Starting phenix.real_space_refine on Tue Mar 12 12:20:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7y_33053/03_2024/7x7y_33053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7y_33053/03_2024/7x7y_33053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7y_33053/03_2024/7x7y_33053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7y_33053/03_2024/7x7y_33053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7y_33053/03_2024/7x7y_33053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7y_33053/03_2024/7x7y_33053.pdb" } resolution = 3.8 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= 0.002 sd= 0.061 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 389 5.16 5 C 39504 2.51 5 N 10986 2.21 5 O 12128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 63007 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4017 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 12, 'TRANS': 516} Chain: "B" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3891 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 9, 'TRANS': 507} Chain: "D" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3902 Classifications: {'peptide': 516} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 500} Chain: "E" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4000 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 17, 'TRANS': 502} Chain: "G" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3979 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain: "H" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3987 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "Q" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3987 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 508} Chain: "Z" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3996 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "a" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3786 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 11, 'TRANS': 487} Chain breaks: 2 Chain: "b" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3891 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 9, 'TRANS': 507} Chain: "d" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3622 Classifications: {'peptide': 479} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 465} Chain breaks: 3 Chain: "e" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4000 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 17, 'TRANS': 502} Chain: "g" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3979 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain: "h" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3987 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "q" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3987 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 508} Chain: "z" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3996 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Time building chain proxies: 23.90, per 1000 atoms: 0.38 Number of scatterers: 63007 At special positions: 0 Unit cell: (194.02, 200.25, 184.23, 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 389 16.00 O 12128 8.00 N 10986 7.00 C 39504 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 - 3.50 Amino acid : False - 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: 18.21 Conformation dependent library (CDL) restraints added in 9.5 seconds 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15372 Finding SS restraints... Secondary structure from input PDB file: 319 helices and 92 sheets defined 55.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 14 through 34 removed outlier: 3.853A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 71 through 86 removed outlier: 3.671A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 109 removed outlier: 3.523A pdb=" N LEU A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 removed outlier: 3.553A pdb=" N GLU A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 4.129A pdb=" N ALA A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.514A pdb=" N ILE A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 3.899A pdb=" N PHE A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 280 removed outlier: 3.769A pdb=" N ASP A 261 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.900A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.604A pdb=" N ARG A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 405 removed outlier: 3.837A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.565A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 434 through 445 removed outlier: 3.548A pdb=" N PHE A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.503A pdb=" N LEU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 removed outlier: 3.665A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.634A pdb=" N SER B 60 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.656A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 118 removed outlier: 3.574A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 removed outlier: 3.548A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.501A pdb=" N ASN B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 4.457A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 182 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.850A pdb=" N ALA B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.626A pdb=" N ALA B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.834A pdb=" N LEU B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.670A pdb=" N GLN B 399 " --> pdb=" O CYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.572A pdb=" N MET B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 removed outlier: 3.935A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.557A pdb=" N THR B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 471 removed outlier: 3.502A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.597A pdb=" N ILE B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.750A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.536A pdb=" N LYS D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.666A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 126 removed outlier: 3.594A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 removed outlier: 3.571A pdb=" N GLN D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.811A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Proline residue: D 185 - end of helix removed outlier: 3.630A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 268 through 294 removed outlier: 3.519A pdb=" N GLU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 289 " --> pdb=" O ASN D 285 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 removed outlier: 3.581A pdb=" N LEU D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.508A pdb=" N PHE D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 443 removed outlier: 3.542A pdb=" N ILE D 430 " --> pdb=" O GLY D 426 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 457 Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 487 removed outlier: 3.603A pdb=" N VAL D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 478 " --> pdb=" O ILE D 474 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 27 through 47 removed outlier: 3.546A pdb=" N ALA E 31 " --> pdb=" O MET E 27 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 32 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 3.599A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 removed outlier: 3.503A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER E 93 " --> pdb=" O MET E 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 123 removed outlier: 3.687A pdb=" N VAL E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 149 removed outlier: 3.544A pdb=" N ARG E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 149 " --> pdb=" O HIS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 172 removed outlier: 3.588A pdb=" N ALA E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 195 removed outlier: 3.619A pdb=" N ALA E 184 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 186 " --> pdb=" O GLN E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 268 through 294 removed outlier: 3.550A pdb=" N TYR E 272 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 315 removed outlier: 3.564A pdb=" N ASN E 309 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.847A pdb=" N LEU E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 332 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 346 removed outlier: 3.629A pdb=" N LEU E 346 " --> pdb=" O PHE E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 413 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 436 through 438 No H-bonds generated for 'chain 'E' and resid 436 through 438' Processing helix chain 'E' and resid 442 through 453 Processing helix chain 'E' and resid 454 through 464 removed outlier: 3.556A pdb=" N SER E 461 " --> pdb=" O PRO E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 479 removed outlier: 3.629A pdb=" N GLU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.759A pdb=" N GLN E 502 " --> pdb=" O ASP E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 527 removed outlier: 3.520A pdb=" N ILE E 515 " --> pdb=" O LYS E 511 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 521 " --> pdb=" O LEU E 517 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 38 removed outlier: 4.139A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE G 27 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 70 removed outlier: 3.554A pdb=" N GLU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 91 removed outlier: 3.759A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 106 removed outlier: 3.719A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.731A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 removed outlier: 3.781A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 removed outlier: 3.707A pdb=" N SER G 166 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 163 through 167' Processing helix chain 'G' and resid 168 through 184 removed outlier: 3.723A pdb=" N ASN G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 260 through 285 removed outlier: 3.622A pdb=" N ARG G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU G 278 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP G 281 " --> pdb=" O GLN G 277 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 306 removed outlier: 3.868A pdb=" N TYR G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 removed outlier: 3.684A pdb=" N ARG G 389 " --> pdb=" O SER G 385 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP G 393 " --> pdb=" O ARG G 389 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA G 394 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP G 404 " --> pdb=" O ASN G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 426 Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 433 through 444 removed outlier: 3.577A pdb=" N VAL G 440 " --> pdb=" O PRO G 436 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA G 441 " --> pdb=" O TYR G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.698A pdb=" N CYS G 455 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 473 removed outlier: 3.579A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA G 468 " --> pdb=" O THR G 464 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS G 469 " --> pdb=" O SER G 465 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS G 470 " --> pdb=" O LEU G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 518 removed outlier: 3.587A pdb=" N GLN G 504 " --> pdb=" O ALA G 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 38 removed outlier: 3.576A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL H 31 " --> pdb=" O SER H 27 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 70 removed outlier: 3.515A pdb=" N LYS H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 90 removed outlier: 3.804A pdb=" N THR H 78 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 108 removed outlier: 3.728A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 108 " --> pdb=" O PHE H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.550A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.687A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 149 removed outlier: 3.721A pdb=" N VAL H 149 " --> pdb=" O ALA H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 163 removed outlier: 4.292A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 185 removed outlier: 3.943A pdb=" N LYS H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.746A pdb=" N TYR H 263 " --> pdb=" O THR H 259 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 277 " --> pdb=" O ILE H 273 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 removed outlier: 3.668A pdb=" N THR H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 352 through 356 removed outlier: 3.665A pdb=" N GLU H 356 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 402 removed outlier: 3.609A pdb=" N MET H 382 " --> pdb=" O ALA H 378 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER H 388 " --> pdb=" O GLU H 384 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET H 394 " --> pdb=" O HIS H 390 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE H 400 " --> pdb=" O VAL H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 425 removed outlier: 3.520A pdb=" N GLU H 415 " --> pdb=" O ALA H 411 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 442 removed outlier: 3.726A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 453 removed outlier: 3.628A pdb=" N LEU H 449 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 470 removed outlier: 3.728A pdb=" N GLN H 470 " --> pdb=" O ALA H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 515 removed outlier: 3.777A pdb=" N ILE H 513 " --> pdb=" O ALA H 509 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 45 removed outlier: 3.564A pdb=" N CYS Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 removed outlier: 3.547A pdb=" N ILE Q 72 " --> pdb=" O ASP Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 94 removed outlier: 3.711A pdb=" N MET Q 85 " --> pdb=" O PRO Q 81 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 122 removed outlier: 3.656A pdb=" N VAL Q 104 " --> pdb=" O GLY Q 100 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU Q 105 " --> pdb=" O THR Q 101 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 116 " --> pdb=" O LEU Q 112 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY Q 122 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 156 through 169 removed outlier: 3.914A pdb=" N ARG Q 165 " --> pdb=" O SER Q 161 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 191 removed outlier: 3.723A pdb=" N LYS Q 181 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA Q 186 " --> pdb=" O LEU Q 182 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER Q 189 " --> pdb=" O GLN Q 185 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 262 through 286 removed outlier: 3.814A pdb=" N MET Q 266 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 removed outlier: 3.870A pdb=" N HIS Q 303 " --> pdb=" O ASP Q 299 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR Q 304 " --> pdb=" O MET Q 300 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN Q 306 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 326 removed outlier: 3.580A pdb=" N LEU Q 321 " --> pdb=" O SER Q 317 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU Q 324 " --> pdb=" O ASP Q 320 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS Q 326 " --> pdb=" O ARG Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 403 removed outlier: 3.522A pdb=" N ASP Q 387 " --> pdb=" O ASN Q 383 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE Q 399 " --> pdb=" O GLY Q 395 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Q 401 " --> pdb=" O ASN Q 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.557A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 444 Processing helix chain 'Q' and resid 446 through 456 Processing helix chain 'Q' and resid 459 through 473 removed outlier: 3.601A pdb=" N VAL Q 463 " --> pdb=" O LYS Q 459 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR Q 468 " --> pdb=" O ILE Q 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA Q 469 " --> pdb=" O SER Q 465 " (cutoff:3.500A) Processing helix chain 'Q' and resid 491 through 496 removed outlier: 3.547A pdb=" N ALA Q 495 " --> pdb=" O ASP Q 491 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 520 removed outlier: 3.612A pdb=" N VAL Q 518 " --> pdb=" O ALA Q 514 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 35 removed outlier: 3.565A pdb=" N VAL Z 33 " --> pdb=" O GLY Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 67 Processing helix chain 'Z' and resid 71 through 88 removed outlier: 3.778A pdb=" N LEU Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA Z 83 " --> pdb=" O LYS Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.615A pdb=" N VAL Z 96 " --> pdb=" O THR Z 92 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU Z 108 " --> pdb=" O LYS Z 104 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.772A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS Z 129 " --> pdb=" O ALA Z 125 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 157 Processing helix chain 'Z' and resid 163 through 180 removed outlier: 4.172A pdb=" N VAL Z 167 " --> pdb=" O GLU Z 163 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE Z 179 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 200 through 204 removed outlier: 3.771A pdb=" N ASP Z 203 " --> pdb=" O SER Z 200 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR Z 204 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 200 through 204' Processing helix chain 'Z' and resid 252 through 281 removed outlier: 