_start: 0.8726 (m-30) cc_final: 0.8296 (m-30) REVERT: O 181 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8654 (tm-30) REVERT: O 242 GLU cc_start: 0.9064 (tt0) cc_final: 0.8615 (tt0) REVERT: U 62 ASP cc_start: 0.8443 (m-30) cc_final: 0.8040 (m-30) REVERT: U 181 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8709 (tm-30) REVERT: U 184 ILE cc_start: 0.9384 (mt) cc_final: 0.9063 (mm) REVERT: U 185 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8649 (tp30) REVERT: U 188 ASP cc_start: 0.8981 (m-30) cc_final: 0.8296 (m-30) REVERT: U 242 GLU cc_start: 0.9078 (tt0) cc_final: 0.8756 (tt0) REVERT: U 308 TRP cc_start: 0.8758 (m100) cc_final: 0.8269 (m100) REVERT: V 55 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8325 (pt0) REVERT: V 59 MET cc_start: 0.9034 (ptm) cc_final: 0.8414 (ppp) REVERT: V 181 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8378 (tp30) REVERT: V 188 ASP cc_start: 0.8937 (m-30) cc_final: 0.8563 (m-30) REVERT: V 197 ASP cc_start: 0.9103 (m-30) cc_final: 0.8880 (m-30) REVERT: V 242 GLU cc_start: 0.9158 (tt0) cc_final: 0.8847 (tt0) REVERT: V 246 TYR cc_start: 0.9151 (t80) cc_final: 0.8927 (t80) REVERT: V 308 TRP cc_start: 0.8924 (m100) cc_final: 0.8398 (m100) REVERT: W 59 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8214 (ppp) REVERT: W 177 ASP cc_start: 0.8750 (m-30) cc_final: 0.8517 (m-30) REVERT: W 181 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8435 (tp30) REVERT: W 184 ILE cc_start: 0.9275 (mt) cc_final: 0.8984 (mm) REVERT: W 188 ASP cc_start: 0.8972 (m-30) cc_final: 0.8494 (m-30) REVERT: W 242 GLU cc_start: 0.9011 (tt0) cc_final: 0.8755 (tt0) REVERT: X 177 ASP cc_start: 0.8850 (m-30) cc_final: 0.8560 (m-30) REVERT: X 181 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8611 (tm-30) REVERT: X 184 ILE cc_start: 0.9324 (mt) cc_final: 0.8969 (mm) REVERT: X 185 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8669 (tp30) REVERT: X 188 ASP cc_start: 0.8889 (m-30) cc_final: 0.8229 (m-30) REVERT: X 242 GLU cc_start: 0.8860 (tt0) cc_final: 0.8432 (tt0) REVERT: X 254 MET cc_start: 0.8873 (mmm) cc_final: 0.8644 (mmm) REVERT: X 268 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8705 (p0) REVERT: Y 59 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8231 (ppp) REVERT: Y 181 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8694 (tm-30) REVERT: Y 184 ILE cc_start: 0.9433 (mt) cc_final: 0.9139 (mt) REVERT: Y 188 ASP cc_start: 0.8850 (m-30) cc_final: 0.8440 (m-30) REVERT: Y 242 GLU cc_start: 0.9102 (tt0) cc_final: 0.8813 (tt0) REVERT: Y 268 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8461 (p0) REVERT: Z 59 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8271 (ppp) REVERT: Z 181 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8362 (tp30) REVERT: Z 190 ILE cc_start: 0.9234 (mt) cc_final: 0.8936 (mm) REVERT: Z 242 GLU cc_start: 0.8865 (tt0) cc_final: 0.8569 (tt0) REVERT: Z 268 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8442 (p0) REVERT: C 275 TRP cc_start: 0.9016 (t60) cc_final: 0.8416 (t60) REVERT: C 284 ASP cc_start: 0.8276 (p0) cc_final: 0.7546 (m-30) REVERT: C 342 ASP cc_start: 0.8696 (t0) cc_final: 0.8379 (t0) REVERT: C 351 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8932 (mp10) REVERT: D 268 MET cc_start: 0.7272 (mtt) cc_final: 0.6516 (mtt) REVERT: D 275 TRP cc_start: 0.8328 (t-100) cc_final: 0.7813 (t-100) REVERT: E 87 MET cc_start: 0.9059 (mmm) cc_final: 0.8646 (mmm) REVERT: E 268 MET cc_start: 0.7242 (mtt) cc_final: 0.6844 (mtt) REVERT: F 275 TRP cc_start: 0.9122 (t60) cc_final: 0.8708 (t60) REVERT: F 284 ASP cc_start: 0.8258 (p0) cc_final: 0.7364 (m-30) REVERT: I 268 MET cc_start: 0.6266 (mtt) cc_final: 0.5263 (ttt) REVERT: I 275 TRP cc_start: 0.8009 (t-100) cc_final: 0.7713 (t-100) REVERT: I 284 ASP cc_start: 0.8352 (p0) cc_final: 0.7478 (m-30) REVERT: I 342 ASP cc_start: 0.8678 (t0) cc_final: 0.8382 (t0) REVERT: I 344 MET cc_start: 0.8822 (ttp) cc_final: 0.8553 (ttm) REVERT: I 351 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8754 (mp10) REVERT: J 275 TRP cc_start: 0.9099 (t60) cc_final: 0.8761 (t60) REVERT: J 284 ASP cc_start: 0.8125 (p0) cc_final: 0.7452 (m-30) REVERT: M 54 TYR cc_start: 0.9181 (t80) cc_final: 0.8917 (t80) REVERT: M 342 ASP cc_start: 0.8631 (t0) cc_final: 0.8315 (t0) REVERT: P 45 LYS cc_start: 0.9124 (ptpt) cc_final: 0.8868 (pttt) REVERT: P 275 TRP cc_start: 0.9058 (t60) cc_final: 0.8491 (t60) REVERT: P 284 ASP cc_start: 0.8284 (p0) cc_final: 0.7310 (m-30) REVERT: P 351 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8704 (mp10) REVERT: Q 299 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8110 (tm-30) REVERT: R 87 MET cc_start: 0.9050 (mmm) cc_final: 0.8595 (mmm) REVERT: R 268 MET cc_start: 0.7453 (pmm) cc_final: 0.7137 (mpp) REVERT: R 275 TRP cc_start: 0.9071 (t60) cc_final: 0.8398 (t60) REVERT: R 342 ASP cc_start: 0.8690 (t0) cc_final: 0.8357 (t0) REVERT: T 268 MET cc_start: 0.7149 (mpp) cc_final: 0.5644 (mpp) REVERT: T 275 TRP cc_start: 0.9055 (t60) cc_final: 0.8210 (t60) REVERT: T 342 ASP cc_start: 0.8705 (t0) cc_final: 0.8414 (t0) outliers start: 127 outliers final: 81 residues processed: 672 average time/residue: 0.6279 time to fit residues: 745.8240 Evaluate side-chains 618 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 519 time to evaluate : 6.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 125 PHE Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain K residue 52 TYR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 268 ASP Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 268 ASP Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 139 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 300 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 328 LEU Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 139 ILE Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 284 LEU Chi-restraints excluded: chain V residue 328 LEU Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 139 ILE Chi-restraints excluded: chain W residue 284 LEU Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 198 MET Chi-restraints excluded: chain X residue 268 ASP Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain X residue 298 LEU Chi-restraints excluded: chain X residue 328 LEU Chi-restraints excluded: chain Y residue 59 MET Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 268 ASP Chi-restraints excluded: chain Y residue 284 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 139 ILE Chi-restraints excluded: chain Z residue 268 ASP Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain R residue 392 LEU Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 322 LEU Chi-restraints excluded: chain T residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 529 optimal weight: 4.9990 chunk 851 optimal weight: 1.9990 chunk 519 optimal weight: 3.9990 chunk 404 optimal weight: 6.9990 chunk 592 optimal weight: 5.9990 chunk 893 optimal weight: 0.1980 chunk 822 optimal weight: 4.9990 chunk 711 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 549 optimal weight: 0.1980 chunk 436 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 HIS ** W 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 73242 Z= 0.176 Angle : 0.581 12.712 98566 Z= 0.302 Chirality : 0.039 0.284 11544 Planarity : 0.003 0.048 12701 Dihedral : 4.196 20.106 9529 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.37 % Allowed : 14.45 % Favored : 84.18 % 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: 2.40 (0.09), residues: 9087 helix: 2.11 (0.06), residues: 7306 sheet: None (None), residues: 0 loop : -0.62 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP S 275 HIS 0.003 0.001 HIS U 316 PHE 0.013 0.001 PHE J 324 TYR 0.023 0.002 TYR A 260 ARG 0.013 0.001 ARG U 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 