Starting phenix.real_space_refine on Thu Sep 26 20:41:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/09_2024/7x3j_32989.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/09_2024/7x3j_32989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/09_2024/7x3j_32989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/09_2024/7x3j_32989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/09_2024/7x3j_32989.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x3j_32989/09_2024/7x3j_32989.cif" } resolution = 4.2 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= 0.020 sd= 0.166 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: 5 Type Number sf(0) Gaussians P 48 5.49 5 S 389 5.16 5 C 39472 2.51 5 N 11001 2.21 5 O 12278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 315 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63188 Number of models: 1 Model: "" Number of chains: 32 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: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3796 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 8, 'TRANS': 495} Chain: "D" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3513 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 455} Chain breaks: 2 Chain: "E" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3914 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 16, 'TRANS': 492} 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: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3913 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain: "Q" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3858 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 13, 'TRANS': 492} Chain: "Z" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3943 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 13, 'TRANS': 500} 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: 4017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4017 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 12, 'TRANS': 516} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 30.12, per 1000 atoms: 0.48 Number of scatterers: 63188 At special positions: 0 Unit cell: (184.52, 217.47, 196.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 389 16.00 P 48 15.00 O 12278 8.00 N 11001 7.00 C 39472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM63058 O3B ATP g 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=26, symmetry=0 Number of additional bonds: simple=26, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.13 Conformation dependent library (CDL) restraints added in 6.3 seconds 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15300 Finding SS restraints... Secondary structure from input PDB file: 324 helices and 96 sheets defined 53.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.510A pdb=" N SER A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.578A pdb=" N LYS A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 removed outlier: 4.151A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.806A pdb=" N VAL A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 134 removed outlier: 3.851A pdb=" N VAL A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.713A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 163 removed outlier: 5.967A pdb=" N ILE A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 161 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 162 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 163' Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.741A pdb=" N PHE A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 4.038A pdb=" N GLU A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 4.065A 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 256 through 279 removed outlier: 3.631A pdb=" N ASP A 261 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.776A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.764A pdb=" N ARG A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 405 removed outlier: 3.610A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.567A pdb=" N ALA A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 472 removed outlier: 3.667A pdb=" N VAL A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.631A 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 removed outlier: 3.647A pdb=" N SER A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.729A pdb=" N LEU B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 72 removed outlier: 3.672A pdb=" N ILE B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.799A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.826A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 removed outlier: 3.646A pdb=" N ILE B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.725A pdb=" N MET B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.795A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 286 removed outlier: 3.590A pdb=" N LYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.927A pdb=" N ALA B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.135A pdb=" N ALA B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.604A pdb=" N ARG B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 395 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.537A pdb=" N ALA B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.859A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 454 removed outlier: 3.692A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 3.697A pdb=" N VAL B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.745A pdb=" N ILE B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 49 removed outlier: 3.612A pdb=" N SER D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 49 " --> pdb=" O ALA D 45 " (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 Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.604A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 removed outlier: 3.996A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 removed outlier: 3.643A pdb=" N ILE D 133 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.614A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 179 through 195 removed outlier: 3.525A pdb=" N SER D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) Proline residue: D 185 - end of helix removed outlier: 3.587A pdb=" N ALA D 190 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D 193 " --> pdb=" O ASN D 189 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 removed outlier: 3.957A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 4.364A pdb=" N PHE D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.949A pdb=" N GLU D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.738A pdb=" N MET D 355 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 356 " --> pdb=" O ALA D 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 352 through 356' Processing helix chain 'D' and resid 394 through 416 removed outlier: 3.524A pdb=" N GLU D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 403 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 415 " --> pdb=" O VAL D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 441 removed outlier: 4.078A pdb=" N GLU D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 448 removed outlier: 4.035A pdb=" N SER D 448 " --> pdb=" O GLY D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.512A pdb=" N GLY D 470 " --> pdb=" O ALA D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 487 removed outlier: 3.550A pdb=" N ASN