3.676A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS Z 273 " --> pdb=" O ASP Z 269 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE Z 274 " --> pdb=" O ARG Z 270 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 308 removed outlier: 3.528A pdb=" N LYS Z 307 " --> pdb=" O ASP Z 303 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 329 removed outlier: 3.538A pdb=" N LEU Z 326 " --> pdb=" O GLU Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 335 through 339 Processing helix chain 'Z' and resid 340 through 344 removed outlier: 3.556A pdb=" N CYS Z 343 " --> pdb=" O SER Z 340 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 404 Processing helix chain 'Z' and resid 412 through 424 removed outlier: 3.606A pdb=" N VAL Z 416 " --> pdb=" O GLY Z 412 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU Z 420 " --> pdb=" O VAL Z 416 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE Z 423 " --> pdb=" O ALA Z 419 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS Z 424 " --> pdb=" O GLU Z 420 " (cutoff:3.500A) Processing helix chain 'Z' and resid 433 through 444 removed outlier: 3.564A pdb=" N LEU Z 444 " --> pdb=" O PHE Z 440 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 455 removed outlier: 3.644A pdb=" N ALA Z 452 " --> pdb=" O PRO Z 448 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER Z 455 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 469 removed outlier: 3.554A pdb=" N THR Z 462 " --> pdb=" O ASP Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 517 removed outlier: 3.590A pdb=" N THR Z 509 " --> pdb=" O LEU Z 505 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Z 510 " --> pdb=" O HIS Z 506 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU Z 516 " --> pdb=" O ALA Z 512 " (cutoff:3.500A) Processing helix chain 'a' and resid 14 through 34 removed outlier: 4.110A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE a 31 " --> pdb=" O SER a 27 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 65 removed outlier: 3.695A pdb=" N LYS a 63 " --> pdb=" O ALA a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 86 removed outlier: 3.707A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP a 80 " --> pdb=" O CYS a 76 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 109 removed outlier: 3.643A pdb=" N LEU a 101 " --> pdb=" O ALA a 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 136 removed outlier: 3.502A pdb=" N LEU a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 156 removed outlier: 3.787A pdb=" N SER a 155 " --> pdb=" O ALA a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 159 through 163 Processing helix chain 'a' and resid 164 through 178 removed outlier: 4.119A pdb=" N PHE a 168 " --> pdb=" O ASN a 164 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET a 171 " --> pdb=" O PHE a 167 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 208 removed outlier: 3.758A pdb=" N GLU a 207 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER a 208 " --> pdb=" O GLN a 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 204 through 208' Processing helix chain 'a' and resid 261 through 281 removed outlier: 3.856A pdb=" N LYS a 272 " --> pdb=" O SER a 268 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU a 273 " --> pdb=" O ASP a 269 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR a 281 " --> pdb=" O LYS a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 304 removed outlier: 3.688A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE a 300 " --> pdb=" O CYS a 296 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL a 301 " --> pdb=" O LEU a 297 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU a 302 " --> pdb=" O LYS a 298 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA a 303 " --> pdb=" O TYR a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 removed outlier: 3.524A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE a 319 " --> pdb=" O ASP a 315 " (cutoff:3.500A) Processing helix chain 'a' and resid 381 through 405 removed outlier: 3.526A pdb=" N CYS a 385 " --> pdb=" O ASN a 381 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL a 402 " --> pdb=" O VAL a 398 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 431 removed outlier: 3.825A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 445 removed outlier: 3.516A pdb=" N LEU a 445 " --> pdb=" O PHE a 441 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.620A pdb=" N VAL a 454 " --> pdb=" O ASN a 450 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.609A pdb=" N LEU a 463 " --> pdb=" O ASP a 459 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN a 477 " --> pdb=" O GLU a 473 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 22 through 40 removed outlier: 3.694A pdb=" N ILE b 35 " --> pdb=" O GLY b 31 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 43 No H-bonds generated for 'chain 'b' and resid 41 through 43' Processing helix chain 'b' and resid 57 through 61 removed outlier: 3.896A pdb=" N SER b 60 " --> pdb=" O ARG b 57 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU b 61 " --> pdb=" O ASP b 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 57 through 61' Processing helix chain 'b' and resid 66 through 74 removed outlier: 3.524A pdb=" N ILE b 70 " --> pdb=" O ASP b 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU b 71 " --> pdb=" O GLY b 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 94 removed outlier: 3.523A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 118 removed outlier: 3.740A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 145 removed outlier: 3.715A pdb=" N GLU b 132 " --> pdb=" O ALA b 128 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS b 135 " --> pdb=" O ARG b 131 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU b 141 " --> pdb=" O ALA b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 167 Processing helix chain 'b' and resid 175 through 191 removed outlier: 4.224A pdb=" N LYS b 181 " --> pdb=" O ASP b 177 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU b 182 " --> pdb=" O HIS b 178 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU b 190 " --> pdb=" O ALA b 186 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS b 191 " --> pdb=" O VAL b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 removed outlier: 3.721A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 307 removed outlier: 3.684A pdb=" N ALA b 307 " --> pdb=" O LEU b 303 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 328 removed outlier: 3.510A pdb=" N VAL b 320 " --> pdb=" O ASP b 316 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU b 321 " --> pdb=" O PHE b 317 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU b 325 " --> pdb=" O GLU b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 403 removed outlier: 3.721A pdb=" N VAL b 396 " --> pdb=" O ASP b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 411 through 425 Processing helix chain 'b' and resid 429 through 444 removed outlier: 3.623A pdb=" N ALA b 433 " --> pdb=" O PRO b 429 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA b 435 " --> pdb=" O LYS b 431 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU b 443 " --> pdb=" O TYR b 439 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 454 Processing helix chain 'b' and resid 457 through 471 removed outlier: 3.578A pdb=" N ALA b 463 " --> pdb=" O ALA b 459 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA b 467 " --> pdb=" O ALA b 463 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU b 471 " --> pdb=" O ALA b 467 " (cutoff:3.500A) Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 removed outlier: 3.719A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU b 515 " --> pdb=" O ALA b 511 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 49 removed outlier: 3.669A pdb=" N ARG d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 52 No H-bonds generated for 'chain 'd' and resid 50 through 52' Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.801A pdb=" N LYS d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN d 80 " --> pdb=" O THR d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 removed outlier: 3.554A pdb=" N MET d 90 " --> pdb=" O PRO d 86 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 125 removed outlier: 3.733A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU d 117 " --> pdb=" O ALA d 113 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 151 removed outlier: 3.583A pdb=" N GLN d 138 " --> pdb=" O SER d 134 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS d 139 " --> pdb=" O GLU d 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 173 removed outlier: 3.830A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 195 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 270 through 294 removed outlier: 3.528A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE d 290 " --> pdb=" O LEU d 286 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 320 Processing helix chain 'd' and resid 329 through 340 removed outlier: 3.562A pdb=" N PHE d 335 " --> pdb=" O GLU d 331 " (cutoff:3.500A) Processing helix chain 'd' and resid 394 through 418 Processing helix chain 'd' and resid 426 through 443 removed outlier: 3.575A pdb=" N THR d 437 " --> pdb=" O ALA d 433 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU d 438 " --> pdb=" O LEU d 434 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG d 441 " --> pdb=" O THR d 437 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU d 443 " --> pdb=" O TYR d 439 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 457 removed outlier: 3.531A pdb=" N CYS d 450 " --> pdb=" O MET d 446 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 469 Processing helix chain 'd' and resid 472 through 487 removed outlier: 3.529A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR d 478 " --> pdb=" O ILE d 474 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 507 Processing helix chain 'd' and resid 512 through 531 Processing helix chain 'e' and resid 28 through 47 removed outlier: 3.796A pdb=" N LEU e 32 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 79 Processing helix chain 'e' and resid 83 through 97 removed outlier: 3.562A pdb=" N VAL e 90 " --> pdb=" O ALA e 86 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER e 93 " --> pdb=" O MET e 89 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS e 94 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 123 removed outlier: 4.157A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU e 121 " --> pdb=" O GLU e 117 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 149 removed outlier: 3.592A pdb=" N ARG e 140 " --> pdb=" O GLU e 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL e 141 " --> pdb=" O GLN e 137 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP e 147 " --> pdb=" O ILE e 143 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE e 149 " --> pdb=" O HIS e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 171 removed outlier: 3.824A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR e 166 " --> pdb=" O PRO e 162 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA e 167 " --> pdb=" O LEU e 163 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR e 170 " --> pdb=" O THR e 166 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 179 removed outlier: 6.069A pdb=" N VAL e 175 " --> pdb=" O GLY e 172 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL e 176 " --> pdb=" O SER e 173 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 195 removed outlier: 4.297A pdb=" N GLU e 185 " --> pdb=" O ARG e 181 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE e 186 " --> pdb=" O GLN e 182 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA e 187 " --> pdb=" O MET e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 203 through 205 No H-bonds generated for 'chain 'e' and resid 203 through 205' Processing helix chain 'e' and resid 216 through 220 removed outlier: 3.562A pdb=" N THR e 220 " --> pdb=" O LEU e 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 268 through 293 removed outlier: 3.725A pdb=" N MET e 286 " --> pdb=" O LYS e 282 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE e 287 " --> pdb=" O PHE e 283 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE e 290 " --> pdb=" O MET e 286 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS e 291 " --> pdb=" O ILE e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 305 through 316 removed outlier: 3.698A pdb=" N GLN e 314 " --> pdb=" O HIS e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 324 through 336 removed outlier: 4.069A pdb=" N GLU e 329 " --> pdb=" O GLY e 325 " (cutoff:3.500A) Processing helix chain 'e' and resid 342 through 346 Processing helix chain 'e' and resid 389 through 413 removed outlier: 3.659A pdb=" N ASP e 402 " --> pdb=" O ARG e 398 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA e 403 " --> pdb=" O SER e 399 " (cutoff:3.500A) Processing helix chain 'e' and resid 421 through 435 removed outlier: 3.556A pdb=" N LEU e 429 " --> pdb=" O ILE e 425 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA e 430 " --> pdb=" O SER e 426 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN e 433 " --> pdb=" O LEU e 429 " (cutoff:3.500A) Processing helix chain 'e' and resid 436 through 438 No H-bonds generated for 'chain 'e' and resid 436 through 438' Processing helix chain 'e' and resid 442 through 454 removed outlier: 3.538A pdb=" N GLU e 454 " --> pdb=" O ALA e 450 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 463 removed outlier: 3.681A pdb=" N SER e 461 " --> pdb=" O PRO e 457 " (cutoff:3.500A) Processing helix chain 'e' and resid 467 through 481 Processing helix chain 'e' and resid 498 through 503 removed outlier: 3.891A pdb=" N GLN e 502 " --> pdb=" O ASP e 498 " (cutoff:3.500A) Processing helix chain 'e' and resid 508 through 527 removed outlier: 3.584A pdb=" N ILE e 515 " --> pdb=" O LYS e 511 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 38 removed outlier: 4.257A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE g 33 " --> pdb=" O ALA g 29 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE g 36 " --> pdb=" O THR g 32 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 41 No H-bonds generated for 'chain 'g' and resid 39 through 41' Processing helix chain 'g' and resid 62 through 70 removed outlier: 3.632A pdb=" N LEU g 67 " --> pdb=" O GLY g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 91 removed outlier: 3.618A pdb=" N GLU g 89 " --> pdb=" O ARG g 85 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU g 90 " --> pdb=" O THR g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 94 through 106 removed outlier: 3.583A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 141 removed outlier: 3.539A pdb=" N ALA g 125 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP g 132 " --> pdb=" O LYS g 128 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU g 137 " --> pdb=" O MET g 133 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS g 138 " --> pdb=" O ILE g 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS g 139 " --> pdb=" O SER g 135 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 removed outlier: 3.842A pdb=" N MET g 152 " --> pdb=" O ASP g 148 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN g 154 " --> pdb=" O ASP g 150 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE g 155 " --> pdb=" O MET g 151 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER g 158 " --> pdb=" O ASN g 154 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER g 159 " --> pdb=" O ILE g 155 " (cutoff:3.500A) Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.578A pdb=" N SER g 166 " --> pdb=" O LYS g 163 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 163 through 167' Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.913A pdb=" N ASN g 174 " --> pdb=" O SER g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 194 through 199 removed outlier: 3.713A pdb=" N TYR g 198 " --> pdb=" O ASP g 194 " (cutoff:3.500A) Processing helix chain 'g' and resid 260 through 283 removed outlier: 3.654A pdb=" N ARG g 266 " --> pdb=" O GLU g 262 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE g 275 " --> pdb=" O GLU g 271 " (cutoff:3.500A) Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.882A pdb=" N TYR g 303 " --> pdb=" O LEU g 299 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 327 removed outlier: 3.618A pdb=" N ILE g 323 " --> pdb=" O ASP g 319 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG g 325 " --> pdb=" O ASN g 321 " (cutoff:3.500A) Processing helix chain 'g' and resid 334 through 338 removed outlier: 3.512A pdb=" N LEU g 338 " --> pdb=" O PRO g 335 " (cutoff:3.500A) Processing helix chain 'g' and resid 380 through 404 removed outlier: 3.578A pdb=" N ARG g 389 " --> pdb=" O SER g 385 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP g 393 " --> pdb=" O ARG g 389 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA g 394 " --> pdb=" O ASN g 390 " (cutoff:3.500A) Processing helix chain 'g' and resid 412 through 426 removed outlier: 3.576A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' Processing helix chain 'g' and resid 433 through 444 removed outlier: 3.676A pdb=" N VAL g 440 " --> pdb=" O PRO g 436 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA g 441 " --> pdb=" O TYR g 437 " (cutoff:3.500A) Processing helix chain 'g' and resid 445 through 456 removed outlier: 3.588A pdb=" N LEU g 451 " --> pdb=" O ILE g 447 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS g 455 " --> pdb=" O LEU g 451 " (cutoff:3.500A) Processing helix chain 'g' and resid 458 through 473 removed outlier: 3.664A pdb=" N LEU g 462 " --> pdb=" O SER g 458 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA g 468 " --> pdb=" O THR g 464 