558 time to evaluate : 6.821 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: A 257 TYR cc_start: 0.9219 (t80) cc_final: 0.8983 (t80) REVERT: A 342 ASP cc_start: 0.8608 (t0) cc_final: 0.8305 (t0) REVERT: A 348 MET cc_start: 0.9033 (ptp) cc_final: 0.8623 (pmm) REVERT: B 21 MET cc_start: 0.8382 (ttt) cc_final: 0.8104 (ttt) REVERT: B 52 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: B 55 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8195 (pt0) REVERT: B 62 ASP cc_start: 0.8669 (m-30) cc_final: 0.8297 (m-30) REVERT: B 181 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8464 (tp30) REVERT: B 188 ASP cc_start: 0.8729 (m-30) cc_final: 0.8190 (m-30) REVERT: B 242 GLU cc_start: 0.8778 (tt0) cc_final: 0.8447 (tt0) REVERT: B 308 TRP cc_start: 0.8729 (m100) cc_final: 0.8414 (m100) REVERT: G 59 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8348 (ppp) REVERT: G 181 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8567 (tm-30) REVERT: G 191 ARG cc_start: 0.8546 (tmm160) cc_final: 0.8322 (ttp80) REVERT: G 242 GLU cc_start: 0.9056 (tt0) cc_final: 0.8738 (tt0) REVERT: H 52 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8157 (m-80) REVERT: H 181 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8511 (tm-30) REVERT: H 188 ASP cc_start: 0.8833 (m-30) cc_final: 0.8425 (m-30) REVERT: H 242 GLU cc_start: 0.8935 (tt0) cc_final: 0.8595 (tt0) REVERT: H 308 TRP cc_start: 0.8755 (m100) cc_final: 0.8458 (m100) REVERT: K 242 GLU cc_start: 0.8991 (tt0) cc_final: 0.8749 (tm-30) REVERT: K 308 TRP cc_start: 0.8742 (m100) cc_final: 0.8303 (m100) REVERT: L 52 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: L 55 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8294 (pt0) REVERT: L 59 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8148 (ppp) REVERT: L 181 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8645 (tm-30) REVERT: L 185 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8692 (tp30) REVERT: L 188 ASP cc_start: 0.8907 (m-30) cc_final: 0.8363 (m-30) REVERT: L 242 GLU cc_start: 0.9077 (tt0) cc_final: 0.8725 (tt0) REVERT: L 268 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8744 (p0) REVERT: L 308 TRP cc_start: 0.8793 (m100) cc_final: 0.8547 (m100) REVERT: N 88 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8572 (tm-30) REVERT: N 181 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8683 (tp30) REVERT: N 184 ILE cc_start: 0.9401 (mt) cc_final: 0.9051 (mt) REVERT: N 188 ASP cc_start: 0.8848 (m-30) cc_final: 0.8364 (m-30) REVERT: N 192 GLN cc_start: 0.9347 (mm-40) cc_final: 0.9102 (tp40) REVERT: N 268 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8711 (p0) REVERT: O 52 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: O 59 MET cc_start: 0.8986 (ptm) cc_final: 0.8493 (ppp) REVERT: O 181 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8667 (tm-30) REVERT: O 242 GLU cc_start: 0.9078 (tt0) cc_final: 0.8615 (tt0) REVERT: U 62 ASP cc_start: 0.8443 (m-30) cc_final: 0.8038 (m-30) REVERT: U 181 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8706 (tm-30) REVERT: U 184 ILE cc_start: 0.9374 (mt) cc_final: 0.9052 (mm) REVERT: U 185 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8600 (tp30) REVERT: U 188 ASP cc_start: 0.8976 (m-30) cc_final: 0.8280 (m-30) REVERT: U 242 GLU cc_start: 0.9049 (tt0) cc_final: 0.8686 (tt0) REVERT: U 308 TRP cc_start: 0.8772 (m100) cc_final: 0.8278 (m100) REVERT: V 55 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8326 (pt0) REVERT: V 59 MET cc_start: 0.9041 (ptm) cc_final: 0.8424 (ppp) REVERT: V 181 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8363 (tp30) REVERT: V 188 ASP cc_start: 0.8936 (m-30) cc_final: 0.8696 (m-30) REVERT: V 197 ASP cc_start: 0.9096 (m-30) cc_final: 0.8880 (m-30) REVERT: V 242 GLU cc_start: 0.9167 (tt0) cc_final: 0.8825 (tt0) REVERT: V 246 TYR cc_start: 0.9128 (t80) cc_final: 0.8916 (t80) REVERT: V 308 TRP cc_start: 0.8911 (m100) cc_final: 0.8375 (m100) REVERT: W 19 LYS cc_start: 0.9388 (tmtt) cc_final: 0.8995 (tptt) REVERT: W 59 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8253 (ppp) REVERT: W 125 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: W 177 ASP cc_start: 0.8745 (m-30) cc_final: 0.8519 (m-30) REVERT: W 181 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8484 (tp30) REVERT: W 184 ILE cc_start: 0.9280 (mt) cc_final: 0.8996 (mm) REVERT: W 188 ASP cc_start: 0.8953 (m-30) cc_final: 0.8481 (m-30) REVERT: W 242 GLU cc_start: 0.8984 (tt0) cc_final: 0.8749 (tt0) REVERT: X 177 ASP cc_start: 0.8848 (m-30) cc_final: 0.8555 (m-30) REVERT: X 181 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8591 (tm-30) REVERT: X 184 ILE cc_start: 0.9317 (mt) cc_final: 0.8961 (mm) REVERT: X 185 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8639 (tp30) REVERT: X 188 ASP cc_start: 0.8887 (m-30) cc_final: 0.8215 (m-30) REVERT: X 242 GLU cc_start: 0.8846 (tt0) cc_final: 0.8450 (tt0) REVERT: X 254 MET cc_start: 0.8864 (mmm) cc_final: 0.8642 (mmm) REVERT: X 268 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8699 (p0) REVERT: Y 59 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8273 (ppp) REVERT: Y 181 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8690 (tm-30) REVERT: Y 184 ILE cc_start: 0.9432 (mt) cc_final: 0.9137 (mt) REVERT: Y 188 ASP cc_start: 0.8846 (m-30) cc_final: 0.8434 (m-30) REVERT: Y 242 GLU cc_start: 0.9095 (tt0) cc_final: 0.8792 (tt0) REVERT: Y 268 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8472 (p0) REVERT: Y 308 TRP cc_start: 0.8794 (m100) cc_final: 0.8072 (m100) REVERT: Z 59 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8278 (ppp) REVERT: Z 181 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8332 (tp30) REVERT: Z 190 ILE cc_start: 0.9250 (mt) cc_final: 0.8997 (mm) REVERT: Z 242 GLU cc_start: 0.8844 (tt0) cc_final: 0.8561 (tt0) REVERT: Z 268 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8447 (p0) REVERT: C 275 TRP cc_start: 0.9052 (t60) cc_final: 0.8471 (t60) REVERT: C 284 ASP cc_start: 0.8244 (p0) cc_final: 0.7509 (m-30) REVERT: C 342 ASP cc_start: 0.8688 (t0) cc_final: 0.8300 (t0) REVERT: C 351 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8924 (mp10) REVERT: D 268 MET cc_start: 0.7214 (mtt) cc_final: 0.6875 (mtt) REVERT: E 87 MET cc_start: 0.9060 (mmm) cc_final: 0.8668 (mmm) REVERT: E 268 MET cc_start: 0.7270 (mtt) cc_final: 0.6869 (mtt) REVERT: F 275 TRP cc_start: 0.9118 (t60) cc_final: 0.8758 (t60) REVERT: F 284 ASP cc_start: 0.8253 (p0) cc_final: 0.7356 (m-30) REVERT: F 322 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8989 (pp) REVERT: F 344 MET cc_start: 0.8594 (ttp) cc_final: 0.7768 (ttm) REVERT: F 348 MET cc_start: 0.9073 (ptp) cc_final: 0.8213 (pmm) REVERT: I 268 MET cc_start: 0.6013 (mtt) cc_final: 0.5321 (ttt) REVERT: I 275 TRP cc_start: 0.8046 (t-100) cc_final: 0.7755 (t-100) REVERT: I 342 ASP cc_start: 0.8677 (t0) cc_final: 0.8401 (t0) REVERT: I 344 MET cc_start: 0.8810 (ttp) cc_final: 0.8564 (ttm) REVERT: I 351 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8561 (mp10) REVERT: J 284 ASP cc_start: 0.8082 (p0) cc_final: 0.7452 (m-30) REVERT: M 54 TYR cc_start: 0.9180 (t80) cc_final: 0.8907 (t80) REVERT: M 275 TRP cc_start: 0.9070 (t60) cc_final: 0.8789 (t60) REVERT: M 342 ASP cc_start: 0.8651 (t0) cc_final: 0.8354 (t0) REVERT: P 45 LYS cc_start: 0.9114 (ptpt) cc_final: 0.8781 (pttt) REVERT: P 244 ASP cc_start: 0.8817 (m-30) cc_final: 0.8530 (m-30) REVERT: P 275 TRP cc_start: 0.9071 (t60) cc_final: 0.8517 (t60) REVERT: P 284 ASP cc_start: 0.8274 (p0) cc_final: 0.7287 (m-30) REVERT: P 348 MET cc_start: 0.8967 (ptp) cc_final: 0.8676 (pmm) REVERT: P 351 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8654 (mp10) REVERT: Q 257 TYR cc_start: 0.9370 (t80) cc_final: 0.8976 (t80) REVERT: Q 299 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8103 (tm-30) REVERT: R 87 MET cc_start: 0.9045 (mmm) cc_final: 0.8596 (mmm) REVERT: R 275 TRP cc_start: 0.9100 (t60) cc_final: 0.8872 (t60) REVERT: R 331 MET cc_start: 0.9085 (mtm) cc_final: 0.8869 (mtp) REVERT: R 342 ASP cc_start: 0.8677 (t0) cc_final: 0.8368 (t0) REVERT: S 275 TRP cc_start: 0.9026 (t60) cc_final: 0.8565 (t60) REVERT: T 45 LYS cc_start: 0.9106 (ptpt) cc_final: 0.8848 (pttt) REVERT: T 275 TRP cc_start: 0.9057 (t60) cc_final: 0.8434 (t60) REVERT: T 342 ASP cc_start: 0.8702 (t0) cc_final: 0.8422 (t0) outliers start: 111 outliers final: 78 residues processed: 649 average time/residue: 0.6275 time to fit residues: 718.9632 Evaluate side-chains 622 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 525 time to evaluate : 6.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 125 PHE Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 268 ASP Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 268 ASP Chi-restraints excluded: chain O residue 52 TYR Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 139 ILE Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 300 GLU Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 328 LEU Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 139 ILE Chi-restraints excluded: chain V residue 144 ILE Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 284 LEU Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 59 MET Chi-restraints excluded: chain W residue 125 PHE Chi-restraints excluded: chain W residue 139 ILE Chi-restraints excluded: chain W residue 142 MET Chi-restraints excluded: chain W residue 284 LEU Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain X residue 139 ILE Chi-restraints excluded: chain X residue 198 MET Chi-restraints excluded: chain X residue 268 ASP Chi-restraints excluded: chain X residue 284 LEU Chi-restraints excluded: chain Y residue 59 MET Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 268 ASP Chi-restraints excluded: chain Y residue 284 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Z residue 28 ILE Chi-restraints excluded: chain Z residue 59 MET Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 139 ILE Chi-restraints excluded: chain Z residue 268 ASP Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 351 GLN Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain R residue 392 LEU Chi-restraints excluded: chain S residue 268 MET Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain T residue 139 ILE Chi-restraints excluded: chain T residue 322 LEU Chi-restraints excluded: chain T residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 565 optimal weight: 1.9990 chunk 758 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 656 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 712 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 chunk 731 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.045058 restraints weight = 390632.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046233 restraints weight = 245730.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.047031 restraints weight = 175895.780| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 73242 Z= 0.165 Angle : 0.580 12.700 98566 Z= 0.299 Chirality : 0.039 0.273 11544 Planarity : 0.003 0.049 12701 Dihedral : 4.151 21.383 9529 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.37 % Allowed : 14.56 % Favored : 84.07 % 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: 2.47 (0.09), residues: 9087 helix: 2.14 (0.06), residues: 7332 sheet: None (None), residues: 0 loop : -0.55 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 275 HIS 0.002 0.001 HIS C 95 PHE 0.016 0.001 PHE C 324 TYR 0.023 0.002 TYR A 260 ARG 0.013 0.001 ARG U 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16042.13 seconds wall clock time: 280 minutes 16.03 seconds (16816.03 seconds total)