D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 removed outlier: 4.131A pdb=" N ALA D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 46 removed outlier: 3.518A pdb=" N ALA E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 3.512A pdb=" N ILE E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.536A pdb=" N LEU E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 104 through 123 removed outlier: 4.147A pdb=" N VAL E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 removed outlier: 3.503A pdb=" N ILE E 131 " --> pdb=" O HIS E 127 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.744A pdb=" N GLN E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 179 through 195 removed outlier: 4.073A pdb=" N MET E 183 " --> pdb=" O CYS E 179 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 184 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 186 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 195 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.684A pdb=" N THR E 220 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 294 removed outlier: 3.666A pdb=" N LYS E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU E 281 " --> pdb=" O LYS E 277 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 292 " --> pdb=" O GLN E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 315 removed outlier: 3.811A pdb=" N LEU E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 removed outlier: 4.382A pdb=" N GLU E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 346 removed outlier: 3.517A pdb=" N GLU E 345 " --> pdb=" O ARG E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 413 removed outlier: 3.848A pdb=" N ILE E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 435 removed outlier: 3.620A pdb=" N ALA E 430 " --> pdb=" O SER E 426 " (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: 3.581A pdb=" N ASP E 451 " --> pdb=" O ARG E 447 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 464 Processing helix chain 'E' and resid 469 through 479 removed outlier: 3.682A pdb=" N ALA E 477 " --> pdb=" O THR E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 513 Processing helix chain 'E' and resid 513 through 527 removed outlier: 3.549A pdb=" N ALA E 518 " --> pdb=" O GLN E 514 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 519 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 522 " --> pdb=" O ALA E 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 37 removed outlier: 3.861A pdb=" N ILE G 27 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 69 removed outlier: 3.534A pdb=" N LEU G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 91 removed outlier: 3.582A pdb=" N ILE G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 106 removed outlier: 3.604A pdb=" N VAL G 98 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 138 removed outlier: 3.771A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 removed outlier: 3.685A pdb=" N MET G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 156 " --> pdb=" O MET G 152 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N SER G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR G 161 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 removed outlier: 3.512A pdb=" N SER G 166 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.055A 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: 4.152A pdb=" N ASN G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.649A pdb=" N TYR G 198 " --> pdb=" O ASP G 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 194 through 198' Processing helix chain 'G' and resid 260 through 283 removed outlier: 3.580A pdb=" N ARG G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP G 281 " --> pdb=" O GLN G 277 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 286 No H-bonds generated for 'chain 'G' and resid 284 through 286' Processing helix chain 'G' and resid 316 through 328 removed outlier: 3.664A pdb=" N ASN G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG G 322 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE G 323 " --> pdb=" O ASP G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 404 removed outlier: 3.548A pdb=" N GLU G 388 " --> pdb=" O LEU G 384 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG G 389 " --> pdb=" O SER G 385 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP G 393 " --> pdb=" O ARG G 389 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN G 396 " --> pdb=" O GLN G 392 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 401 " --> pdb=" O VAL G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 426 removed outlier: 3.674A pdb=" N THR G 423 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU G 424 " --> pdb=" O HIS G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 removed outlier: 3.625A pdb=" N ALA G 439 " --> pdb=" O TRP G 435 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL G 440 " --> pdb=" O PRO G 436 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA G 441 " --> pdb=" O TYR G 437 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN G 442 " --> pdb=" O ARG G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.673A pdb=" N LEU G 451 " --> pdb=" O ILE G 447 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE G 452 " --> pdb=" O PRO G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 473 removed outlier: 3.888A pdb=" N SER G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN G 472 " --> pdb=" O ALA G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 517 removed outlier: 3.509A pdb=" N TYR G 506 " --> pdb=" O LYS G 502 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G 515 " --> pdb=" O GLU G 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 28 removed outlier: 3.909A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA H 28 " --> pdb=" O SER H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 61 through 70 removed outlier: 3.567A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.718A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 113 removed outlier: 3.516A pdb=" N ALA H 101 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN H 107 " --> pdb=" O GLU H 103 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL H 108 " --> pdb=" O PHE H 104 " (cutoff:3.500A) Proline residue: H 110 - end of helix removed outlier: 3.924A 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: 3.763A pdb=" N THR H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 163 removed outlier: 3.577A pdb=" N MET H 160 " --> pdb=" O GLU H 156 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 185 removed outlier: 3.672A pdb=" N LYS H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET H 178 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 179 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 285 removed outlier: 3.700A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 267 " --> pdb=" O TYR H 263 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 removed outlier: 3.557A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET H 324 " --> pdb=" O LYS H 320 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 356 removed outlier: 3.681A pdb=" N GLU H 356 " --> pdb=" O ILE H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 402 removed outlier: 4.245A pdb=" N THR H 385 " --> pdb=" O PHE H 381 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE H 400 " --> pdb=" O VAL H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 423 removed outlier: 3.650A pdb=" N ARG H 421 " --> pdb=" O SER H 417 