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS g 470 " --> pdb=" O LEU g 466 " (cutoff:3.500A) Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 36 removed outlier: 3.552A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL h 31 " --> pdb=" O SER h 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 70 removed outlier: 3.947A pdb=" N ASP h 70 " --> pdb=" O LEU h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 90 removed outlier: 3.777A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA h 88 " --> pdb=" O LYS h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 108 removed outlier: 3.520A pdb=" N PHE h 104 " --> pdb=" O LEU h 100 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU h 105 " --> pdb=" O ALA h 101 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS h 106 " --> pdb=" O ALA h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 114 removed outlier: 3.554A pdb=" N GLU h 113 " --> pdb=" O LYS h 109 " (cutoff:3.500A) Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.660A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU h 138 " --> pdb=" O ASN h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 145 through 149 Processing helix chain 'h' and resid 150 through 163 removed outlier: 3.618A pdb=" N LEU h 154 " --> pdb=" O GLU h 150 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA h 162 " --> pdb=" O CYS h 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 185 removed outlier: 4.052A pdb=" N LYS h 177 " --> pdb=" O ALA h 173 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET h 178 " --> pdb=" O PHE h 174 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 259 through 285 removed outlier: 3.660A pdb=" N TYR h 263 " --> pdb=" O THR h 259 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN h 264 " --> pdb=" O VAL h 260 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU h 274 " --> pdb=" O GLU h 270 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE h 281 " --> pdb=" O LYS h 277 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 306 removed outlier: 3.536A pdb=" N TYR h 302 " --> pdb=" O VAL h 298 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE h 303 " --> pdb=" O ALA h 299 " (cutoff:3.500A) Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 378 through 402 removed outlier: 3.757A pdb=" N MET h 382 " --> pdb=" O ALA h 378 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG h 387 " --> pdb=" O GLU h 383 " (cutoff:3.500A) Processing helix chain 'h' and resid 410 through 425 removed outlier: 3.522A pdb=" N GLU h 415 " --> pdb=" O ALA h 411 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG h 425 " --> pdb=" O ARG h 421 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 442 removed outlier: 3.783A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU h 442 " --> pdb=" O TYR h 438 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 453 removed outlier: 3.784A pdb=" N CYS h 450 " --> pdb=" O PRO h 446 " (cutoff:3.500A) Processing helix chain 'h' and resid 456 through 469 removed outlier: 3.565A pdb=" N ALA h 469 " --> pdb=" O ARG h 465 " (cutoff:3.500A) Processing helix chain 'h' and resid 496 through 515 removed outlier: 3.532A pdb=" N ILE h 513 " --> pdb=" O ALA h 509 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 45 removed outlier: 3.592A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU q 39 " --> pdb=" O ALA q 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 removed outlier: 3.536A pdb=" N ILE q 72 " --> pdb=" O ASP q 68 " (cutoff:3.500A) Processing helix chain 'q' and resid 80 through 94 removed outlier: 3.640A pdb=" N MET q 85 " --> pdb=" O PRO q 81 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 121 removed outlier: 3.503A pdb=" N LEU q 105 " --> pdb=" O THR q 101 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY q 109 " --> pdb=" O LEU q 105 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE q 121 " --> pdb=" O GLU q 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 124 through 143 removed outlier: 3.569A pdb=" N ARG q 137 " --> pdb=" O GLU q 133 " (cutoff:3.500A) Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 156 through 169 removed outlier: 3.623A pdb=" N LEU q 164 " --> pdb=" O VAL q 160 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG q 165 " --> pdb=" O SER q 161 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 175 through 191 removed outlier: 3.501A pdb=" N ALA q 180 " --> pdb=" O GLU q 176 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS q 181 " --> pdb=" O VAL q 177 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER q 189 " --> pdb=" O GLN q 185 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE q 190 " --> pdb=" O ALA q 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 287 removed outlier: 3.628A pdb=" N GLU q 273 " --> pdb=" O SER q 269 " (cutoff:3.500A) Processing helix chain 'q' and resid 300 through 308 removed outlier: 3.537A pdb=" N ASN q 306 " --> pdb=" O LEU q 302 " (cutoff:3.500A) Processing helix chain 'q' and resid 317 through 326 removed outlier: 3.755A pdb=" N LEU q 321 " --> pdb=" O SER q 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU q 324 " --> pdb=" O ASP q 320 " (cutoff:3.500A) Processing helix chain 'q' and resid 381 through 403 removed outlier: 3.578A pdb=" N ASP q 387 " --> pdb=" O ASN q 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU q 389 " --> pdb=" O MET q 385 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL q 401 " --> pdb=" O ASN q 397 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU q 402 " --> pdb=" O THR q 398 " (cutoff:3.500A) Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.601A pdb=" N ILE q 417 " --> pdb=" O GLY q 413 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER q 425 " --> pdb=" O LYS q 421 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.541A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 455 Processing helix chain 'q' and resid 459 through 473 removed outlier: 3.563A pdb=" N VAL q 463 " --> pdb=" O LYS q 459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA q 469 " --> pdb=" O SER q 465 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU q 473 " --> pdb=" O ALA q 469 " (cutoff:3.500A) Processing helix chain 'q' and resid 491 through 496 removed outlier: 3.527A pdb=" N ALA q 495 " --> pdb=" O ASP q 491 " (cutoff:3.500A) Processing helix chain 'q' and resid 501 through 520 removed outlier: 3.524A pdb=" N ALA q 507 " --> pdb=" O GLY q 503 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL q 518 " --> pdb=" O ALA q 514 " (cutoff:3.500A) Processing helix chain 'z' and resid 17 through 35 removed outlier: 3.632A pdb=" N ASN z 23 " --> pdb=" O ALA z 19 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL z 33 " --> pdb=" O GLY z 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 59 through 66 Processing helix chain 'z' and resid 71 through 88 removed outlier: 3.902A pdb=" N LEU z 76 " --> pdb=" O PRO z 72 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE z 77 " --> pdb=" O THR z 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA z 83 " --> pdb=" O LYS z 79 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR z 88 " --> pdb=" O GLN z 84 " (cutoff:3.500A) Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.530A pdb=" N VAL z 96 " --> pdb=" O THR z 92 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.781A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS z 129 " --> pdb=" O ALA z 125 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL z 137 " --> pdb=" O PHE z 133 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 3.554A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS z 159 " --> pdb=" O SER z 155 " (cutoff:3.500A) Processing helix chain 'z' and resid 163 through 179 removed outlier: 4.422A pdb=" N VAL z 167 " --> pdb=" O GLU z 163 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA z 178 " --> pdb=" O ASP z 174 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE z 179 " --> pdb=" O SER z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 200 through 204 removed outlier: 4.028A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 252 through 281 removed outlier: 3.502A pdb=" N GLU z 257 " --> pdb=" O ALA z 253 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS z 261 " --> pdb=" O GLU z 257 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 329 removed outlier: 3.544A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU z 326 " --> pdb=" O GLU z 322 " (cutoff:3.500A) Processing helix chain 'z' and resid 335 through 339 removed outlier: 3.537A pdb=" N ASP z 338 " --> pdb=" O SER z 335 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.627A pdb=" N LEU z 384 " --> pdb=" O ASN z 380 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 424 removed outlier: 3.552A pdb=" N VAL z 416 " --> pdb=" O GLY z 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA z 421 " --> pdb=" O ALA z 417 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE z 423 " --> pdb=" O ALA z 419 " (cutoff:3.500A) Processing helix chain 'z' and resid 430 through 432 No H-bonds generated for 'chain 'z' and resid 430 through 432' Processing helix chain 'z' and resid 433 through 444 Processing helix chain 'z' and resid 445 through 455 removed outlier: 3.552A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 468 removed outlier: 3.610A pdb=" N THR z 462 " --> pdb=" O ASP z 458 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU z 463 " --> pdb=" O LEU z 459 " (cutoff:3.500A) Processing helix chain 'z' and resid 498 through 517 removed outlier: 3.710A pdb=" N LEU z 505 " --> pdb=" O LYS z 501 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS z 506 " --> pdb=" O LYS z 502 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR z 509 " --> pdb=" O LEU z 505 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU z 516 " --> pdb=" O ALA z 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 4.810A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.626A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP A 42 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP G 521 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 200 Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 217 removed outlier: 3.535A pdb=" N TYR A 214 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 364 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 361 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.290A pdb=" N ILE B 520 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 517 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET E 58 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 519 " --> pdb=" O MET E 58 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL E 60 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 521 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.547A pdb=" N MET B 62 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 52 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.641A pdb=" N HIS B 200 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 375 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLY B 377 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.769A pdb=" N ILE B 232 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 349 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 240 Processing sheet with id=AB4, first strand: chain 'B' and resid 406 through 407 Processing sheet with id=AB5, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.802A pdb=" N LYS D 209 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 227 through 229 Processing sheet with id=AB8, first strand: chain 'D' and resid 323 through 328 removed outlier: 3.894A pdb=" N ASP D 327 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 247 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 299 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 301 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N VAL D 345 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU D 248 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.680A pdb=" N GLY D 492 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 207 through 211 removed outlier: 3.635A pdb=" N THR E 382 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE E 223 " --> pdb=" O THR E 382 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 384 " --> pdb=" O LYS E 221 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 227 through 228 removed outlier: 3.941A pdb=" N VAL E 228 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET E 369 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE E 360 " --> pdb=" O MET E 369 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 357 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 319 through 320 removed outlier: 6.687A pdb=" N ALA E 298 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA E 247 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL E 340 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 248 " --> pdb=" O VAL E 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AC6, first strand: chain 'E' and resid 528 through 532 removed outlier: 4.889A pdb=" N ILE E 528 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU H 48 " --> pdb=" O ILE E 528 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP E 530 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL H 50 " --> pdb=" O ASP E 530 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG E 532 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS H 47 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER H 59 " --> pdb=" O LYS H 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 58 removed outlier: 3.519A pdb=" N VAL G 58 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AC9, first strand: chain 'G' and resid 201 through 205 removed outlier: 3.546A pdb=" N GLU G 202 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU G 376 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY G 378 " --> pdb=" O ILE G 204 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD2, first strand: chain 'G' and resid 310 through 312 removed outlier: 6.230A pdb=" N VAL G 290 " --> pdb=" O ILE G 312 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL G 239 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N VAL G 332 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU G 240 " --> pdb=" O VAL G 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'G' and resid 479 through 480 removed outlier: 3.794A pdb=" N VAL G 488 " --> pdb=" O GLY G 479 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 141 through 142 removed outlier: 4.047A pdb=" N VAL H 141 " --> pdb=" O VAL H 405 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 196 through 201 removed outlier: 6.483A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY H 376 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL H 200 " --> pdb=" O GLY H 376 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.353A pdb=" N VAL H 289 " --> pdb=" O ALA H 311 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 347 through 351 removed outlier: 4.029A pdb=" N GLU H 349 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE H 360 " --> pdb=" O GLU H 349 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR H 351 " --> pdb=" O TYR H 358 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 358 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AD9, first strand: chain 'H' and resid 516 through 521 removed outlier: 6.995A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.518A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLY Q 379 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE Q 207 " --> pdb=" O GLY Q 379 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 221 through 223 Processing sheet with id=AE3, first strand: chain 'Q' and resid 239 through 242 Processing sheet with id=AE4, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id=AE5, first strand: chain 'Q' and resid 521 through 526 removed outlier: 4.289A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS Z 45 " --> pdb=" O THR Z 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR Z 57 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.258A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 211 through 212 removed outlier: 3.665A pdb=" N THR Z 361 " --> pdb=" O LEU Z 212 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 229 through 231 removed outlier: 3.579A pdb=" N VAL Z 290 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id=AF1, first strand: chain 'Z' and resid 478 through 479 Processing sheet with id=AF2, first strand: chain 'a' and resid 11 through 13 removed outlier: 4.251A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS d 59 " --> pdb=" O THR d 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 52 through 55 removed outlier: 3.623A pdb=" N LYS a 43 " --> pdb=" O THR a 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET a 44 " --> pdb=" O ASP g 521 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL g 523 " --> pdb=" O MET a 44 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU g 17 " --> pdb=" O ILE g 522 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 137 through 138 removed outlier: 3.574A pdb=" N ILE a 137 " --> pdb=" O VAL a 408 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 196 through 201 removed outlier: 4.045A pdb=" N SER a 374 " --> pdb=" O ILE a 211 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE a 376 " --> pdb=" O MET a 209 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET a 209 " --> pdb=" O ILE a 376 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 214 through 217 removed outlier: 3.715A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 234 through 237 Processing sheet with id=AF8, first strand: chain 'a' and resid 486 through 488 Processing sheet with id=AF9, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.199A pdb=" N ILE b 520 " --> pdb=" O GLU b 19 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP e 56 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN b 519 " --> pdb=" O ASP e 56 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS e 57 " --> pdb=" O THR e 69 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR e 69 " --> pdb=" O LYS e 57 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 49 through 54 removed outlier: 7.460A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR d 538 " --> pdb=" O ILE b 51 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU b 53 " --> pdb=" O THR d 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.495A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU b 375 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE b 202 " --> pdb=" O LEU b 375 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLY b 377 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS b 204 " --> pdb=" O GLY b 377 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 219 through 220 removed outlier: 3.637A pdb=" N ILE b 360 " --> pdb=" O LEU b 220 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 239 through 240 Processing sheet with id=AG5, first strand: chain 'b' and resid 406 through 407 Processing sheet with id=AG6, first strand: chain 'b' and resid 476 through 479 removed outlier: 3.588A pdb=" N GLY b 486 " --> pdb=" O GLY b 477 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.388A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU d 222 " --> pdb=" O VAL d 389 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.563A pdb=" N THR d 377 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 246 through 248 removed outlier: 6.913A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU d 298 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE d 325 " --> pdb=" O LEU d 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'd' and resid 421 through 423 Processing sheet with id=AH2, first strand: chain 'd' and resid 491 through 494 removed outlier: 3.663A pdb=" N GLY d 492 " --> pdb=" O SER d 501 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER d 501 " --> pdb=" O GLY d 492 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'e' and resid 24 through 26 removed outlier: 3.655A pdb=" N LYS e 533 " --> pdb=" O SER e 24 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU e 26 " --> pdb=" O ILE e 531 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE e 531 " --> pdb=" O LEU e 26 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP h 46 " --> pdb=" O ILE e 528 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'e' and resid 207 through 213 removed outlier: 6.479A pdb=" N LYS e 208 " --> pdb=" O ILE e 383 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE e 385 " --> pdb=" O LYS e 208 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N GLY e 387 " --> pdb=" O GLU e 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS e 212 " --> pdb=" O GLY e 387 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE e 223 " --> pdb=" O THR e 382 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE e 384 " --> pdb=" O LYS e 221 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS e 221 " --> pdb=" O PHE e 384 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'e' and resid 246 through 249 removed outlier: 6.153A pdb=" N ALA e 247 " --> pdb=" O ILE e 299 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA e 298 " --> pdb=" O VAL e 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'e' and resid 356 through 362 removed outlier: 7.176A pdb=" N PHE e 362 " --> pdb=" O ASP e 367 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASP e 367 " --> pdb=" O PHE e 362 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 416 through 418 Processing sheet with id=AH8, first strand: chain 'g' and resid 57 through 58 removed outlier: 7.959A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI1, first strand: chain 'g' and resid 201 through 203 removed outlier: 3.540A pdb=" N GLU g 202 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU g 376 " --> pdb=" O GLU g 202 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS g 213 " --> pdb=" O LEU g 375 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 232 through 233 Processing sheet with id=AI3, first strand: chain 'g' and resid 310 through 312 removed outlier: 5.718A pdb=" N VAL g 290 " --> pdb=" O ILE g 312 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N VAL g 332 " --> pdb=" O ILE g 238 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU g 240 " --> pdb=" O VAL g 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'g' and resid 479 through 480 removed outlier: 3.834A pdb=" N VAL g 488 " --> pdb=" O GLY g 479 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'h' and resid 141 through 142 removed outlier: 3.555A pdb=" N VAL h 141 " --> pdb=" O VAL h 405 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL h 405 " --> pdb=" O VAL h 141 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'h' and resid 196 through 201 removed outlier: 3.771A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'h' and resid 215 through 216 removed outlier: 4.176A pdb=" N ASN h 359 " --> pdb=" O PHE h 216 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE h 360 " --> pdb=" O GLU h 349 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU h 349 " --> pdb=" O PHE h 360 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 309 through 311 removed outlier: 6.170A pdb=" N VAL h 289 " --> pdb=" O ALA h 311 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLN h 331 " --> pdb=" O ILE h 237 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU h 239 " --> pdb=" O GLN h 331 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 475 through 477 Processing sheet with id=AJ1, first strand: chain 'h' and resid 516 through 521 removed outlier: 6.479A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'q' and resid 202 through 208 Processing sheet with id=AJ3, first strand: chain 'q' and resid 221 through 223 removed outlier: 3.507A pdb=" N TYR q 351 " --> pdb=" O VAL q 362 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'q' and resid 311 through 314 removed outlier: 9.478A pdb=" N LEU q 333 " --> pdb=" O ILE q 239 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL q 241 " --> pdb=" O LEU q 333 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'q' and resid 408 through 410 Processing sheet with id=AJ6, first strand: chain 'q' and resid 521 through 526 removed outlier: 4.527A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS z 45 " --> pdb=" O THR z 57 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR z 57 " --> pdb=" O LYS z 45 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.337A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER z 205 " --> pdb=" O LEU z 375 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'z' and resid 211 through 212 Processing sheet with id=AJ9, first strand: chain 'z' and resid 229 through 231 removed outlier: 6.121A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL z 311 " --> pdb=" O PHE z 289 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'z' and resid 407 through 409 Processing sheet with id=AK2, first strand: chain 'z' and resid 478 through 479 3083 hydrogen bonds defined for protein. 8979 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: 23.95 Time building geometry restraints manager: 20.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 21382 1.34 - 1.46: 11034 1.46 - 1.58: 30657 1.58 - 1.69: 0 1.69 - 1.81: 643 Bond restraints: 63716 Sorted by residual: bond pdb=" C CYS E 438 " pdb=" N PRO E 439 " ideal model delta sigma weight residual 1.334 1.512 -0.178 2.34e-02 1.83e+03 5.79e+01 bond pdb=" CA SER A 405 " pdb=" C SER A 405 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.32e-02 5.74e+03 9.75e+00 bond pdb=" C ASP G 404 " pdb=" N PRO G 405 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.76e+00 bond pdb=" N SER A 405 " pdb=" CA SER A 405 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.28e-02 6.10e+03 3.81e+00 bond pdb=" C CYS e 438 " pdb=" N PRO e 439 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.22e+00 ... (remaining 63711 not shown) Histogram of bond angle deviations from ideal: 91.62 - 100.09: 3 100.09 - 108.56: 2373 108.56 - 117.03: 43860 117.03 - 125.50: 39214 125.50 - 133.97: 495 Bond angle restraints: 85945 Sorted by residual: angle pdb=" N CYS A 147 " pdb=" CA CYS A 147 " pdb=" C CYS A 147 " ideal model delta sigma weight residual 114.16 91.62 22.54 1.48e+00 4.57e-01 2.32e+02 angle pdb=" N SER A 405 " pdb=" CA SER A 405 " pdb=" C SER A 405 " ideal model delta sigma weight residual 110.10 92.20 17.90 1.49e+00 4.50e-01 1.44e+02 angle pdb=" N CYS a 147 " pdb=" CA CYS a 147 " pdb=" C CYS a 147 " ideal model delta sigma weight residual 114.64 101.40 13.24 1.52e+00 4.33e-01 7.59e+01 angle pdb=" N GLY A 202 " pdb=" CA GLY A 202 " pdb=" C GLY A 202 " ideal model delta sigma weight residual 110.97 118.46 -7.49 1.56e+00 4.11e-01 2.30e+01 angle pdb=" N GLU a 404 " pdb=" CA GLU a 404 " pdb=" C GLU a 404 " ideal model delta sigma weight residual 112.68 106.42 6.26 1.33e+00 5.65e-01 2.22e+01 ... (remaining 85940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 38854 15.94 - 31.88: 362 31.88 - 47.82: 253 47.82 - 63.76: 72 63.76 - 79.70: 14 Dihedral angle restraints: 39555 sinusoidal: 15827 harmonic: 23728 Sorted by residual: dihedral pdb=" CA GLN A 187 " pdb=" C GLN A 187 " pdb=" N PRO A 188 " pdb=" CA PRO A 188 " ideal model delta harmonic sigma weight residual 180.00 -128.69 -51.31 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA GLN a 187 " pdb=" C GLN a 187 " pdb=" N PRO a 188 " pdb=" CA PRO a 188 " ideal model delta harmonic sigma weight residual -180.00 -132.21 -47.79 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ILE A 184 " pdb=" C ILE A 184 " pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 39552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 9470 0.071 - 0.142: 813 0.142 - 0.213: 7 0.213 - 0.284: 0 0.284 - 0.355: 2 Chirality restraints: 10292 Sorted by residual: chirality pdb=" CA SER A 405 " pdb=" N SER A 405 " pdb=" C SER A 405 " pdb=" CB SER A 405 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA CYS A 147 " pdb=" N CYS A 147 " pdb=" C CYS A 147 " pdb=" CB CYS A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA GLU a 404 " pdb=" N GLU a 404 " pdb=" C GLU a 404 " pdb=" CB GLU a 404 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 10289 not shown) Planarity restraints: 11042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 187 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO a 188 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO a 188 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO a 188 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 187 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO A 188 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 381 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO D 382 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 382 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 382 " 0.031 5.00e-02 4.00e+02 ... (remaining 11039 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 663 2.66 - 3.22: 58544 3.22 - 3.78: 88327 3.78 - 4.34: 125823 4.34 - 4.90: 204774 Nonbonded interactions: 478131 Sorted by model distance: nonbonded pdb=" O ARG G 216 " pdb=" OG1 THR G 364 " model vdw 2.098 2.440 nonbonded pdb=" N CYS A 147 " pdb=" N LEU A 148 " model vdw 2.138 2.560 nonbonded pdb=" NZ LYS b 204 " pdb=" OD2 ASP b 357 " model vdw 2.219 2.520 nonbonded pdb=" OD1 ASP d 99 " pdb=" OG1 THR d 106 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASP D 99 " pdb=" OG1 THR D 106 " model vdw 2.221 2.440 ... (remaining 478126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 243 or resid 260 through 327 or resid 342 throug \ h 533)) selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'D' and (resid 24 through 249 or resid 269 through 300 or resid 312 throu \ gh 340 or resid 348 through 539)) selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 11.860 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 128.650 Find NCS groups from input model: 5.860 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 0.002 0.178 63716 Z= 0.120 Angle : 0.524 22.543 85945 Z= 0.346 Chirality : 0.039 0.355 10292 Planarity : 0.003 0.073 11042 Dihedral : 7.693 79.701 24183 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.06 % Allowed : 0.07 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: -3.46 (0.07), residues: 8205 helix: -3.12 (0.05), residues: 4021 sheet: -1.10 (0.16), residues: 805 loop : -1.21 (0.09), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 302 HIS 0.007 0.000 HIS q 196 PHE 0.013 0.001 PHE h 220 TYR 0.010 0.001 TYR q 30 ARG 0.004 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1605 time to evaluate : 6.583 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: A 246 MET cc_start: 0.0245 (tpp) cc_final: -0.0110 (ttm) REVERT: B 48 MET cc_start: 0.8866 (mmm) cc_final: 0.8573 (mmm) REVERT: B 362 PHE cc_start: 0.5920 (m-10) cc_final: 0.5456 (m-80) REVERT: B 488 MET cc_start: 0.8188 (mmp) cc_final: 0.7983 (mmm) REVERT: B 493 ILE cc_start: 0.8696 (mt) cc_final: 0.8349 (mt) REVERT: D 195 ILE cc_start: 0.7772 (mm) cc_final: 0.7480 (mm) REVERT: D 432 LEU cc_start: 0.9533 (tp) cc_final: 0.9222 (tt) REVERT: E 92 LEU cc_start: 0.8208 (tp) cc_final: 0.7661 (tp) REVERT: E 357 VAL cc_start: 0.4566 (t) cc_final: 0.4143 (t) REVERT: G 66 ILE cc_start: 0.9116 (mt) cc_final: 0.8894 (tt) REVERT: G 145 ASP cc_start: 0.7219 (t0) cc_final: 0.6863 (p0) REVERT: G 198 TYR cc_start: 0.6801 (m-10) cc_final: 0.6175 (m-10) REVERT: G 229 MET cc_start: 0.3727 (mtt) cc_final: 0.3497 (mmm) REVERT: G 313 ARG cc_start: 0.6508 (ptt180) cc_final: 0.5864 (ttt180) REVERT: G 362 PHE cc_start: 0.6503 (m-10) cc_final: 0.6039 (m-80) REVERT: G 416 MET cc_start: 0.7999 (mmm) cc_final: 0.7657 (mmm) REVERT: G 520 ASP cc_start: 0.7701 (p0) cc_final: 0.7493 (p0) REVERT: H 382 MET cc_start: 0.5388 (mtm) cc_final: 0.4904 (mmp) REVERT: H 414 MET cc_start: 0.8638 (mmm) cc_final: 0.8375 (tpp) REVERT: Q 75 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8300 (mm-30) REVERT: Q 88 MET cc_start: 0.7636 (mtm) cc_final: 0.7314 (mtp) REVERT: Q 249 MET cc_start: -0.0482 (mtp) cc_final: -0.2520 (ttm) REVERT: Q 266 MET cc_start: 0.5668 (mmt) cc_final: 0.5467 (mmm) REVERT: Q 320 ASP cc_start: 0.7987 (m-30) cc_final: 0.7440 (t0) REVERT: Q 358 THR cc_start: 0.6953 (m) cc_final: 0.6692 (m) REVERT: Q 382 ASP cc_start: 0.7886 (m-30) cc_final: 0.6754 (t0) REVERT: Q 386 ASP cc_start: 0.8868 (m-30) cc_final: 0.8429 (m-30) REVERT: Z 221 MET cc_start: -0.0393 (mmt) cc_final: -0.0861 (mmm) REVERT: Z 351 TYR cc_start: 0.7374 (p90) cc_final: 0.6919 (p90) REVERT: a 171 MET cc_start: 0.7965 (mtp) cc_final: 0.7395 (ttt) REVERT: a 388 MET cc_start: 0.7833 (mtt) cc_final: 0.7180 (mmt) REVERT: b 141 LEU cc_start: 0.8957 (mt) cc_final: 0.8633 (mp) REVERT: b 160 MET cc_start: 0.8313 (mtp) cc_final: 0.7823 (mmt) REVERT: b 182 LEU cc_start: 0.8485 (mt) cc_final: 0.8164 (tp) REVERT: b 396 VAL cc_start: 0.9540 (m) cc_final: 0.9288 (p) REVERT: b 417 MET cc_start: 0.8531 (mtm) cc_final: 0.8300 (mtm) REVERT: b 480 MET cc_start: 0.7817 (mmp) cc_final: 0.7305 (mmm) REVERT: e 65 ASP cc_start: 0.7541 (m-30) cc_final: 0.7245 (m-30) REVERT: e 183 MET cc_start: 0.8385 (mtp) cc_final: 0.7703 (ptm) REVERT: e 197 MET cc_start: 0.4593 (ttm) cc_final: 0.4015 (tpp) REVERT: e 360 ILE cc_start: 0.3539 (mm) cc_final: 0.3218 (mt) REVERT: g 191 LYS cc_start: 0.8309 (mttt) cc_final: 0.7995 (mtpt) REVERT: g 440 VAL cc_start: 0.8588 (t) cc_final: 0.8293 (t) REVERT: h 156 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8131 (tt0) REVERT: h 185 MET cc_start: 0.8774 (mmm) cc_final: 0.8306 (ttt) REVERT: h 382 MET cc_start: 0.7750 (mtm) cc_final: 0.7240 (mtm) REVERT: h 391 ASP cc_start: 0.8671 (m-30) cc_final: 0.8422 (t0) REVERT: h 517 ASP cc_start: 0.8552 (t70) cc_final: 0.8278 (t0) REVERT: q 172 GLN cc_start: 0.8639 (tp40) cc_final: 0.8232 (tp40) REVERT: q 204 VAL cc_start: 0.8881 (t) cc_final: 0.8424 (t) REVERT: q 223 PHE cc_start: 0.7658 (m-10) cc_final: 0.6676 (m-10) REVERT: q 492 MET cc_start: 0.8381 (mmp) cc_final: 0.8106 (mmm) REVERT: z 229 TYR cc_start: 0.8092 (m-10) cc_final: 0.7647 (m-80) outliers start: 4 outliers final: 1 residues processed: 1608 average time/residue: 0.6293 time to fit residues: 1659.1700 Evaluate side-chains 800 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 799 time to evaluate : 5.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 689 optimal weight: 8.9990 chunk 619 optimal weight: 2.9990 chunk 343 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 chunk 417 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 640 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 389 optimal weight: 20.0000 chunk 476 optimal weight: 5.9990 chunk 741 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN B 91 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN D 129 HIS D 406 HIS D 482 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN E 20 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 514 GLN E 520 GLN G 116 GLN G 157 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 396 GLN ** G 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 ASN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 ASN Q 93 GLN ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN Z 65 HIS Z 434 GLN a 135 ASN ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 435 GLN a 471 HIS a 475 GLN b 148 HIS b 419 HIS d 482 ASN ** e 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 358 GLN ** e 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 400 ASN h 21 GLN h 25 ASN h 30 GLN h 234 ASN h 301 GLN ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN q 198 ASN q 475 ASN q 477 ASN z 65 HIS ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 438 GLN z 497 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 63716 Z= 0.284 Angle : 0.672 14.599 85945 Z= 0.352 Chirality : 0.046 0.458 10292 Planarity : 0.005 0.080 11042 Dihedral : 4.034 57.337 8759 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.59 % Allowed : 7.01 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: -1.09 (0.08), residues: 8205 helix: -0.29 (0.07), residues: 4169 sheet: -0.78 (0.16), residues: 862 loop : -1.11 (0.10), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 495 HIS 0.008 0.001 HIS z 65 PHE 0.046 0.002 PHE B 317 TYR 0.026 0.002 TYR q 304 ARG 0.015 0.001 ARG d 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 852 time to evaluate : 5.547 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 42 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7787 (p0) REVERT: A 81 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8886 (tp) REVERT: A 246 MET cc_start: -0.0037 (tpp) cc_final: -0.0433 (ttm) REVERT: B 144 SER cc_start: 0.8952 (m) cc_final: 0.8514 (t) REVERT: B 362 PHE cc_start: 0.5938 (m-10) cc_final: 0.5682 (m-80) REVERT: B 384 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: B 388 ARG cc_start: 0.9084 (ptp-170) cc_final: 0.8661 (ptp-170) REVERT: B 488 MET cc_start: 0.8417 (mmp) cc_final: 0.8118 (mmm) REVERT: B 493 ILE cc_start: 0.8799 (mt) cc_final: 0.8500 (mt) REVERT: D 67 ASP cc_start: 0.6853 (t0) cc_final: 0.6628 (t0) REVERT: D 90 MET cc_start: 0.8370 (mtm) cc_final: 0.8161 (mtm) REVERT: D 320 MET cc_start: 0.0374 (mtt) cc_final: 0.0022 (mtt) REVERT: E 27 MET cc_start: 0.6637 (mpp) cc_final: 0.6304 (mpp) REVERT: E 237 MET cc_start: 0.4701 (mmm) cc_final: 0.4410 (mtp) REVERT: G 104 GLU cc_start: 0.8252 (tp30) cc_final: 0.7999 (tm-30) REVERT: G 145 ASP cc_start: 0.7484 (t0) cc_final: 0.7048 (p0) REVERT: G 198 TYR cc_start: 0.6370 (m-10) cc_final: 0.6040 (m-10) REVERT: G 388 GLU cc_start: 0.8978 (pt0) cc_final: 0.8757 (pp20) REVERT: G 415 GLU cc_start: 0.8281 (mp0) cc_final: 0.8033 (mp0) REVERT: H 61 ASP cc_start: 0.8169 (t70) cc_final: 0.7922 (t0) REVERT: H 382 MET cc_start: 0.5294 (mtm) cc_final: 0.4748 (mmm) REVERT: H 390 HIS cc_start: 0.8548 (m-70) cc_final: 0.8241 (t-90) REVERT: H 394 MET cc_start: 0.9077 (mmm) cc_final: 0.8848 (mmm) REVERT: Q 75 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8342 (mm-30) REVERT: Q 130 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7726 (mp0) REVERT: Q 238 LYS cc_start: 0.7423 (mmtt) cc_final: 0.7218 (tppt) REVERT: Q 276 MET cc_start: 0.6163 (ptt) cc_final: 0.5618 (ptm) REVERT: Q 382 ASP cc_start: 0.8012 (m-30) cc_final: 0.7672 (m-30) REVERT: Q 385 MET cc_start: 0.7752 (mtm) cc_final: 0.7521 (mtm) REVERT: Z 121 GLU cc_start: 0.7860 (tp30) cc_final: 0.7583 (tp30) REVERT: Z 190 MET cc_start: 0.7810 (ttm) cc_final: 0.7336 (ttm) REVERT: Z 221 MET cc_start: -0.0498 (mmt) cc_final: -0.0703 (mmt) REVERT: Z 351 TYR cc_start: 0.6503 (p90) cc_final: 0.6270 (p90) REVERT: a 53 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8554 (p) REVERT: a 99 GLU cc_start: 0.8446 (tp30) cc_final: 0.8115 (tm-30) REVERT: a 171 MET cc_start: 0.7933 (mtp) cc_final: 0.7531 (ttt) REVERT: a 206 MET cc_start: 0.6473 (ptm) cc_final: 0.6204 (ptm) REVERT: a 388 MET cc_start: 0.7765 (mtt) cc_final: 0.7248 (mmt) REVERT: b 52 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8493 (pt) REVERT: b 160 MET cc_start: 0.8582 (mtp) cc_final: 0.7908 (mmt) REVERT: b 213 TYR cc_start: 0.6476 (m-80) cc_final: 0.6163 (m-80) REVERT: b 396 VAL cc_start: 0.9564 (m) cc_final: 0.9338 (p) REVERT: b 400 THR cc_start: 0.9338 (m) cc_final: 0.9088 (p) REVERT: d 150 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8161 (p0) REVERT: d 151 MET cc_start: 0.8054 (tpp) cc_final: 0.7678 (tpp) REVERT: d 355 MET cc_start: 0.5134 (ptt) cc_final: 0.3064 (tpp) REVERT: d 452 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8242 (ttm-80) REVERT: e 63 ASP cc_start: 0.6691 (p0) cc_final: 0.6442 (p0) REVERT: e 183 MET cc_start: 0.8316 (mtp) cc_final: 0.7607 (ptm) REVERT: e 197 MET cc_start: 0.4035 (ttm) cc_final: 0.3826 (tpp) REVERT: e 297 LEU cc_start: 0.6864 (tp) cc_final: 0.6311 (mp) REVERT: e 489 ILE cc_start: 0.8482 (mt) cc_final: 0.8007 (mt) REVERT: g 104 GLU cc_start: 0.8434 (tp30) cc_final: 0.8170 (tm-30) REVERT: g 152 MET cc_start: 0.8990 (mpp) cc_final: 0.8217 (mpp) REVERT: g 186 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7060 (mp0) REVERT: g 191 LYS cc_start: 0.8471 (mttt) cc_final: 0.8054 (mtpt) REVERT: g 196 LYS cc_start: 0.9395 (ptmt) cc_final: 0.8912 (pptt) REVERT: g 229 MET cc_start: 0.1634 (mtt) cc_final: 0.1386 (mtp) REVERT: g 320 ASN cc_start: 0.7329 (m-40) cc_final: 0.7050 (t0) REVERT: h 185 MET cc_start: 0.8812 (mmm) cc_final: 0.8371 (ttt) REVERT: h 199 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7369 (mtpt) REVERT: h 382 MET cc_start: 0.7878 (mtm) cc_final: 0.7326 (mtm) REVERT: h 391 ASP cc_start: 0.8745 (m-30) cc_final: 0.8449 (t0) REVERT: q 34 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: q 75 GLU cc_start: 0.8026 (tp30) cc_final: 0.7669 (tp30) REVERT: q 242 TYR cc_start: 0.4866 (OUTLIER) cc_final: 0.4171 (m-80) REVERT: q 351 TYR cc_start: 0.6595 (p90) cc_final: 0.6158 (p90) REVERT: q 481 ASP cc_start: 0.8108 (t0) cc_final: 0.7905 (t70) REVERT: q 492 MET cc_start: 0.8715 (mmp) cc_final: 0.8411 (mmm) REVERT: z 194 MET cc_start: 0.7677 (tpt) cc_final: 0.7228 (tpt) REVERT: z 207 ILE cc_start: 0.8020 (mm) cc_final: 0.7585 (mm) REVERT: z 229 TYR cc_start: 0.8272 (m-80) cc_final: 0.7757 (m-80) outliers start: 178 outliers final: 103 residues processed: 976 average time/residue: 0.5747 time to fit residues: 949.7243 Evaluate side-chains 764 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 651 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 372 CYS Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 174 PHE Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 210 SER Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 346 HIS Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain Z residue 393 ASP Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 508 CYS Chi-restraints excluded: chain Z residue 521 ILE Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain a residue 398 VAL Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 289 CYS Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 394 LEU Chi-restraints excluded: chain b residue 462 VAL Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 150 ASP Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain d residue 452 ARG Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 188 VAL Chi-restraints excluded: chain e residue 405 CYS Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 171 LEU Chi-restraints excluded: chain g residue 197 LYS Chi-restraints excluded: chain g residue 372 CYS Chi-restraints excluded: chain h residue 29 CYS Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain q residue 34 GLN Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 242 TYR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 321 LEU Chi-restraints excluded: chain q residue 358 THR Chi-restraints excluded: chain q residue 403 THR Chi-restraints excluded: chain q residue 426 TYR Chi-restraints excluded: chain q residue 475 ASN Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 93 THR Chi-restraints excluded: chain z residue 156 LEU Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 320 ASN Chi-restraints excluded: chain z residue 500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 412 optimal weight: 30.0000 chunk 230 optimal weight: 30.0000 chunk 617 optimal weight: 6.9990 chunk 505 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 743 optimal weight: 0.9980 chunk 802 optimal weight: 0.0020 chunk 661 optimal weight: 6.9990 chunk 737 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 596 optimal weight: 5.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN D 406 HIS D 484 HIS D 494 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN G 157 ASN G 269 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 ASN ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 ASN Q 13 GLN ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Z 65 HIS ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 435 GLN ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 175 HIS e 289 GLN e 479 GLN g 442 GLN ** h 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 432 GLN ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN z 65 HIS z 70 GLN z 198 HIS z 497 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 63716 Z= 0.236 Angle : 0.571 15.143 85945 Z= 0.295 Chirality : 0.043 0.254 10292 Planarity : 0.004 0.086 11042 Dihedral : 3.817 47.156 8757 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.47 % Allowed : 8.48 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: -0.10 (0.09), residues: 8205 helix: 0.83 (0.08), residues: 4152 sheet: -0.57 (0.16), residues: 889 loop : -1.04 (0.10), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 168 HIS 0.013 0.001 HIS z 198 PHE 0.025 0.002 PHE B 317 TYR 0.021 0.002 TYR A 181 ARG 0.006 0.000 ARG E 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 689 time to evaluate : 5.552 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: A 42 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7999 (p0) REVERT: A 62 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8861 (mm) REVERT: A 246 MET cc_start: -0.0001 (tpp) cc_final: -0.0330 (ttm) REVERT: B 144 SER cc_start: 0.9103 (m) cc_final: 0.8699 (t) REVERT: B 244 MET cc_start: 0.2375 (ptm) cc_final: 0.2092 (ptm) REVERT: B 362 PHE cc_start: 0.6202 (m-10) cc_final: 0.5907 (m-80) REVERT: B 388 ARG cc_start: 0.9188 (ptp-170) cc_final: 0.8855 (ptp-170) REVERT: B 488 MET cc_start: 0.8455 (mmp) cc_final: 0.8121 (mmm) REVERT: B 493 ILE cc_start: 0.8815 (mt) cc_final: 0.8488 (mt) REVERT: D 67 ASP cc_start: 0.6755 (t0) cc_final: 0.6537 (t0) REVERT: D 320 MET cc_start: 0.0200 (mtt) cc_final: -0.0207 (mtt) REVERT: E 27 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.6156 (mpp) REVERT: E 237 MET cc_start: 0.4759 (mmm) cc_final: 0.4409 (mtp) REVERT: E 397 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7903 (pptt) REVERT: E 521 MET cc_start: 0.7899 (ptm) cc_final: 0.7679 (ptm) REVERT: E 530 ASP cc_start: 0.8344 (t0) cc_final: 0.7762 (t0) REVERT: G 104 GLU cc_start: 0.8282 (tp30) cc_final: 0.7952 (tm-30) REVERT: G 145 ASP cc_start: 0.7386 (t0) cc_final: 0.7067 (p0) REVERT: G 151 MET cc_start: 0.8897 (tpp) cc_final: 0.8694 (tpp) REVERT: G 198 TYR cc_start: 0.6411 (m-10) cc_final: 0.6102 (m-10) REVERT: G 415 GLU cc_start: 0.8226 (mp0) cc_final: 0.7992 (mp0) REVERT: H 61 ASP cc_start: 0.8256 (t70) cc_final: 0.7985 (t0) REVERT: H 359 ASN cc_start: 0.6206 (m-40) cc_final: 0.5911 (m-40) REVERT: H 382 MET cc_start: 0.5267 (mtm) cc_final: 0.4866 (mmm) REVERT: H 390 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8297 (t-90) REVERT: Q 130 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7848 (mt-10) REVERT: Q 215 SER cc_start: 0.8532 (m) cc_final: 0.8286 (p) REVERT: Q 249 MET cc_start: -0.0106 (mtt) cc_final: -0.3388 (ttm) REVERT: Q 276 MET cc_start: 0.6305 (ptt) cc_final: 0.5971 (tmm) REVERT: Z 190 MET cc_start: 0.7983 (ttm) cc_final: 0.7649 (ttm) REVERT: Z 221 MET cc_start: -0.0432 (mmt) cc_final: -0.1030 (mmm) REVERT: Z 321 MET cc_start: 0.8906 (tmm) cc_final: 0.8261 (ptm) REVERT: a 171 MET cc_start: 0.7848 (mtp) cc_final: 0.7503 (ttt) REVERT: a 206 MET cc_start: 0.6456 (ptm) cc_final: 0.6233 (ptm) REVERT: a 388 MET cc_start: 0.7826 (mtt) cc_final: 0.7241 (mmt) REVERT: b 52 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8476 (pt) REVERT: b 160 MET cc_start: 0.8544 (mtp) cc_final: 0.7911 (mmt) REVERT: b 400 THR cc_start: 0.9325 (m) cc_final: 0.9103 (p) REVERT: d 151 MET cc_start: 0.8255 (tpp) cc_final: 0.8029 (tpp) REVERT: d 355 MET cc_start: 0.5379 (ptt) cc_final: 0.4609 (ppp) REVERT: e 100 ILE cc_start: 0.7606 (tp) cc_final: 0.6734 (pt) REVERT: e 117 GLU cc_start: 0.8582 (tp30) cc_final: 0.8333 (tp30) REVERT: e 183 MET cc_start: 0.8378 (mtp) cc_final: 0.7649 (ptm) REVERT: e 297 LEU cc_start: 0.6754 (tp) cc_final: 0.6245 (mp) REVERT: e 472 MET cc_start: 0.7899 (tpp) cc_final: 0.7677 (tpp) REVERT: g 152 MET cc_start: 0.9049 (mpp) cc_final: 0.8270 (mpp) REVERT: g 191 LYS cc_start: 0.8566 (mttt) cc_final: 0.8028 (tptp) REVERT: g 196 LYS cc_start: 0.9406 (ptmt) cc_final: 0.8940 (pptt) REVERT: g 229 MET cc_start: 0.1773 (mtt) cc_final: 0.1500 (mtp) REVERT: g 362 PHE cc_start: 0.6618 (m-10) cc_final: 0.6355 (m-80) REVERT: h 185 MET cc_start: 0.8803 (mmm) cc_final: 0.8303 (ttt) REVERT: h 199 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7179 (mtpp) REVERT: h 352 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6770 (tp-100) REVERT: h 382 MET cc_start: 0.7941 (mtm) cc_final: 0.6964 (mtm) REVERT: h 391 ASP cc_start: 0.8747 (m-30) cc_final: 0.8488 (t0) REVERT: q 31 ARG cc_start: 0.7274 (mtt180) cc_final: 0.6952 (mtt-85) REVERT: q 75 GLU cc_start: 0.8037 (tp30) cc_final: 0.7733 (tp30) REVERT: q 102 ASN cc_start: 0.2331 (OUTLIER) cc_final: 0.0952 (p0) REVERT: q 492 MET cc_start: 0.8792 (mmp) cc_final: 0.8295 (mmm) REVERT: z 221 MET cc_start: 0.1872 (mmp) cc_final: 0.1351 (tpp) REVERT: z 229 TYR cc_start: 0.8279 (m-80) cc_final: 0.7739 (m-80) REVERT: z 355 LEU cc_start: 0.7307 (mp) cc_final: 0.6895 (mt) outliers start: 170 outliers final: 119 residues processed: 810 average time/residue: 0.5531 time to fit residues: 775.4766 Evaluate side-chains 757 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 629 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 397 LYS Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 168 TRP Chi-restraints excluded: chain G residue 372 CYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 149 CYS Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 213 ASP Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 346 HIS Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 521 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 394 LEU Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 129 ILE Chi-restraints excluded: chain e residue 164 ILE Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 517 LEU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 155 ILE Chi-restraints excluded: chain g residue 168 TRP Chi-restraints excluded: chain g residue 197 LYS Chi-restraints excluded: chain g residue 495 ILE Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 216 PHE Chi-restraints excluded: chain h residue 220 PHE Chi-restraints excluded: chain h residue 352 GLN Chi-restraints excluded: chain h residue 468 HIS Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 102 ASN Chi-restraints excluded: chain q residue 124 SER Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 321 LEU Chi-restraints excluded: chain q residue 403 THR Chi-restraints excluded: chain q residue 426 TYR Chi-restraints excluded: chain q residue 454 GLU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 93 THR Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 320 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 734 optimal weight: 0.2980 chunk 558 optimal weight: 1.9990 chunk 385 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 499 optimal weight: 2.9990 chunk 745 optimal weight: 20.0000 chunk 789 optimal weight: 2.9990 chunk 389 optimal weight: 6.9990 chunk 706 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 482 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 361 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS E 497 ASN E 520 GLN G 157 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 HIS ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 358 GLN e 401 HIS h 171 GLN ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN q 303 HIS z 65 HIS ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 63716 Z= 0.171 Angle : 0.515 12.427 85945 Z= 0.264 Chirality : 0.041 0.280 10292 Planarity : 0.003 0.083 11042 Dihedral : 3.724 48.297 8757 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.44 % Allowed : 9.21 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: 0.33 (0.09), residues: 8205 helix: 1.31 (0.08), residues: 4155 sheet: -0.47 (0.16), residues: 937 loop : -1.02 (0.10), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 168 HIS 0.023 0.001 HIS D 484 PHE 0.021 0.001 PHE B 317 TYR 0.022 0.001 TYR B 299 ARG 0.007 0.000 ARG z 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 684 time to evaluate : 5.490 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: A 62 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 246 MET cc_start: 0.0061 (tpp) cc_final: -0.0320 (ttm) REVERT: B 353 MET cc_start: 0.0595 (mmt) cc_final: 0.0169 (mmt) REVERT: B 388 ARG cc_start: 0.9184 (ptp-170) cc_final: 0.8897 (ptp90) REVERT: B 488 MET cc_start: 0.8434 (mmp) cc_final: 0.8135 (mmm) REVERT: B 493 ILE cc_start: 0.8777 (mt) cc_final: 0.8478 (mt) REVERT: D 67 ASP cc_start: 0.6763 (t0) cc_final: 0.6552 (t0) REVERT: D 320 MET cc_start: 0.0118 (mtt) cc_final: -0.0117 (mmt) REVERT: E 27 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6275 (mpp) REVERT: E 56 ASP cc_start: 0.8126 (m-30) cc_final: 0.7857 (t0) REVERT: E 237 MET cc_start: 0.4554 (mmm) cc_final: 0.4341 (mtp) REVERT: E 397 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7989 (pptt) REVERT: E 515 ILE cc_start: 0.9125 (pt) cc_final: 0.8773 (mt) REVERT: E 530 ASP cc_start: 0.8289 (t0) cc_final: 0.7555 (t0) REVERT: G 104 GLU cc_start: 0.8287 (tp30) cc_final: 0.7914 (tm-30) REVERT: G 145 ASP cc_start: 0.7419 (t0) cc_final: 0.7134 (p0) REVERT: G 198 TYR cc_start: 0.6223 (m-10) cc_final: 0.5970 (m-10) REVERT: H 61 ASP cc_start: 0.8204 (t70) cc_final: 0.7920 (t0) REVERT: H 359 ASN cc_start: 0.6208 (m-40) cc_final: 0.5904 (m-40) REVERT: H 382 MET cc_start: 0.5276 (mtm) cc_final: 0.4804 (mmm) REVERT: H 390 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8302 (t-90) REVERT: Q 206 LYS cc_start: 0.8835 (ptpt) cc_final: 0.8577 (mtpt) REVERT: Q 249 MET cc_start: -0.0326 (mtt) cc_final: -0.3399 (ttm) REVERT: Q 276 MET cc_start: 0.6466 (ptt) cc_final: 0.6057 (tmm) REVERT: Q 385 MET cc_start: 0.8129 (mtm) cc_final: 0.7369 (mtt) REVERT: Z 17 GLN cc_start: 0.8164 (pt0) cc_final: 0.7935 (pt0) REVERT: Z 68 GLN cc_start: 0.5223 (mp10) cc_final: 0.4498 (mp10) REVERT: Z 190 MET cc_start: 0.8066 (ttm) cc_final: 0.7725 (ttm) REVERT: Z 221 MET cc_start: -0.0489 (mmt) cc_final: -0.0975 (mmm) REVERT: Z 278 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6147 (pttp) REVERT: a 171 MET cc_start: 0.7946 (mtp) cc_final: 0.7601 (tmm) REVERT: a 388 MET cc_start: 0.7944 (mtt) cc_final: 0.7345 (mmt) REVERT: b 52 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8470 (pt) REVERT: b 156 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8480 (mtp-110) REVERT: b 160 MET cc_start: 0.8573 (mtp) cc_final: 0.7950 (mmt) REVERT: d 355 MET cc_start: 0.5253 (ptt) cc_final: 0.3041 (mmm) REVERT: d 409 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8737 (pp) REVERT: e 100 ILE cc_start: 0.7658 (tp) cc_final: 0.6752 (pt) REVERT: e 183 MET cc_start: 0.8381 (mtp) cc_final: 0.7578 (ptm) REVERT: e 297 LEU cc_start: 0.6791 (tp) cc_final: 0.6340 (mm) REVERT: g 152 MET cc_start: 0.8983 (mpp) cc_final: 0.8363 (mpp) REVERT: g 185 PHE cc_start: 0.7082 (t80) cc_final: 0.6779 (t80) REVERT: g 191 LYS cc_start: 0.8586 (mttt) cc_final: 0.8032 (tptp) REVERT: g 196 LYS cc_start: 0.9364 (ptmt) cc_final: 0.8870 (pptt) REVERT: g 229 MET cc_start: 0.1645 (mtt) cc_final: 0.1382 (mtp) REVERT: h 185 MET cc_start: 0.8768 (mmm) cc_final: 0.8329 (ttt) REVERT: h 199 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7191 (mtpp) REVERT: h 352 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6491 (tp-100) REVERT: h 382 MET cc_start: 0.7855 (mtm) cc_final: 0.6612 (mtm) REVERT: h 391 ASP cc_start: 0.8743 (m-30) cc_final: 0.8450 (t0) REVERT: q 75 GLU cc_start: 0.7993 (tp30) cc_final: 0.7753 (tp30) REVERT: q 351 TYR cc_start: 0.6751 (p90) cc_final: 0.6548 (p90) REVERT: q 385 MET cc_start: 0.8034 (ptp) cc_final: 0.7713 (ptm) REVERT: q 387 ASP cc_start: 0.8404 (p0) cc_final: 0.8031 (m-30) REVERT: q 492 MET cc_start: 0.8781 (mmp) cc_final: 0.8278 (mmm) REVERT: z 194 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6245 (tmm) REVERT: z 221 MET cc_start: 0.1825 (mmp) cc_final: 0.1320 (tpp) REVERT: z 229 TYR cc_start: 0.8305 (m-80) cc_final: 0.7765 (m-80) outliers start: 168 outliers final: 116 residues processed: 793 average time/residue: 0.5479 time to fit residues: 752.3676 Evaluate side-chains 741 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 614 time to evaluate : 5.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 397 LYS Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 372 CYS Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 210 SER Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain Z residue 142 GLU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 213 ASP Chi-restraints excluded: chain Z residue 278 LYS Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 346 HIS Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 508 CYS Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 156 ARG Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 394 LEU Chi-restraints excluded: chain b residue 478 LEU Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 409 LEU Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 405 CYS Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 155 ILE Chi-restraints excluded: chain g residue 168 TRP Chi-restraints excluded: chain g residue 495 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 216 PHE Chi-restraints excluded: chain h residue 220 PHE Chi-restraints excluded: chain h residue 352 GLN Chi-restraints excluded: chain h residue 468 HIS Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 242 TYR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 321 LEU Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain q residue 426 TYR Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 93 THR Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 194 MET Chi-restraints excluded: chain z residue 320 ASN Chi-restraints excluded: chain z residue 359 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 657 optimal weight: 5.9990 chunk 448 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 587 optimal weight: 20.0000 chunk 325 optimal weight: 0.8980 chunk 673 optimal weight: 6.9990 chunk 545 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 403 optimal weight: 6.9990 chunk 708 optimal weight: 0.4980 chunk 199 optimal weight: 0.8980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 GLN ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 HIS ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 361 HIS b 469 HIS e 493 HIS ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 86 GLN ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 468 HIS q 50 ASN z 65 HIS ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 63716 Z= 0.214 Angle : 0.543 11.936 85945 Z= 0.278 Chirality : 0.042 0.283 10292 Planarity : 0.003 0.086 11042 Dihedral : 3.792 48.557 8757 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.87 % Allowed : 9.53 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: 0.58 (0.09), residues: 8205 helix: 1.57 (0.08), residues: 4169 sheet: -0.41 (0.17), residues: 918 loop : -0.97 (0.10), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.036 0.001 HIS B 361 PHE 0.022 0.001 PHE B 317 TYR 0.019 0.001 TYR A 181 ARG 0.006 0.000 ARG d 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 646 time to evaluate : 5.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8851 (mm) REVERT: A 246 MET cc_start: 0.0038 (tpp) cc_final: -0.0319 (ttm) REVERT: B 353 MET cc_start: 0.0905 (mmt) cc_final: 0.0396 (mmt) REVERT: B 388 ARG cc_start: 0.9165 (ptp-170) cc_final: 0.8881 (ptp90) REVERT: B 399 GLN cc_start: 0.8450 (mp10) cc_final: 0.7906 (mp10) REVERT: D 439 TYR cc_start: 0.6557 (m-80) cc_final: 0.6262 (m-10) REVERT: D 489 LYS cc_start: 0.8803 (pttm) cc_final: 0.8597 (pttm) REVERT: E 27 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5987 (mpp) REVERT: E 397 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8085 (pptt) REVERT: E 515 ILE cc_start: 0.9123 (pt) cc_final: 0.8846 (mt) REVERT: E 530 ASP cc_start: 0.8423 (t0) cc_final: 0.7083 (t0) REVERT: G 104 GLU cc_start: 0.8315 (tp30) cc_final: 0.7946 (tm-30) REVERT: G 145 ASP cc_start: 0.7433 (t0) cc_final: 0.7185 (p0) REVERT: G 151 MET cc_start: 0.8877 (tpp) cc_final: 0.8473 (tpp) REVERT: G 196 LYS cc_start: 0.7810 (mttt) cc_final: 0.7515 (tptp) REVERT: G 198 TYR cc_start: 0.6271 (m-10) cc_final: 0.6020 (m-10) REVERT: G 395 MET cc_start: 0.8957 (mtp) cc_final: 0.8746 (ptm) REVERT: H 61 ASP cc_start: 0.8190 (t70) cc_final: 0.7928 (t0) REVERT: H 382 MET cc_start: 0.5278 (mtm) cc_final: 0.4825 (mmm) REVERT: H 390 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.8333 (t-90) REVERT: Q 206 LYS cc_start: 0.8888 (ptpt) cc_final: 0.8603 (mtpt) REVERT: Q 249 MET cc_start: -0.0632 (mtt) cc_final: -0.3485 (ttm) REVERT: Q 276 MET cc_start: 0.6382 (ptt) cc_final: 0.6047 (tmm) REVERT: Q 311 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6930 (mtm) REVERT: Q 385 MET cc_start: 0.8187 (mtm) cc_final: 0.7517 (mtt) REVERT: Z 190 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7817 (ttt) REVERT: Z 221 MET cc_start: -0.0586 (mmt) cc_final: -0.0999 (mmm) REVERT: Z 278 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6182 (pttp) REVERT: Z 321 MET cc_start: 0.8893 (tmm) cc_final: 0.8364 (ptm) REVERT: Z 485 GLU cc_start: 0.7665 (pm20) cc_final: 0.7382 (pm20) REVERT: a 99 GLU cc_start: 0.8455 (tp30) cc_final: 0.7846 (tm-30) REVERT: a 171 MET cc_start: 0.7789 (mtp) cc_final: 0.7480 (tmm) REVERT: a 388 MET cc_start: 0.8042 (mtt) cc_final: 0.7332 (mmt) REVERT: b 52 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8386 (pt) REVERT: b 156 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8541 (mtp-110) REVERT: b 160 MET cc_start: 0.8544 (mtp) cc_final: 0.7972 (mmt) REVERT: b 392 ASP cc_start: 0.7875 (m-30) cc_final: 0.7374 (t0) REVERT: d 355 MET cc_start: 0.5208 (ptt) cc_final: 0.3016 (mmm) REVERT: d 410 CYS cc_start: 0.9121 (m) cc_final: 0.8639 (m) REVERT: e 100 ILE cc_start: 0.7818 (tp) cc_final: 0.6949 (pt) REVERT: e 117 GLU cc_start: 0.8692 (tp30) cc_final: 0.8409 (tp30) REVERT: e 183 MET cc_start: 0.8427 (mtp) cc_final: 0.7628 (ptm) REVERT: e 297 LEU cc_start: 0.6794 (tp) cc_final: 0.6316 (mm) REVERT: g 152 MET cc_start: 0.8997 (mpp) cc_final: 0.8450 (mpp) REVERT: g 177 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8387 (pp) REVERT: g 191 LYS cc_start: 0.8637 (mttt) cc_final: 0.7953 (tttp) REVERT: g 196 LYS cc_start: 0.9377 (ptmt) cc_final: 0.8905 (pptt) REVERT: g 404 ASP cc_start: 0.7521 (t0) cc_final: 0.7258 (t0) REVERT: h 57 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8645 (t) REVERT: h 172 LYS cc_start: 0.8618 (pttt) cc_final: 0.8373 (pttt) REVERT: h 185 MET cc_start: 0.8755 (mmm) cc_final: 0.8354 (ttt) REVERT: h 199 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7125 (mtpp) REVERT: h 227 MET cc_start: -0.0996 (ptp) cc_final: -0.2162 (ttt) REVERT: h 352 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6388 (tp-100) REVERT: h 372 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: h 382 MET cc_start: 0.7863 (mtm) cc_final: 0.6758 (mtm) REVERT: h 391 ASP cc_start: 0.8743 (m-30) cc_final: 0.8487 (t0) REVERT: q 75 GLU cc_start: 0.8054 (tp30) cc_final: 0.7801 (tp30) REVERT: q 102 ASN cc_start: 0.2325 (OUTLIER) cc_final: 0.0935 (p0) REVERT: q 492 MET cc_start: 0.8843 (mmp) cc_final: 0.8398 (mmm) REVERT: z 194 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.5817 (ttm) REVERT: z 221 MET cc_start: 0.1652 (mmp) cc_final: 0.1153 (tpp) REVERT: z 229 TYR cc_start: 0.8359 (m-80) cc_final: 0.7718 (m-80) REVERT: z 526 MET cc_start: 0.1653 (tpt) cc_final: 0.1151 (tpt) outliers start: 197 outliers final: 135 residues processed: 776 average time/residue: 0.5575 time to fit residues: 751.1152 Evaluate side-chains 750 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 599 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 397 LYS Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 372 CYS Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 149 CYS Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 190 MET Chi-restraints excluded: chain Z residue 278 LYS Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 346 HIS Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 508 CYS Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 156 ARG Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 304 PHE Chi-restraints excluded: chain b residue 361 HIS Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 394 LEU Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain d residue 452 ARG Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 129 ILE Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 517 LEU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 155 ILE Chi-restraints excluded: chain g residue 168 TRP Chi-restraints excluded: chain g residue 177 LEU Chi-restraints excluded: chain g residue 495 ILE Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 90 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 216 PHE Chi-restraints excluded: chain h residue 220 PHE Chi-restraints excluded: chain h residue 352 GLN Chi-restraints excluded: chain h residue 372 PHE Chi-restraints excluded: chain h residue 456 ASP Chi-restraints excluded: chain h residue 468 HIS Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 102 ASN Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 217 VAL Chi-restraints excluded: chain q residue 242 TYR Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain q residue 401 VAL Chi-restraints excluded: chain q residue 403 THR Chi-restraints excluded: chain q residue 426 TYR Chi-restraints excluded: chain q residue 428 GLU Chi-restraints excluded: chain q residue 443 GLU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 156 LEU Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 194 MET Chi-restraints excluded: chain z residue 320 ASN Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 389 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 265 optimal weight: 9.9990 chunk 711 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 463 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 790 optimal weight: 30.0000 chunk 656 optimal weight: 0.9980 chunk 365 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 414 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 17 GLN Z 65 HIS ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 361 HIS d 406 HIS g 221 ASN h 30 GLN ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 172 GLN z 65 HIS ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 63716 Z= 0.208 Angle : 0.539 10.660 85945 Z= 0.274 Chirality : 0.042 0.273 10292 Planarity : 0.003 0.085 11042 Dihedral : 3.799 49.299 8757 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.82 % Allowed : 9.95 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: 0.72 (0.09), residues: 8205 helix: 1.72 (0.08), residues: 4162 sheet: -0.31 (0.17), residues: 884 loop : -0.97 (0.10), residues: 3159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 478 HIS 0.026 0.001 HIS h 468 PHE 0.021 0.001 PHE Q 399 TYR 0.024 0.001 TYR b 213 ARG 0.007 0.000 ARG q 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 624 time to evaluate : 5.721 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: A 62 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8814 (mm) REVERT: A 246 MET cc_start: 0.0115 (tpp) cc_final: -0.0277 (mtm) REVERT: B 287 ILE cc_start: 0.3239 (pt) cc_final: 0.2856 (pt) REVERT: B 388 ARG cc_start: 0.9160 (ptp-170) cc_final: 0.8870 (ptp90) REVERT: E 56 ASP cc_start: 0.8243 (m-30) cc_final: 0.7956 (t0) REVERT: E 397 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8089 (pptt) REVERT: E 515 ILE cc_start: 0.9093 (pt) cc_final: 0.8855 (mt) REVERT: E 530 ASP cc_start: 0.8420 (t0) cc_final: 0.7643 (m-30) REVERT: G 104 GLU cc_start: 0.8318 (tp30) cc_final: 0.8001 (tm-30) REVERT: G 151 MET cc_start: 0.8878 (tpp) cc_final: 0.8438 (tpp) REVERT: G 196 LYS cc_start: 0.7834 (mttt) cc_final: 0.7569 (tptp) REVERT: G 198 TYR cc_start: 0.6244 (m-10) cc_final: 0.6025 (m-10) REVERT: H 61 ASP cc_start: 0.8205 (t70) cc_final: 0.7949 (t0) REVERT: H 382 MET cc_start: 0.5379 (mtm) cc_final: 0.4849 (mmm) REVERT: H 390 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8323 (t-90) REVERT: Q 30 TYR cc_start: 0.6504 (t80) cc_final: 0.6284 (t80) REVERT: Q 67 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9088 (p0) REVERT: Q 249 MET cc_start: -0.0640 (mtt) cc_final: -0.3475 (ttm) REVERT: Q 276 MET cc_start: 0.6429 (ptt) cc_final: 0.6137 (tmm) REVERT: Q 311 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6980 (mtm) REVERT: Z 53 ASP cc_start: 0.7184 (t70) cc_final: 0.6927 (t70) REVERT: Z 68 GLN cc_start: 0.5602 (mp10) cc_final: 0.4885 (mp10) REVERT: Z 190 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7884 (ttt) REVERT: Z 221 MET cc_start: -0.0581 (mmt) cc_final: -0.1108 (mmm) REVERT: Z 278 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6045 (pttt) REVERT: a 99 GLU cc_start: 0.8485 (tp30) cc_final: 0.7930 (tm-30) REVERT: a 171 MET cc_start: 0.7812 (mtp) cc_final: 0.7476 (tmm) REVERT: a 388 MET cc_start: 0.8140 (mtt) cc_final: 0.7522 (mmt) REVERT: b 52 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8412 (pt) REVERT: b 160 MET cc_start: 0.8544 (mtp) cc_final: 0.8053 (mmt) REVERT: b 310 MET cc_start: 0.2528 (OUTLIER) cc_final: 0.2258 (ttp) REVERT: b 392 ASP cc_start: 0.8059 (m-30) cc_final: 0.7599 (t0) REVERT: d 67 ASP cc_start: 0.7685 (t0) cc_final: 0.7325 (t0) REVERT: d 355 MET cc_start: 0.5209 (ptt) cc_final: 0.3006 (mmm) REVERT: d 410 CYS cc_start: 0.9183 (m) cc_final: 0.8619 (m) REVERT: e 100 ILE cc_start: 0.7966 (tp) cc_final: 0.7128 (pt) REVERT: e 117 GLU cc_start: 0.8756 (tp30) cc_final: 0.8459 (tp30) REVERT: e 183 MET cc_start: 0.8445 (mtp) cc_final: 0.7641 (ptm) REVERT: e 297 LEU cc_start: 0.6825 (tp) cc_final: 0.6373 (mm) REVERT: g 152 MET cc_start: 0.8987 (mpp) cc_final: 0.8464 (mpp) REVERT: g 177 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8420 (pp) REVERT: g 191 LYS cc_start: 0.8601 (mttt) cc_final: 0.8061 (tptm) REVERT: g 196 LYS cc_start: 0.9375 (ptmt) cc_final: 0.8942 (pptt) REVERT: g 229 MET cc_start: 0.0574 (mtt) cc_final: 0.0292 (mtp) REVERT: g 404 ASP cc_start: 0.7600 (t0) cc_final: 0.7326 (t0) REVERT: h 57 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8647 (t) REVERT: h 172 LYS cc_start: 0.8701 (pttt) cc_final: 0.8451 (pttt) REVERT: h 185 MET cc_start: 0.8777 (mmm) cc_final: 0.8382 (ttt) REVERT: h 199 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7144 (mtpp) REVERT: h 227 MET cc_start: -0.1063 (ptp) cc_final: -0.2329 (ttt) REVERT: h 352 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6434 (tp-100) REVERT: h 372 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: h 382 MET cc_start: 0.7793 (mtm) cc_final: 0.6731 (mtm) REVERT: h 391 ASP cc_start: 0.8747 (m-30) cc_final: 0.8490 (t0) REVERT: q 31 ARG cc_start: 0.7304 (mtt-85) cc_final: 0.7064 (mtt-85) REVERT: q 75 GLU cc_start: 0.8061 (tp30) cc_final: 0.7491 (tp30) REVERT: q 102 ASN cc_start: 0.2156 (OUTLIER) cc_final: 0.0798 (p0) REVERT: q 385 MET cc_start: 0.8246 (ptp) cc_final: 0.7927 (ptm) REVERT: q 492 MET cc_start: 0.8859 (mmp) cc_final: 0.8452 (mmm) REVERT: z 194 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6020 (ttm) REVERT: z 221 MET cc_start: 0.1603 (mmp) cc_final: 0.1074 (tpp) REVERT: z 229 TYR cc_start: 0.8327 (m-80) cc_final: 0.7644 (m-80) REVERT: z 522 MET cc_start: 0.8095 (mmm) cc_final: 0.7862 (mmp) REVERT: z 523 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7642 (mtp-110) outliers start: 194 outliers final: 142 residues processed: 752 average time/residue: 0.5657 time to fit residues: 740.4063 Evaluate side-chains 746 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 588 time to evaluate : 5.