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP H 422 " --> pdb=" O LYS H 418 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 423 " --> pdb=" O TYR H 419 " (cutoff:3.500A) Processing helix chain 'H' and resid 424 through 427 Processing helix chain 'H' and resid 431 through 442 removed outlier: 3.713A pdb=" N ALA H 437 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS H 440 " --> pdb=" O GLY H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 453 removed outlier: 3.728A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA H 453 " --> pdb=" O LEU H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 471 removed outlier: 3.678A pdb=" N GLN H 470 " --> pdb=" O ALA H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 515 removed outlier: 3.658A pdb=" N ILE H 513 " --> pdb=" O ALA H 509 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 45 removed outlier: 3.585A pdb=" N ALA Q 35 " --> pdb=" O ARG Q 31 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N CYS Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 removed outlier: 3.614A pdb=" N LEU Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU Q 75 " --> pdb=" O THR Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 94 removed outlier: 3.612A pdb=" N VAL Q 87 " --> pdb=" O ALA Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 120 removed outlier: 3.618A pdb=" N VAL Q 104 " --> pdb=" O GLY Q 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU Q 105 " --> pdb=" O THR Q 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU Q 116 " --> pdb=" O LEU Q 112 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG Q 120 " --> pdb=" O GLU Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 143 removed outlier: 3.625A pdb=" N VAL Q 128 " --> pdb=" O SER Q 124 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Q 130 " --> pdb=" O SER Q 126 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 147 removed outlier: 3.548A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 144 through 147' Processing helix chain 'Q' and resid 156 through 169 removed outlier: 3.603A pdb=" N SER Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU Q 163 " --> pdb=" O GLU Q 159 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET Q 169 " --> pdb=" O ARG Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 188 removed outlier: 3.810A pdb=" N LEU Q 179 " --> pdb=" O ASN Q 175 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS Q 181 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU Q 182 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE Q 183 " --> pdb=" O LEU Q 179 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Q 184 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 215 removed outlier: 3.595A pdb=" N SER Q 214 " --> pdb=" O GLY Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 261 through 286 removed outlier: 3.552A pdb=" N GLU Q 273 " --> pdb=" O SER Q 269 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE Q 283 " --> pdb=" O GLN Q 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 removed outlier: 3.805A pdb=" N TYR Q 308 " --> pdb=" O TYR Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 326 removed outlier: 3.858A pdb=" N LEU Q 324 " --> pdb=" O ASP Q 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS Q 325 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS Q 326 " --> pdb=" O ARG Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 402 removed outlier: 4.020A pdb=" N ASP Q 387 " --> pdb=" O ASN Q 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE Q 399 " --> pdb=" O GLY Q 395 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 430 removed outlier: 3.796A pdb=" N ILE Q 417 " --> pdb=" O GLY Q 413 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU Q 418 " --> pdb=" O ALA Q 414 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA Q 420 " --> pdb=" O GLU Q 416 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR Q 424 " --> pdb=" O ALA Q 420 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 444 removed outlier: 3.583A pdb=" N ILE Q 438 " --> pdb=" O GLU Q 434 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU Q 443 " --> pdb=" O LYS Q 439 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 456 Processing helix chain 'Q' and resid 459 through 473 removed outlier: 3.591A pdb=" N VAL Q 463 " --> pdb=" O LYS Q 459 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER Q 465 " --> pdb=" O ASN Q 461 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL Q 470 " --> pdb=" O LYS Q 466 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU Q 473 " --> pdb=" O ALA Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 removed outlier: 3.692A pdb=" N ALA Q 507 " --> pdb=" O GLY Q 503 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE Q 508 " --> pdb=" O LYS Q 504 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR Q 517 " --> pdb=" O ASN Q 513 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 35 removed outlier: 3.615A pdb=" N ALA Z 21 " --> pdb=" O GLN Z 17 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN Z 23 " --> pdb=" O ALA Z 19 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL Z 33 " --> pdb=" O GLY Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 71 through 85 removed outlier: 3.747A pdb=" N LEU Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Z 81 " --> pdb=" O ILE Z 77 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA Z 83 " --> pdb=" O LYS Z 79 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 111 removed outlier: 3.637A pdb=" N VAL Z 96 " --> pdb=" O THR Z 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE Z 98 " --> pdb=" O SER Z 94 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE Z 99 " --> pdb=" O ASN Z 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU Z 101 " --> pdb=" O LEU Z 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP Z 107 " --> pdb=" O LEU Z 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU Z 108 " --> pdb=" O LYS Z 104 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER Z 111 " --> pdb=" O ASP Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.704A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA Z 125 " --> pdb=" O GLU Z 121 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS Z 129 " --> pdb=" O ALA Z 125 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Z 137 " --> pdb=" O PHE Z 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS Z 138 " --> pdb=" O LEU Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 157 removed outlier: 3.624A pdb=" N LEU Z 148 " --> pdb=" O ASP Z 144 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP Z 150 " --> pdb=" O GLU Z 146 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER Z 155 " --> pdb=" O VAL Z 151 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG Z 157 " --> pdb=" O ARG Z 153 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 179 removed outlier: 4.652A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL Z 172 " --> pdb=" O LEU Z 168 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP Z 174 " --> pdb=" O GLU Z 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER Z 175 " --> pdb=" O ALA Z 171 " (cutoff:3.500A) removed outlier: 3.651A 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 252 through 281 removed outlier: 3.619A pdb=" N LYS Z 261 " --> pdb=" O GLU Z 257 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP Z 269 " --> pdb=" O LYS Z 265 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE Z 275 " --> pdb=" O VAL Z 271 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 removed outlier: 3.822A pdb=" N ASP Z 303 " --> pdb=" O PRO Z 299 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Z 304 " --> pdb=" O PHE Z 300 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS Z 307 " --> pdb=" O ASP Z 303 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 328 removed outlier: 3.595A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 335 through 339 removed outlier: 3.939A pdb=" N ASP Z 338 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU Z 339 " --> pdb=" O PHE Z 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 335 through 339' Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 removed outlier: 3.501A pdb=" N ASP Z 393 " --> pdb=" O ASP Z 389 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG Z 396 " --> pdb=" O ARG Z 392 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 424 Processing helix chain 'Z' and resid 433 through 444 removed outlier: 3.577A pdb=" N VAL Z 437 " --> pdb=" O ALA Z 433 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.645A pdb=" N ALA Z 452 " --> pdb=" O PRO Z 448 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN Z 453 " --> pdb=" O LYS Z 449 " (cutoff:3.500A) Processing helix chain 'Z' and resid 460 through 469 removed outlier: 3.645A pdb=" N LYS Z 465 " --> pdb=" O GLU Z 461 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU Z 469 " --> pdb=" O LYS Z 465 " (cutoff:3.500A) Processing helix chain 'Z' and resid 488 through 493 removed outlier: 3.601A pdb=" N VAL Z 492 " --> pdb=" O VAL Z 488 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 517 removed outlier: 3.611A pdb=" N THR Z 509 " --> pdb=" O LEU Z 505 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL Z 510 " --> pdb=" O HIS Z 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 37 removed outlier: 3.548A pdb=" N LEU b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE b 29 " --> pdb=" O ARG b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 74 removed outlier: 3.730A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 95 removed outlier: 3.682A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP b 86 " --> pdb=" O LYS b 82 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET b 87 " --> pdb=" O VAL b 83 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU b 94 " --> pdb=" O VAL b 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 119 removed outlier: 3.749A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA b 106 " --> pdb=" O VAL b 102 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU b 116 " --> pdb=" O GLU b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 145 removed outlier: 3.587A pdb=" N ILE b 126 " --> pdb=" O HIS b 122 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU b 132 " --> pdb=" O ALA b 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS b 135 " --> pdb=" O ARG b 131 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU b 141 " --> pdb=" O ALA b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 167 removed outlier: 3.640A pdb=" N GLN b 157 " --> pdb=" O VAL b 153 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.703A pdb=" N THR b 173 " --> pdb=" O LYS b 170 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 170 through 174' Processing helix chain 'b' and resid 175 through 189 removed outlier: 3.528A pdb=" N PHE b 179 " --> pdb=" O HIS b 175 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS b 181 " --> pdb=" O ASP b 177 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU b 182 " --> pdb=" O HIS b 178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL b 184 " --> pdb=" O THR b 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU b 185 " --> pdb=" O LYS b 181 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL b 187 " --> pdb=" O ALA b 183 " (cutoff:3.500A) Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 260 through 284 removed outlier: 3.631A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS b 284 " --> pdb=" O GLU b 280 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 307 removed outlier: 3.515A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 327 removed outlier: 3.753A pdb=" N ARG b 322 " --> pdb=" O ALA b 318 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU b 325 " --> pdb=" O GLU b 321 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR b 327 " --> pdb=" O LEU b 323 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 403 removed outlier: 4.024A pdb=" N ALA b 393 " --> pdb=" O SER b 389 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL b 396 " --> pdb=" O ASP b 392 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL b 401 " --> pdb=" O LEU b 397 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS b 402 " --> pdb=" O ALA b 398 " (cutoff:3.500A) Processing helix chain 'b' and resid 411 through 425 Processing helix chain 'b' and resid 429 through 445 removed outlier: 3.743A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA b 435 " --> pdb=" O LYS b 431 " (cutoff:3.500A) Processing helix chain 'b' and resid 445 through 454 removed outlier: 3.768A pdb=" N ILE b 450 " --> pdb=" O LEU b 446 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 462 Processing helix chain 'b' and resid 463 through 471 removed outlier: 3.908A pdb=" N ALA b 467 " --> pdb=" O ALA b 463 " (cutoff:3.500A) removed outlier: 4.254A 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: 3.635A pdb=" N LEU b 504 " --> pdb=" O LYS b 500 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA b 507 " --> pdb=" O VAL b 503 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA b 511 " --> pdb=" O ALA b 507 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU b 515 " --> pdb=" O ALA b 511 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 48 removed outlier: 3.834A pdb=" N ARG d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA d 45 " --> pdb=" O ALA d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 52 Processing helix chain 'd' and resid 73 through 82 removed outlier: 3.645A pdb=" N LYS d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN d 82 " --> pdb=" O LEU d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 90 Processing helix chain 'd' and resid 91 through 102 removed outlier: 3.716A pdb=" N ILE d 100 " --> pdb=" O LYS d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.746A pdb=" N VAL d 109 " --> pdb=" O GLY d 105 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN d 125 " --> pdb=" O THR d 121 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS d 126 " --> pdb=" O LYS d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 151 removed outlier: 3.570A pdb=" N ILE d 133 " --> pdb=" O HIS d 129 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU d 135 " --> pdb=" O THR d 131 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU d 148 " --> pdb=" O GLY d 144 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP d 150 " --> pdb=" O GLU d 146 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET d 151 " --> pdb=" O ILE d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 172 removed outlier: 3.815A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA d 167 " --> pdb=" O LEU d 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR d 168 " --> pdb=" O LEU d 164 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR d 169 " --> pdb=" O ASN d 165 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER d 170 " --> pdb=" O SER d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 195 removed outlier: 3.814A pdb=" N MET d 186 " --> pdb=" O LEU d 182 