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 397 LYS Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 372 CYS Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 149 CYS Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 176 ILE Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 190 MET Chi-restraints excluded: chain Z residue 213 ASP Chi-restraints excluded: chain Z residue 278 LYS Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 346 HIS Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 508 CYS Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 304 PHE Chi-restraints excluded: chain b residue 310 MET Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 147 ILE Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain d residue 452 ARG Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 517 LEU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 155 ILE Chi-restraints excluded: chain g residue 168 TRP Chi-restraints excluded: chain g residue 177 LEU Chi-restraints excluded: chain g residue 495 ILE Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 90 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 216 PHE Chi-restraints excluded: chain h residue 220 PHE Chi-restraints excluded: chain h residue 352 GLN Chi-restraints excluded: chain h residue 372 PHE Chi-restraints excluded: chain h residue 456 ASP Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 102 ASN Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 208 LEU Chi-restraints excluded: chain q residue 217 VAL Chi-restraints excluded: chain q residue 242 TYR Chi-restraints excluded: chain q residue 285 ASP Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 377 LEU Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain q residue 403 THR Chi-restraints excluded: chain q residue 426 TYR Chi-restraints excluded: chain q residue 428 GLU Chi-restraints excluded: chain q residue 454 GLU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 156 LEU Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 194 MET Chi-restraints excluded: chain z residue 320 ASN Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain z residue 389 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 762 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 450 optimal weight: 7.9990 chunk 577 optimal weight: 20.0000 chunk 447 optimal weight: 5.9990 chunk 665 optimal weight: 9.9990 chunk 441 optimal weight: 0.4980 chunk 787 optimal weight: 3.9990 chunk 492 optimal weight: 2.9990 chunk 480 optimal weight: 30.0000 chunk 363 optimal weight: 0.5980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 140 HIS q 198 ASN q 201 ASN z 65 HIS ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 63716 Z= 0.211 Angle : 0.550 13.102 85945 Z= 0.278 Chirality : 0.042 0.330 10292 Planarity : 0.003 0.086 11042 Dihedral : 3.835 49.278 8757 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.91 % Allowed : 10.18 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: 0.79 (0.09), residues: 8205 helix: 1.81 (0.08), residues: 4161 sheet: -0.39 (0.17), residues: 874 loop : -0.94 (0.10), residues: 3170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.025 0.001 HIS B 361 PHE 0.027 0.001 PHE B 362 TYR 0.028 0.001 TYR Q 30 ARG 0.014 0.000 ARG G 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 619 time to evaluate : 5.498 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: A 62 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8807 (mm) REVERT: A 246 MET cc_start: 0.0150 (tpp) cc_final: -0.0268 (mtm) REVERT: B 388 ARG cc_start: 0.9147 (ptp-170) cc_final: 0.8837 (ptp90) REVERT: D 320 MET cc_start: 0.0823 (mmt) cc_final: -0.0417 (mtt) REVERT: E 27 MET cc_start: 0.6166 (mpp) cc_final: 0.5543 (mpp) REVERT: E 56 ASP cc_start: 0.8245 (m-30) cc_final: 0.7953 (t0) REVERT: E 397 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8117 (pptt) REVERT: E 515 ILE cc_start: 0.9090 (pt) cc_final: 0.8877 (mt) REVERT: E 530 ASP cc_start: 0.8184 (t0) cc_final: 0.7388 (m-30) REVERT: G 104 GLU cc_start: 0.8316 (tp30) cc_final: 0.8002 (tm-30) REVERT: G 196 LYS cc_start: 0.7826 (mttt) cc_final: 0.7613 (tptp) REVERT: G 232 TYR cc_start: 0.6321 (m-80) cc_final: 0.5829 (m-80) REVERT: H 178 MET cc_start: 0.8645 (mmm) cc_final: 0.8116 (mtm) REVERT: H 382 MET cc_start: 0.5348 (mtm) cc_final: 0.4770 (mmm) REVERT: H 390 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8351 (t-90) REVERT: Q 67 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.9073 (p0) REVERT: Q 117 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8234 (mm-30) REVERT: Q 249 MET cc_start: -0.0801 (mtt) cc_final: -0.3558 (ttm) REVERT: Q 276 MET cc_start: 0.6407 (ptt) cc_final: 0.6130 (tmm) REVERT: Q 311 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.7015 (mtm) REVERT: Z 53 ASP cc_start: 0.7241 (t70) cc_final: 0.6991 (t70) REVERT: Z 190 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7964 (ttt) REVERT: Z 221 MET cc_start: -0.0609 (mmt) cc_final: -0.1028 (mmm) REVERT: Z 278 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6093 (pttt) REVERT: Z 321 MET cc_start: 0.8886 (tmm) cc_final: 0.8355 (ptm) REVERT: a 99 GLU cc_start: 0.8485 (tp30) cc_final: 0.7932 (tm-30) REVERT: a 171 MET cc_start: 0.7857 (mtp) cc_final: 0.7590 (ppp) REVERT: a 388 MET cc_start: 0.8095 (mtt) cc_final: 0.7472 (mmt) REVERT: b 51 ILE cc_start: 0.9246 (mt) cc_final: 0.9004 (tt) REVERT: b 52 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8424 (pt) REVERT: b 160 MET cc_start: 0.8559 (mtp) cc_final: 0.8104 (mmt) REVERT: b 310 MET cc_start: 0.2573 (OUTLIER) cc_final: 0.2303 (ttp) REVERT: b 392 ASP cc_start: 0.8056 (m-30) cc_final: 0.7603 (t0) REVERT: d 355 MET cc_start: 0.5223 (ptt) cc_final: 0.2884 (mmm) REVERT: d 410 CYS cc_start: 0.9126 (m) cc_final: 0.8534 (m) REVERT: e 117 GLU cc_start: 0.8817 (tp30) cc_final: 0.8484 (tp30) REVERT: e 183 MET cc_start: 0.8456 (mtp) cc_final: 0.7678 (ptm) REVERT: e 297 LEU cc_start: 0.6895 (tp) cc_final: 0.6453 (mm) REVERT: g 54 MET cc_start: 0.7653 (mtm) cc_final: 0.7271 (mpp) REVERT: g 152 MET cc_start: 0.9004 (mpp) cc_final: 0.8490 (mpp) REVERT: g 177 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8472 (pp) REVERT: g 185 PHE cc_start: 0.7063 (t80) cc_final: 0.6753 (t80) REVERT: g 191 LYS cc_start: 0.8678 (mttt) cc_final: 0.8147 (tptp) REVERT: g 196 LYS cc_start: 0.9346 (ptmt) cc_final: 0.9003 (pptt) REVERT: g 229 MET cc_start: 0.0689 (mtt) cc_final: 0.0451 (mtp) REVERT: g 404 ASP cc_start: 0.7661 (t0) cc_final: 0.7367 (t0) REVERT: h 199 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7230 (mtpt) REVERT: h 352 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6467 (tp-100) REVERT: h 382 MET cc_start: 0.7804 (mtm) cc_final: 0.7141 (mtm) REVERT: h 391 ASP cc_start: 0.8760 (m-30) cc_final: 0.8510 (t0) REVERT: q 31 ARG cc_start: 0.7328 (mtt-85) cc_final: 0.7065 (mtt-85) REVERT: q 75 GLU cc_start: 0.8078 (tp30) cc_final: 0.7524 (tp30) REVERT: q 102 ASN cc_start: 0.2177 (OUTLIER) cc_final: 0.0849 (p0) REVERT: q 385 MET cc_start: 0.8396 (ptp) cc_final: 0.8121 (ptm) REVERT: z 221 MET cc_start: 0.1671 (mmp) cc_final: 0.1190 (tpp) REVERT: z 229 TYR cc_start: 0.8425 (m-80) cc_final: 0.7679 (m-80) outliers start: 200 outliers final: 147 residues processed: 759 average time/residue: 0.5397 time to fit residues: 713.9700 Evaluate side-chains 752 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 591 time to evaluate : 5.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 129 HIS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 397 LYS Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 372 CYS Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 480 ASN Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain Q residue 149 CYS Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 190 MET Chi-restraints excluded: chain Z residue 278 LYS Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 346 HIS Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 508 CYS Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 304 PHE Chi-restraints excluded: chain b residue 310 MET Chi-restraints excluded: chain b residue 394 LEU Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 150 ASP Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain d residue 452 ARG Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 129 ILE Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 517 LEU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 155 ILE Chi-restraints excluded: chain g residue 168 TRP Chi-restraints excluded: chain g residue 177 LEU Chi-restraints excluded: chain g residue 495 ILE Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 90 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 216 PHE Chi-restraints excluded: chain h residue 352 GLN Chi-restraints excluded: chain h residue 456 ASP Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 55 MET Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 102 ASN Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 208 LEU Chi-restraints excluded: chain q residue 217 VAL Chi-restraints excluded: chain q residue 242 TYR Chi-restraints excluded: chain q residue 285 ASP Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 377 LEU Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain q residue 401 VAL Chi-restraints excluded: chain q residue 403 THR Chi-restraints excluded: chain q residue 428 GLU Chi-restraints excluded: chain q residue 454 GLU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 521 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 320 ASN Chi-restraints excluded: chain z residue 359 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 487 optimal weight: 2.9990 chunk 314 optimal weight: 0.4980 chunk 470 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 500 optimal weight: 6.9990 chunk 536 optimal weight: 5.9990 chunk 389 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 618 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 234 HIS ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 GLN ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 HIS ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 502 GLN ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 331 GLN h 380 GLN h 390 HIS ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 471 HIS z 65 HIS ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 63716 Z= 0.248 Angle : 0.593 13.790 85945 Z= 0.301 Chirality : 0.043 0.334 10292 Planarity : 0.004 0.087 11042 Dihedral : 3.999 49.605 8757 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.66 % Allowed : 11.01 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: 0.72 (0.09), residues: 8205 helix: 1.77 (0.08), residues: 4163 sheet: -0.41 (0.18), residues: 854 loop : -1.00 (0.10), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 478 HIS 0.012 0.001 HIS B 361 PHE 0.035 0.002 PHE Q 191 TYR 0.026 0.002 TYR B 299 ARG 0.013 0.000 ARG z 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 620 time to evaluate : 5.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8842 (mm) REVERT: A 246 MET cc_start: -0.0114 (tpp) cc_final: -0.0464 (mtm) REVERT: A 473 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: B 388 ARG cc_start: 0.9153 (ptp-170) cc_final: 0.8832 (ptp90) REVERT: D 48 ILE cc_start: 0.9475 (tp) cc_final: 0.9176 (tt) REVERT: D 320 MET cc_start: 0.0614 (mmt) cc_final: -0.0502 (mtt) REVERT: E 27 MET cc_start: 0.6492 (mpp) cc_final: 0.5994 (mpp) REVERT: E 56 ASP cc_start: 0.8261 (m-30) cc_final: 0.7964 (t0) REVERT: E 397 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7646 (pptt) REVERT: E 530 ASP cc_start: 0.8277 (t0) cc_final: 0.7482 (m-30) REVERT: G 104 GLU cc_start: 0.8379 (tp30) cc_final: 0.8006 (tm-30) REVERT: G 196 LYS cc_start: 0.7975 (mttt) cc_final: 0.7683 (tptp) REVERT: G 232 TYR cc_start: 0.6382 (m-80) cc_final: 0.5928 (m-80) REVERT: G 520 ASP cc_start: 0.7955 (p0) cc_final: 0.7691 (t0) REVERT: H 170 GLN cc_start: 0.7061 (mm110) cc_final: 0.6812 (mp10) REVERT: H 172 LYS cc_start: 0.7437 (pttt) cc_final: 0.6979 (mttm) REVERT: H 178 MET cc_start: 0.8602 (mmm) cc_final: 0.8254 (mtt) REVERT: H 382 MET cc_start: 0.5541 (mtm) cc_final: 0.4951 (mmm) REVERT: H 390 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.8364 (t-90) REVERT: H 402 ASN cc_start: 0.6627 (t0) cc_final: 0.5957 (t0) REVERT: H 403 ASP cc_start: 0.6828 (m-30) cc_final: 0.6004 (t0) REVERT: Q 31 ARG cc_start: 0.8227 (mmt180) cc_final: 0.7957 (mtt180) REVERT: Q 67 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.9083 (p0) REVERT: Q 249 MET cc_start: -0.0987 (mtt) cc_final: -0.3690 (ttm) REVERT: Q 276 MET cc_start: 0.6576 (ptt) cc_final: 0.6239 (tmm) REVERT: Q 311 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7239 (mtm) REVERT: Q 323 ARG cc_start: 0.8469 (tpt170) cc_final: 0.7935 (tpt170) REVERT: Z 53 ASP cc_start: 0.7356 (t70) cc_final: 0.7111 (t70) REVERT: Z 190 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: Z 221 MET cc_start: -0.0726 (mmt) cc_final: -0.1130 (mmm) REVERT: Z 278 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6121 (pttt) REVERT: Z 321 MET cc_start: 0.8874 (tmm) cc_final: 0.8370 (ptm) REVERT: a 99 GLU cc_start: 0.8510 (tp30) cc_final: 0.7977 (tm-30) REVERT: a 171 MET cc_start: 0.7873 (mtp) cc_final: 0.7617 (tmm) REVERT: a 388 MET cc_start: 0.8096 (mtt) cc_final: 0.7434 (mmt) REVERT: b 52 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8397 (pt) REVERT: b 87 MET cc_start: 0.8437 (tpp) cc_final: 0.8210 (tpp) REVERT: b 160 MET cc_start: 0.8591 (mtp) cc_final: 0.8206 (mmt) REVERT: b 310 MET cc_start: 0.2738 (OUTLIER) cc_final: 0.2501 (ttp) REVERT: b 392 ASP cc_start: 0.8064 (m-30) cc_final: 0.7645 (t0) REVERT: d 186 MET cc_start: 0.5360 (tpp) cc_final: 0.5140 (tpp) REVERT: d 355 MET cc_start: 0.5334 (ptt) cc_final: 0.3009 (mmm) REVERT: d 410 CYS cc_start: 0.9176 (m) cc_final: 0.8597 (m) REVERT: e 117 GLU cc_start: 0.8866 (tp30) cc_final: 0.8593 (tp30) REVERT: e 401 HIS cc_start: 0.8898 (m90) cc_final: 0.8630 (m-70) REVERT: g 54 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7444 (mpp) REVERT: g 104 GLU cc_start: 0.8625 (tp30) cc_final: 0.8275 (tm-30) REVERT: g 152 MET cc_start: 0.9027 (mpp) cc_final: 0.8499 (mpp) REVERT: g 177 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8587 (pp) REVERT: g 191 LYS cc_start: 0.8705 (mttt) cc_final: 0.8162 (tptp) REVERT: g 196 LYS cc_start: 0.9285 (ptmt) cc_final: 0.8973 (pptt) REVERT: g 404 ASP cc_start: 0.7755 (t0) cc_final: 0.7454 (t0) REVERT: h 172 LYS cc_start: 0.8801 (pttt) cc_final: 0.8549 (pttt) REVERT: h 199 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7259 (mtpt) REVERT: h 352 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6632 (tp-100) REVERT: h 382 MET cc_start: 0.7835 (mtm) cc_final: 0.7222 (mtm) REVERT: h 387 ARG cc_start: 0.7900 (ptp90) cc_final: 0.7633 (ptt180) REVERT: h 391 ASP cc_start: 0.8768 (m-30) cc_final: 0.8513 (t0) REVERT: h 479 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7478 (mp) REVERT: q 75 GLU cc_start: 0.8117 (tp30) cc_final: 0.7575 (tp30) REVERT: q 102 ASN cc_start: 0.2559 (OUTLIER) cc_final: 0.1156 (p0) REVERT: q 276 MET cc_start: 0.2033 (ttp) cc_final: 0.1804 (ttp) REVERT: q 311 MET cc_start: 0.5822 (mpp) cc_final: 0.5572 (mmt) REVERT: q 385 MET cc_start: 0.8514 (ptp) cc_final: 0.8257 (ptm) REVERT: q 416 GLU cc_start: 0.8060 (mp0) cc_final: 0.7840 (mp0) REVERT: z 221 MET cc_start: 0.1574 (mmp) cc_final: 0.1043 (tpp) outliers start: 183 outliers final: 142 residues processed: 747 average time/residue: 0.5552 time to fit residues: 723.1713 Evaluate side-chains 735 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 577 time to evaluate : 5.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 397 LYS Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 149 CYS Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 190 MET Chi-restraints excluded: chain Z residue 278 LYS Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 508 CYS Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 304 PHE Chi-restraints excluded: chain b residue 310 MET Chi-restraints excluded: chain b residue 394 LEU Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain d residue 452 ARG Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 129 ILE Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 517 LEU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 54 MET Chi-restraints excluded: chain g residue 155 ILE Chi-restraints excluded: chain g residue 168 TRP Chi-restraints excluded: chain g residue 171 LEU Chi-restraints excluded: chain g residue 177 LEU Chi-restraints excluded: chain g residue 495 ILE Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 90 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 216 PHE Chi-restraints excluded: chain h residue 352 GLN Chi-restraints excluded: chain h residue 372 PHE Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 102 ASN Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 208 LEU Chi-restraints excluded: chain q residue 217 VAL Chi-restraints excluded: chain q residue 242 TYR Chi-restraints excluded: chain q residue 285 ASP Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 377 LEU Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain q residue 401 VAL Chi-restraints excluded: chain q residue 403 THR Chi-restraints excluded: chain q residue 428 GLU Chi-restraints excluded: chain q residue 454 GLU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 521 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 320 ASN Chi-restraints excluded: chain z residue 359 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 716 optimal weight: 5.9990 chunk 754 optimal weight: 0.7980 chunk 688 optimal weight: 4.9990 chunk 733 optimal weight: 10.0000 chunk 441 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 chunk 576 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 663 optimal weight: 4.9990 chunk 694 optimal weight: 50.0000 chunk 731 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS E 182 GLN E 296 ASN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 153 ASN ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 228 GLN h 390 HIS ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 63716 Z= 0.190 Angle : 0.568 12.350 85945 Z= 0.285 Chirality : 0.042 0.307 10292 Planarity : 0.003 0.086 11042 Dihedral : 3.918 49.495 8757 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.49 % Allowed : 11.42 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: 0.83 (0.09), residues: 8205 helix: 1.89 (0.08), residues: 4167 sheet: -0.43 (0.17), residues: 899 loop : -0.99 (0.10), residues: 3139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.010 0.001 HIS E 401 PHE 0.026 0.001 PHE d 35 TYR 0.022 0.001 TYR A 181 ARG 0.008 0.000 ARG z 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 610 time to evaluate : 5.