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL d 191 " --> pdb=" O SER d 187 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS d 193 " --> pdb=" O ASN d 189 " (cutoff:3.500A) removed outlier: 3.756A 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 293 removed outlier: 3.593A pdb=" N MET d 272 " --> pdb=" O ASP d 268 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP d 273 " --> pdb=" O TYR d 269 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE d 283 " --> pdb=" O GLU d 279 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS d 292 " --> pdb=" O LYS d 288 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 removed outlier: 3.614A pdb=" N LEU d 314 " --> pdb=" O SER d 310 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS d 315 " --> pdb=" O ASP d 311 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU d 317 " --> pdb=" O ALA d 313 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN d 318 " --> pdb=" O LEU d 314 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET d 320 " --> pdb=" O PHE d 316 " (cutoff:3.500A) Processing helix chain 'd' and resid 329 through 338 removed outlier: 3.689A pdb=" N GLU d 334 " --> pdb=" O ARG d 330 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE d 335 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.718A 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 removed outlier: 3.765A pdb=" N ILE d 398 " --> pdb=" O ASN d 394 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU d 399 " --> pdb=" O LYS d 395 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU d 400 " --> pdb=" O LEU d 396 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL d 411 " --> pdb=" O ASP d 407 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE d 412 " --> pdb=" O ALA d 408 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU d 415 " --> pdb=" O VAL d 411 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS d 417 " --> pdb=" O ARG d 413 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS d 418 " --> pdb=" O CYS d 414 " (cutoff:3.500A) Processing helix chain 'd' and resid 426 through 441 removed outlier: 3.854A pdb=" N THR d 437 " --> pdb=" O ALA d 433 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG d 441 " --> pdb=" O THR d 437 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 457 removed outlier: 3.714A pdb=" N CYS d 450 " --> pdb=" O MET d 446 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL d 451 " --> pdb=" O GLU d 447 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 469 Processing helix chain 'd' and resid 472 through 487 removed outlier: 4.154A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU d 479 " --> pdb=" O SER d 475 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN d 486 " --> pdb=" O ASN d 482 " (cutoff:3.500A) Processing helix chain 'd' and resid 512 through 531 removed outlier: 3.642A pdb=" N THR d 520 " --> pdb=" O VAL d 516 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA d 522 " --> pdb=" O ALA d 518 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 47 removed outlier: 3.639A pdb=" N LYS e 33 " --> pdb=" O LEU e 29 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR e 45 " --> pdb=" O ALA e 41 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET e 46 " --> pdb=" O VAL e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 79 removed outlier: 3.533A pdb=" N ILE e 75 " --> pdb=" O ASP e 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER e 77 " --> pdb=" O ALA e 73 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET e 78 " --> pdb=" O THR e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 92 removed outlier: 3.561A pdb=" N MET e 89 " --> pdb=" O ILE e 85 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU e 92 " --> pdb=" O LEU e 88 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 97 removed outlier: 3.840A pdb=" N ASP e 97 " --> pdb=" O SER e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 125 removed outlier: 3.962A pdb=" N VAL e 108 " --> pdb=" O THR e 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL e 109 " --> pdb=" O THR e 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG e 124 " --> pdb=" O GLN e 120 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY e 125 " --> pdb=" O LEU e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 150 removed outlier: 3.534A pdb=" N ASP e 133 " --> pdb=" O ILE e 129 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG e 140 " --> pdb=" O GLU e 136 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL e 141 " --> pdb=" O GLN e 137 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 172 removed outlier: 3.818A pdb=" N ILE e 164 " --> pdb=" O THR e 160 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR e 170 " --> pdb=" O THR e 166 " (cutoff:3.500A) Processing helix chain 'e' and resid 174 through 179 removed outlier: 3.537A pdb=" N ASN e 177 " --> pdb=" O LYS e 174 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS e 179 " --> pdb=" O VAL e 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 174 through 179' Processing helix chain 'e' and resid 180 through 195 removed outlier: 3.623A pdb=" N ALA e 184 " --> pdb=" O HIS e 180 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU e 185 " --> pdb=" O ARG e 181 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE e 186 " --> pdb=" O GLN e 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA e 187 " --> pdb=" O MET e 183 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL e 188 " --> pdb=" O ALA e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 216 through 220 removed outlier: 3.636A pdb=" N ASP e 219 " --> pdb=" O ARG e 216 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR e 220 " --> pdb=" O LEU e 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 216 through 220' Processing helix chain 'e' and resid 268 through 289 removed outlier: 3.615A pdb=" N ALA e 274 " --> pdb=" O GLU e 270 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS e 277 " --> pdb=" O LYS e 273 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS e 282 " --> pdb=" O TYR e 278 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET e 286 " --> pdb=" O LYS e 282 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE e 287 " --> pdb=" O PHE e 283 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN e 288 " --> pdb=" O GLU e 284 " (cutoff:3.500A) Processing helix chain 'e' and resid 305 through 315 removed outlier: 3.651A pdb=" N LEU e 311 " --> pdb=" O GLU e 307 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU e 313 " --> pdb=" O ASN e 309 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN e 314 " --> pdb=" O HIS e 310 " (cutoff:3.500A) Processing helix chain 'e' and resid 324 through 335 removed outlier: 3.593A pdb=" N ILE e 328 " --> pdb=" O GLY e 324 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU e 329 " --> pdb=" O GLY e 325 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE e 331 " --> pdb=" O GLU e 327 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA e 334 " --> pdb=" O LEU e 330 " (cutoff:3.500A) Processing helix chain 'e' and resid 342 through 346 removed outlier: 3.719A pdb=" N GLU e 345 " --> pdb=" O ARG e 342 " (cutoff:3.500A) Processing helix chain 'e' and resid 389 through 413 removed outlier: 3.570A pdb=" N ARG e 398 " --> pdb=" O GLU e 394 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS e 405 " --> pdb=" O HIS e 401 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL e 406 " --> pdb=" O ASP e 402 " (cutoff:3.500A) Processing helix chain 'e' and resid 421 through 435 removed outlier: 3.582A pdb=" N SER e 426 " --> pdb=" O ALA e 422 " (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: 3.656A pdb=" N GLU e 454 " --> pdb=" O ALA e 450 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 464 removed outlier: 3.569A pdb=" N SER e 461 " --> pdb=" O PRO e 457 " (cutoff:3.500A) Processing helix chain 'e' and resid 467 through 479 removed outlier: 3.743A pdb=" N GLU e 474 " --> pdb=" O GLN e 470 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL e 475 " --> pdb=" O THR e 471 " (cutoff:3.500A) Processing helix chain 'e' and resid 508 through 528 removed outlier: 3.555A pdb=" N ILE e 515 " --> pdb=" O LYS e 511 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE e 528 " --> pdb=" O MET e 524 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 35 removed outlier: 4.332A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE g 33 " --> pdb=" O ALA g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 70 removed outlier: 3.626A pdb=" N LEU g 67 " --> pdb=" O GLY g 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG g 68 " --> pdb=" O ASN g 64 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE g 70 " --> pdb=" O ILE g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 91 removed outlier: 3.809A pdb=" N MET g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE g 81 " --> pdb=" O ALA g 77 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER g 84 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU g 89 " --> pdb=" O ARG g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 94 through 106 removed outlier: 3.507A pdb=" N VAL g 98 " --> pdb=" O GLY g 94 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.537A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP g 132 " --> pdb=" O LYS g 128 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU g 137 " --> pdb=" O MET g 133 " (cutoff:3.500A) Processing helix chain 'g' and resid 156 through 161 removed outlier: 3.610A pdb=" N THR g 161 " --> pdb=" O ASN g 157 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 167 removed outlier: 4.170A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 164 through 167' Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.700A pdb=" N MET g 182 " --> pdb=" O ASP g 178 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL g 183 " --> pdb=" O ALA g 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN g 184 " --> pdb=" O VAL g 180 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 189 removed outlier: 3.878A pdb=" N ASN g 188 " --> pdb=" O PHE g 185 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY g 189 " --> pdb=" O GLU g 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 185 through 189' Processing helix chain 'g' and resid 194 through 199 Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 281 removed outlier: 3.826A pdb=" N ARG g 266 " --> pdb=" O GLU g 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU g 268 " --> pdb=" O PHE g 264 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET g 270 " --> pdb=" O ARG g 266 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP g 281 " --> pdb=" O GLN g 277 " (cutoff:3.500A) Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.607A pdb=" N TYR g 303 " --> pdb=" O LEU g 299 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 328 removed outlier: 3.635A pdb=" N ARG g 322 " --> pdb=" O THR g 318 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG g 325 " --> pdb=" O ASN g 321 " (cutoff:3.500A) Processing helix chain 'g' and resid 334 through 338 removed outlier: 4.119A pdb=" N LEU g 338 " --> pdb=" O PRO g 335 " (cutoff:3.500A) Processing helix chain 'g' and resid 380 through 404 removed outlier: 3.654A pdb=" N ARG g 389 " --> pdb=" O SER g 385 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP g 393 " --> pdb=" O ARG g 389 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN g 400 " --> pdb=" O GLN g 396 " (cutoff:3.500A) Processing helix chain 'g' and resid 412 through 426 removed outlier: 3.573A pdb=" N ALA g 419 " --> pdb=" O GLU g 415 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 444 removed outlier: 3.656A pdb=" N ALA g 439 " --> pdb=" O TRP g 435 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA g 441 " --> pdb=" O TYR g 437 " (cutoff:3.500A) Processing helix chain 'g' and resid 445 through 456 removed outlier: 3.860A pdb=" N LEU g 451 " --> pdb=" O ILE g 447 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE g 452 " --> pdb=" O PRO g 448 " (cutoff:3.500A) Processing helix chain 'g' and resid 458 through 471 removed outlier: 3.581A pdb=" N THR g 464 " --> pdb=" O ILE g 460 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER g 465 " --> pdb=" O ARG g 461 " (cutoff:3.500A) Processing helix chain 'g' and resid 499 through 519 removed outlier: 3.552A pdb=" N LEU g 517 " --> pdb=" O ALA g 513 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG g 518 " --> pdb=" O VAL g 514 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE g 519 " --> pdb=" O LEU g 515 " (cutoff:3.500A) Processing helix chain 'h' and resid 18 through 36 removed outlier: 3.887A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN h 30 " --> pdb=" O ILE h 26 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL h 31 " --> pdb=" O SER h 27 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 67 removed outlier: 3.542A pdb=" N LYS h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 78 removed outlier: 3.648A pdb=" N THR h 78 " --> pdb=" O PRO h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 90 removed outlier: 3.595A pdb=" N ALA h 83 " --> pdb=" O LEU h 79 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP h 87 " --> pdb=" O ALA h 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA h 88 " --> pdb=" O LYS h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 108 removed outlier: 3.675A pdb=" N LEU h 99 " --> pdb=" O THR h 95 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE h 104 " --> pdb=" O LEU h 100 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU h 105 " --> pdb=" O ALA h 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN h 107 " --> pdb=" O GLU h 103 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL h 108 " --> pdb=" O PHE h 104 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 114 removed outlier: 3.751A pdb=" N GLU h 113 " --> pdb=" O LYS h 109 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU h 114 " --> pdb=" O PRO h 110 " (cutoff:3.500A) Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.850A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR h 127 " --> pdb=" O ARG h 123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN h 134 " --> pdb=" O GLN h 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS h 137 " --> pdb=" O VAL h 133 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU h 138 " --> pdb=" O ASN h 134 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE h 139 " --> pdb=" O LYS h 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 145 through 149 removed outlier: 3.780A pdb=" N LYS h 148 " --> pdb=" O LYS h 145 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL h 149 " --> pdb=" O ALA h 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 145 through 149' Processing helix chain 'h' and resid 150 through 163 removed outlier: 3.696A pdb=" N ALA h 159 " --> pdb=" O LEU h 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR h 161 " --> pdb=" O LYS h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 185 removed