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8857 (mm) REVERT: A 246 MET cc_start: -0.0159 (tpp) cc_final: -0.0533 (mtm) REVERT: A 388 MET cc_start: 0.7537 (mtt) cc_final: 0.7302 (mmp) REVERT: A 473 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: B 353 MET cc_start: 0.1796 (mmp) cc_final: 0.1382 (mmp) REVERT: B 388 ARG cc_start: 0.9146 (ptp-170) cc_final: 0.8833 (ptp90) REVERT: D 48 ILE cc_start: 0.9435 (tp) cc_final: 0.9117 (tt) REVERT: D 320 MET cc_start: 0.0644 (mmt) cc_final: -0.0457 (mtt) REVERT: E 27 MET cc_start: 0.6497 (mpp) cc_final: 0.6043 (mpp) REVERT: E 56 ASP cc_start: 0.8226 (m-30) cc_final: 0.7927 (t0) REVERT: E 530 ASP cc_start: 0.8215 (t0) cc_final: 0.7442 (m-30) REVERT: G 104 GLU cc_start: 0.8326 (tp30) cc_final: 0.8042 (tm-30) REVERT: G 196 LYS cc_start: 0.7833 (mttt) cc_final: 0.7602 (tptp) REVERT: G 232 TYR cc_start: 0.6422 (m-80) cc_final: 0.5959 (m-80) REVERT: G 520 ASP cc_start: 0.7935 (p0) cc_final: 0.7678 (t0) REVERT: H 178 MET cc_start: 0.8532 (mmm) cc_final: 0.8167 (mtm) REVERT: H 382 MET cc_start: 0.5525 (mtm) cc_final: 0.4926 (mmm) REVERT: H 390 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8407 (t-90) REVERT: H 402 ASN cc_start: 0.6669 (t0) cc_final: 0.5953 (t0) REVERT: H 403 ASP cc_start: 0.6741 (m-30) cc_final: 0.6020 (t0) REVERT: Q 31 ARG cc_start: 0.8141 (mmt180) cc_final: 0.7860 (mtt180) REVERT: Q 67 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.9068 (p0) REVERT: Q 249 MET cc_start: -0.1123 (mtt) cc_final: -0.3770 (ttm) REVERT: Q 276 MET cc_start: 0.6624 (ptt) cc_final: 0.6243 (tmm) REVERT: Q 311 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7264 (mtm) REVERT: Q 323 ARG cc_start: 0.8310 (tpt170) cc_final: 0.7737 (tpt90) REVERT: Z 53 ASP cc_start: 0.7340 (t70) cc_final: 0.7100 (t70) REVERT: Z 190 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8169 (ttm) REVERT: Z 221 MET cc_start: -0.0764 (mmt) cc_final: -0.1104 (mmm) REVERT: Z 278 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6034 (pttt) REVERT: Z 321 MET cc_start: 0.8872 (tmm) cc_final: 0.8385 (ptm) REVERT: a 171 MET cc_start: 0.7837 (mtp) cc_final: 0.7539 (tmm) REVERT: a 388 MET cc_start: 0.8077 (mtt) cc_final: 0.7416 (mmt) REVERT: b 51 ILE cc_start: 0.9259 (mt) cc_final: 0.9040 (tt) REVERT: b 52 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8429 (pt) REVERT: b 87 MET cc_start: 0.8409 (tpp) cc_final: 0.8165 (tpp) REVERT: b 160 MET cc_start: 0.8601 (mtp) cc_final: 0.8239 (mmt) REVERT: b 310 MET cc_start: 0.2707 (OUTLIER) cc_final: 0.2446 (ttp) REVERT: b 392 ASP cc_start: 0.8111 (m-30) cc_final: 0.7653 (t0) REVERT: d 186 MET cc_start: 0.5396 (tpp) cc_final: 0.5190 (tpp) REVERT: d 355 MET cc_start: 0.5196 (ptt) cc_final: 0.2848 (mmm) REVERT: d 410 CYS cc_start: 0.9102 (m) cc_final: 0.8552 (m) REVERT: e 117 GLU cc_start: 0.8854 (tp30) cc_final: 0.8622 (tp30) REVERT: e 297 LEU cc_start: 0.6954 (tp) cc_final: 0.6520 (mm) REVERT: e 401 HIS cc_start: 0.8905 (m90) cc_final: 0.8620 (m-70) REVERT: e 533 LYS cc_start: 0.8723 (pptt) cc_final: 0.8519 (pptt) REVERT: g 53 PRO cc_start: 0.7638 (Cg_exo) cc_final: 0.7152 (Cg_endo) REVERT: g 104 GLU cc_start: 0.8593 (tp30) cc_final: 0.8271 (tm-30) REVERT: g 152 MET cc_start: 0.9044 (mpp) cc_final: 0.8552 (mpp) REVERT: g 177 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8597 (pp) REVERT: g 191 LYS cc_start: 0.8706 (mttt) cc_final: 0.8151 (tptp) REVERT: g 196 LYS cc_start: 0.9268 (ptmt) cc_final: 0.8973 (pptt) REVERT: g 229 MET cc_start: 0.0354 (mtp) cc_final: 0.0079 (mtp) REVERT: g 404 ASP cc_start: 0.7681 (t0) cc_final: 0.7359 (t0) REVERT: h 172 LYS cc_start: 0.8846 (pttt) cc_final: 0.8588 (pttt) REVERT: h 199 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7261 (mtpt) REVERT: h 352 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6551 (tp-100) REVERT: h 382 MET cc_start: 0.7837 (mtm) cc_final: 0.7221 (mtm) REVERT: h 391 ASP cc_start: 0.8761 (m-30) cc_final: 0.8513 (t0) REVERT: h 479 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7498 (mp) REVERT: q 75 GLU cc_start: 0.8092 (tp30) cc_final: 0.7566 (tp30) REVERT: q 344 MET cc_start: 0.3766 (ttp) cc_final: 0.3563 (ttp) REVERT: z 221 MET cc_start: 0.1572 (mmp) cc_final: 0.1047 (tpp) REVERT: z 229 TYR cc_start: 0.8936 (m-80) cc_final: 0.7788 (m-80) REVERT: z 526 MET cc_start: 0.3084 (mmm) cc_final: 0.1555 (mmp) outliers start: 171 outliers final: 136 residues processed: 729 average time/residue: 0.5417 time to fit residues: 695.6330 Evaluate side-chains 734 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 585 time to evaluate : 5.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 149 CYS Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 190 MET Chi-restraints excluded: chain Z residue 278 LYS Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 508 CYS Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 304 PHE Chi-restraints excluded: chain b residue 310 MET Chi-restraints excluded: chain b residue 394 LEU Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 150 ASP Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain d residue 452 ARG Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 129 ILE Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 517 LEU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 155 ILE Chi-restraints excluded: chain g residue 168 TRP Chi-restraints excluded: chain g residue 177 LEU Chi-restraints excluded: chain g residue 241 LEU Chi-restraints excluded: chain g residue 495 ILE Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 90 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 113 GLU Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 199 LYS Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 216 PHE Chi-restraints excluded: chain h residue 352 GLN Chi-restraints excluded: chain h residue 372 PHE Chi-restraints excluded: chain h residue 456 ASP Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 149 CYS Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 208 LEU Chi-restraints excluded: chain q residue 217 VAL Chi-restraints excluded: chain q residue 242 TYR Chi-restraints excluded: chain q residue 285 ASP Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 377 LEU Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 521 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 320 ASN Chi-restraints excluded: chain z residue 359 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 481 optimal weight: 9.9990 chunk 775 optimal weight: 6.9990 chunk 473 optimal weight: 6.9990 chunk 368 optimal weight: 4.9990 chunk 539 optimal weight: 7.9990 chunk 813 optimal weight: 0.0020 chunk 749 optimal weight: 4.9990 chunk 648 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 500 optimal weight: 5.9990 chunk 397 optimal weight: 3.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 242 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 GLN H 241 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 153 ASN ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 HIS ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 282 HIS h 390 HIS ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 63716 Z= 0.278 Angle : 0.639 12.974 85945 Z= 0.321 Chirality : 0.044 0.381 10292 Planarity : 0.004 0.087 11042 Dihedral : 4.110 49.871 8757 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.31 % Allowed : 11.85 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: 0.71 (0.09), residues: 8205 helix: 1.79 (0.08), residues: 4167 sheet: -0.45 (0.18), residues: 873 loop : -1.06 (0.10), residues: 3165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 478 HIS 0.015 0.001 HIS B 361 PHE 0.026 0.002 PHE Q 191 TYR 0.023 0.002 TYR A 181 ARG 0.018 0.001 ARG A 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16410 Ramachandran restraints generated. 8205 Oldfield, 0 Emsley, 8205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 606 time to evaluate : 5.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7880 (ppp) cc_final: 0.7639 (ppp) REVERT: A 62 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 384 MET cc_start: 0.2946 (tpt) cc_final: 0.2101 (ptm) REVERT: A 473 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: B 388 ARG cc_start: 0.9163 (ptp-170) cc_final: 0.8820 (ptp90) REVERT: B 488 MET cc_start: 0.8723 (mmm) cc_final: 0.8187 (tpp) REVERT: D 48 ILE cc_start: 0.9514 (tp) cc_final: 0.9201 (tt) REVERT: D 320 MET cc_start: 0.0582 (mmt) cc_final: -0.0410 (mtt) REVERT: E 27 MET cc_start: 0.6709 (mpp) cc_final: 0.6396 (mpp) REVERT: E 56 ASP cc_start: 0.8230 (m-30) cc_final: 0.7933 (t0) REVERT: E 530 ASP cc_start: 0.8323 (t0) cc_final: 0.7658 (m-30) REVERT: G 104 GLU cc_start: 0.8373 (tp30) cc_final: 0.8095 (tm-30) REVERT: H 178 MET cc_start: 0.8526 (mmm) cc_final: 0.8153 (mtm) REVERT: H 382 MET cc_start: 0.5604 (mtm) cc_final: 0.4941 (mmm) REVERT: H 390 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8286 (t-90) REVERT: H 402 ASN cc_start: 0.7219 (t0) cc_final: 0.6554 (t0) REVERT: H 403 ASP cc_start: 0.7075 (m-30) cc_final: 0.6444 (t0) REVERT: Q 31 ARG cc_start: 0.8174 (mmt180) cc_final: 0.7885 (mtt180) REVERT: Q 67 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9072 (p0) REVERT: Q 249 MET cc_start: -0.1132 (mtt) cc_final: -0.3762 (ttm) REVERT: Q 276 MET cc_start: 0.6577 (ptt) cc_final: 0.6109 (tmm) REVERT: Q 311 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7264 (mtm) REVERT: Z 53 ASP cc_start: 0.7350 (t70) cc_final: 0.7117 (t70) REVERT: Z 190 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8211 (ttm) REVERT: Z 221 MET cc_start: -0.0695 (mmt) cc_final: -0.1051 (mmm) REVERT: Z 278 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.5977 (pttt) REVERT: Z 321 MET cc_start: 0.8852 (tmm) cc_final: 0.8406 (ptm) REVERT: a 99 GLU cc_start: 0.8590 (tp30) cc_final: 0.8072 (tm-30) REVERT: a 171 MET cc_start: 0.7865 (mtp) cc_final: 0.7629 (tmm) REVERT: a 388 MET cc_start: 0.8102 (mtt) cc_final: 0.7455 (mmt) REVERT: b 52 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8375 (pt) REVERT: b 87 MET cc_start: 0.8443 (tpp) cc_final: 0.8200 (tpp) REVERT: b 160 MET cc_start: 0.8660 (mtp) cc_final: 0.8396 (mmt) REVERT: b 310 MET cc_start: 0.2817 (OUTLIER) cc_final: 0.2569 (ttp) REVERT: b 392 ASP cc_start: 0.8164 (m-30) cc_final: 0.7752 (t0) REVERT: d 67 ASP cc_start: 0.7889 (t0) cc_final: 0.7462 (t0) REVERT: d 355 MET cc_start: 0.5282 (ptt) cc_final: 0.2951 (mmm) REVERT: d 410 CYS cc_start: 0.9192 (m) cc_final: 0.8675 (m) REVERT: d 452 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8363 (ttt-90) REVERT: e 117 GLU cc_start: 0.8866 (tp30) cc_final: 0.8641 (tp30) REVERT: e 297 LEU cc_start: 0.6707 (tp) cc_final: 0.6350 (mm) REVERT: e 533 LYS cc_start: 0.8639 (pptt) cc_final: 0.8424 (pptt) REVERT: g 152 MET cc_start: 0.9056 (mpp) cc_final: 0.8551 (mpp) REVERT: g 177 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8723 (pp) REVERT: g 191 LYS cc_start: 0.8736 (mttt) cc_final: 0.8171 (tptp) REVERT: g 196 LYS cc_start: 0.9239 (ptmt) cc_final: 0.8979 (pptt) REVERT: g 229 MET cc_start: 0.0339 (mtp) cc_final: 0.0063 (mtp) REVERT: g 404 ASP cc_start: 0.7756 (t0) cc_final: 0.7449 (t0) REVERT: h 352 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6617 (tp-100) REVERT: h 382 MET cc_start: 0.7916 (mtm) cc_final: 0.7316 (mtm) REVERT: h 391 ASP cc_start: 0.8806 (m-30) cc_final: 0.8540 (t0) REVERT: h 479 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7475 (mp) REVERT: q 75 GLU cc_start: 0.8138 (tp30) cc_final: 0.7623 (tp30) REVERT: q 276 MET cc_start: 0.1955 (ttp) cc_final: 0.1625 (tmm) REVERT: q 344 MET cc_start: 0.3965 (ttp) cc_final: 0.3741 (ttp) REVERT: z 221 MET cc_start: 0.1597 (mmp) cc_final: 0.1083 (tpp) REVERT: z 526 MET cc_start: 0.3286 (mmm) cc_final: 0.2953 (mmm) outliers start: 159 outliers final: 130 residues processed: 718 average time/residue: 0.5537 time to fit residues: 694.7764 Evaluate side-chains 714 residues out of total 6876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 571 time to evaluate : 5.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 408 VAL Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 170 GLN Chi-restraints excluded: chain H residue 175 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 390 HIS Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 67 ASN Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 149 CYS Chi-restraints excluded: chain Q residue 232 THR Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 313 VAL Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 384 LEU Chi-restraints excluded: chain Q residue 518 VAL Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain Z residue 190 MET Chi-restraints excluded: chain Z residue 278 LYS Chi-restraints excluded: chain Z residue 300 PHE Chi-restraints excluded: chain Z residue 406 CYS Chi-restraints excluded: chain Z residue 429 VAL Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 479 VAL Chi-restraints excluded: chain Z residue 508 CYS Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 107 LEU Chi-restraints excluded: chain a residue 113 HIS Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 117 ILE Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 304 PHE Chi-restraints excluded: chain b residue 310 MET Chi-restraints excluded: chain b residue 394 LEU Chi-restraints excluded: chain b residue 515 LEU Chi-restraints excluded: chain b residue 517 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 150 ASP Chi-restraints excluded: chain d residue 422 ILE Chi-restraints excluded: chain d residue 452 ARG Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain e residue 56 ASP Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 129 ILE Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain e residue 517 LEU Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 155 ILE Chi-restraints excluded: chain g residue 168 TRP Chi-restraints excluded: chain g residue 177 LEU Chi-restraints excluded: chain g residue 495 ILE Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 90 VAL Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 139 ILE Chi-restraints excluded: chain h residue 216 PHE Chi-restraints excluded: chain h residue 352 GLN Chi-restraints excluded: chain h residue 372 PHE Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain q residue 205 CYS Chi-restraints excluded: chain q residue 208 LEU Chi-restraints excluded: chain q residue 217 VAL Chi-restraints excluded: chain q residue 242 TYR Chi-restraints excluded: chain q residue 285 ASP Chi-restraints excluded: chain q residue 299 ASP Chi-restraints excluded: chain q residue 377 LEU Chi-restraints excluded: chain q residue 384 LEU Chi-restraints excluded: chain q residue 403 THR Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 521 VAL Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 57 THR Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 166 ASP Chi-restraints excluded: chain z residue 192 GLU Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 320 ASN Chi-restraints excluded: chain z residue 359 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 817 random chunks: chunk 514 optimal weight: 0.5980 chunk 690 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 597 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 649 optimal weight: 7.9990 chunk 271 optimal weight: 0.8980 chunk 666 optimal weight: 0.6980 chunk 82 optimal weight: 40.0000 chunk 119 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS D 502 ASN ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 390 HIS ** h 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.156101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107945 restraints weight = 155555.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.106099 restraints weight = 108374.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.107188 restraints weight = 86571.018| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.457 63716 Z= 0.338 Angle : 0.702 58.995 85945 Z= 0.363 Chirality : 0.044 0.779 10292 Planarity : 0.004 0.087 11042 Dihedral : 4.104 49.876 8757 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.41 % Allowed : 12.13 % Favored : 85.46 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.02 % Twisted Proline : 0.92 % 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: 0.71 (0.09), residues: 8205 helix: 1.79 (0.08), residues: 4167 sheet: -0.46 (0.18), residues: 873 loop : -1.06 (0.10), residues: 3165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 478 HIS 0.023 0.001 HIS e 401 PHE 0.019 0.002 PHE Q 191 TYR 0.022 0.002 TYR Q 351 ARG 0.021 0.000 ARG h 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13390.40 seconds wall clock time: 236 minutes 51.17 seconds (14211.17 seconds total)