outlier: 3.596A pdb=" N PHE h 175 " --> pdb=" O GLN h 171 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS h 177 " --> pdb=" O ALA h 173 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET h 178 " --> pdb=" O PHE h 174 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL h 179 " --> pdb=" O PHE h 175 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL h 180 " --> pdb=" O ALA h 176 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP h 181 " --> pdb=" O LYS h 177 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL h 183 " --> pdb=" O VAL h 179 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 208 removed outlier: 3.604A pdb=" N ASP h 207 " --> pdb=" O ALA h 204 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER h 208 " --> pdb=" O LEU h 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 204 through 208' Processing helix chain 'h' and resid 261 through 285 removed outlier: 4.046A pdb=" N ALA h 265 " --> pdb=" O GLU h 261 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL h 267 " --> pdb=" O TYR h 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU h 274 " --> pdb=" O GLU h 270 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS h 277 " --> pdb=" O ILE h 273 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE h 281 " --> pdb=" O LYS h 277 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 306 removed outlier: 3.608A pdb=" N THR h 300 " --> pdb=" O GLY h 296 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP h 305 " --> pdb=" O GLN h 301 " (cutoff:3.500A) Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 352 through 356 removed outlier: 4.020A pdb=" N GLU h 356 " --> pdb=" O ILE h 353 " (cutoff:3.500A) Processing helix chain 'h' and resid 378 through 402 removed outlier: 3.517A pdb=" N VAL h 396 " --> pdb=" O ALA h 392 " (cutoff:3.500A) Processing helix chain 'h' and resid 410 through 425 removed outlier: 3.529A pdb=" N ARG h 425 " --> pdb=" O ARG h 421 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 442 removed outlier: 4.005A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE h 435 " --> pdb=" O GLN h 431 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 453 removed outlier: 3.624A pdb=" N CYS h 450 " --> pdb=" O PRO h 446 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA h 453 " --> pdb=" O LEU h 449 " (cutoff:3.500A) Processing helix chain 'h' and resid 456 through 471 removed outlier: 3.656A pdb=" N LEU h 461 " --> pdb=" O ALA h 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS h 463 " --> pdb=" O ASN h 459 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA h 466 " --> pdb=" O ASN h 462 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY h 471 " --> pdb=" O ARG h 467 " (cutoff:3.500A) Processing helix chain 'h' and resid 496 through 515 removed outlier: 3.668A pdb=" N ILE h 513 " --> pdb=" O ALA h 509 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 45 removed outlier: 3.529A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE q 33 " --> pdb=" O VAL q 29 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU q 39 " --> pdb=" O ALA q 35 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 removed outlier: 3.576A pdb=" N ILE q 72 " --> pdb=" O ASP q 68 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 95 removed outlier: 3.698A pdb=" N VAL q 87 " --> pdb=" O ALA q 83 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 120 removed outlier: 3.515A pdb=" N GLY q 109 " --> pdb=" O LEU q 105 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU q 118 " --> pdb=" O LEU q 114 " (cutoff:3.500A) Processing helix chain 'q' and resid 124 through 146 removed outlier: 3.846A pdb=" N GLU q 130 " --> pdb=" O SER q 126 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU q 133 " --> pdb=" O ILE q 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU q 141 " --> pdb=" O ARG q 137 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE q 142 " --> pdb=" O LYS q 138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU q 143 " --> pdb=" O ALA q 139 " (cutoff:3.500A) Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 156 through 164 removed outlier: 3.611A pdb=" N VAL q 160 " --> pdb=" O ASP q 156 " (cutoff:3.500A) Processing helix chain 'q' and resid 164 through 169 Processing helix chain 'q' and resid 178 through 183 removed outlier: 3.537A pdb=" N ILE q 183 " --> pdb=" O LEU q 179 " (cutoff:3.500A) Processing helix chain 'q' and resid 183 through 188 removed outlier: 4.014A pdb=" N VAL q 188 " --> pdb=" O ALA q 184 " (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 removed outlier: 3.619A pdb=" N SER q 214 " --> pdb=" O GLY q 211 " (cutoff:3.500A) Processing helix chain 'q' and resid 262 through 285 removed outlier: 3.683A pdb=" N ASN q 267 " --> pdb=" O GLU q 263 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE q 283 " --> pdb=" O GLN q 279 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 removed outlier: 3.591A pdb=" N HIS q 303 " --> pdb=" O ASP q 299 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN q 306 " --> pdb=" O LEU q 302 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR q 308 " --> pdb=" O TYR q 304 " (cutoff:3.500A) Processing helix chain 'q' and resid 317 through 326 removed outlier: 3.732A pdb=" N LEU q 324 " --> pdb=" O ASP q 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS q 325 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS q 326 " --> pdb=" O ARG q 322 " (cutoff:3.500A) Processing helix chain 'q' and resid 381 through 401 removed outlier: 3.635A pdb=" N ASP q 387 " --> pdb=" O ASN q 383 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP q 393 " --> pdb=" O GLU q 389 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR q 398 " --> pdb=" O ASP q 394 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL q 401 " --> pdb=" O ASN q 397 " (cutoff:3.500A) Processing helix chain 'q' and resid 402 through 404 No H-bonds generated for 'chain 'q' and resid 402 through 404' Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.648A pdb=" N GLU q 418 " --> pdb=" O ALA q 414 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU q 419 " --> pdb=" O THR q 415 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR q 424 " --> pdb=" O ALA q 420 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 444 removed outlier: 3.677A pdb=" N ILE q 438 " --> pdb=" O GLU q 434 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 455 removed outlier: 3.531A pdb=" N ASN q 455 " --> pdb=" O ALA q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 459 through 473 removed outlier: 3.611A pdb=" N VAL q 463 " --> pdb=" O LYS q 459 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL q 470 " --> pdb=" O LYS q 466 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU q 473 " --> pdb=" O ALA q 469 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 removed outlier: 3.596A pdb=" N ALA q 507 " --> pdb=" O GLY q 503 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE q 508 " --> pdb=" O LYS q 504 " (cutoff:3.500A) Processing helix chain 'z' and resid 17 through 35 removed outlier: 3.933A pdb=" N ALA z 21 " --> pdb=" O GLN z 17 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN z 23 " --> pdb=" O ALA z 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP z 32 " --> pdb=" O ARG z 28 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL z 33 " --> pdb=" O GLY z 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 73 through 79 removed outlier: 4.241A pdb=" N ILE z 77 " --> pdb=" O THR z 73 " (cutoff:3.500A) Processing helix chain 'z' and resid 79 through 88 removed outlier: 3.522A pdb=" N ALA z 83 " --> pdb=" O LYS z 79 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP z 86 " --> pdb=" O THR z 82 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR z 88 " --> pdb=" O GLN z 84 " (cutoff:3.500A) Processing helix chain 'z' and resid 92 through 111 removed outlier: 3.734A pdb=" N VAL z 96 " --> pdb=" O THR z 92 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE z 98 " --> pdb=" O SER z 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE z 99 " --> pdb=" O ASN z 95 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS z 104 " --> pdb=" O GLY z 100 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.508A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU z 124 " --> pdb=" O THR z 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU z 128 " --> pdb=" O GLU z 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS z 129 " --> pdb=" O ALA z 125 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL z 137 " --> pdb=" O PHE z 133 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 156 removed outlier: 3.536A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) Processing helix chain 'z' and resid 157 through 159 No H-bonds generated for 'chain 'z' and resid 157 through 159' Processing helix chain 'z' and resid 164 through 178 removed outlier: 3.972A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL z 172 " --> pdb=" O LEU z 168 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP z 174 " --> pdb=" O GLU z 170 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER z 175 " --> pdb=" O ALA z 171 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE z 176 " --> pdb=" O VAL z 172 " (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: 3.588A pdb=" N ASP z 203 " --> pdb=" O SER z 200 " (cutoff:3.500A) removed outlier: 4.080A 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 255 through 264 Processing helix chain 'z' and resid 264 through 281 removed outlier: 4.363A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE z 274 " --> pdb=" O ARG z 270 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE z 275 " --> pdb=" O VAL z 271 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS z 280 " --> pdb=" O GLU z 276 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL z 281 " --> pdb=" O LEU z 277 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 308 removed outlier: 3.955A pdb=" N ALA z 304 " --> pdb=" O PHE z 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU z 305 " --> pdb=" O SER z 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS z 307 " --> pdb=" O ASP z 303 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 317 through 328 removed outlier: 3.740A pdb=" N ARG z 323 " --> pdb=" O ARG z 319 " (cutoff:3.500A) removed outlier: 3.668A 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 342 No H-bonds generated for 'chain 'z' and resid 340 through 342' Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.632A pdb=" N ARG z 396 " --> pdb=" O ARG z 392 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA z 397 " --> pdb=" O ASP z 393 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL z 398 " --> pdb=" O GLY z 394 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA z 401 " --> pdb=" O ALA z 397 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE z 402 " --> pdb=" O VAL z 398 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 424 Processing helix chain 'z' and resid 433 through 444 removed outlier: 3.665A pdb=" N LEU z 444 " --> pdb=" O PHE z 440 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.533A pdb=" N LEU z 451 " --> pdb=" O ILE z 447 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA z 452 " --> pdb=" O PRO z 448 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN z 453 " --> pdb=" O LYS z 449 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 468 removed outlier: 3.713A pdb=" N LYS z 465 " --> pdb=" O GLU z 461 " (cutoff:3.500A) Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 498 through 517 removed outlier: 3.647A pdb=" N CYS z 508 " --> pdb=" O LEU z 504 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR z 509 " --> pdb=" O LEU z 505 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR z 513 " --> pdb=" O THR z 509 " (cutoff:3.500A) Processing helix chain 'a' and resid 15 through 32 removed outlier: 3.511A pdb=" N SER a 27 " --> pdb=" O MET a 23 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE a 31 " --> pdb=" O SER a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 65 removed outlier: 3.579A pdb=" N LYS a 63 " --> pdb=" O ALA a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 84 removed outlier: 4.153A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS a 76 " --> pdb=" O ALA a 72 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU a 77 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU a 78 " --> pdb=" O VAL a 74 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP a 80 " --> pdb=" O CYS a 76 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS a 84 " --> pdb=" O ASP a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.807A pdb=" N VAL a 93 " --> pdb=" O GLY a 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS a 109 " --> pdb=" O ASP a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 134 removed outlier: 3.852A pdb=" N VAL a 117 " --> pdb=" O HIS a 113 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 156 removed outlier: 3.715A pdb=" N THR a 154 " --> pdb=" O ASN a 150 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER a 155 " --> pdb=" O ALA a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 163 removed outlier: 5.968A pdb=" N ILE a 160 " --> pdb=" O SER a 157 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE a 161 " --> pdb=" O SER a 158 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY a 162 " --> pdb=" O LYS a 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 157 through 163' Processing helix chain 'a' and resid 164 through 177 removed outlier: 3.740A pdb=" N PHE a 168 " --> pdb=" O ASN a 164 " (cutoff:3.500A) removed outlier: 3.954A 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: 3.750A pdb=" N VAL a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP a 174 " --> pdb=" O ASN a 170 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA a 175 " --> pdb=" O MET a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 208 removed outlier: 4.038A pdb=" N GLU a 207 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 4.067A 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 256 through 279 removed outlier: 3.630A pdb=" N ASP a 261 " --> pdb=" O PRO a 257 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE a 263 " --> pdb=" O LYS a 259 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG a 264 " --> pdb=" O LEU a 260 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS a 272 " --> pdb=" O SER a 268 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU a 273 " --> pdb=" O ASP a 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE a 275 " --> pdb=" O THR a 271 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN a 276 " --> pdb=" O LYS a 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS a 277 " --> pdb=" O GLU a 273 " (cutoff:3.500A) Processing helix chain 'a' and resid 295 through 304 removed outlier: 3.776A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE a 300 " --> pdb=" O CYS a 296 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL a 301 " --> pdb=" O LEU a 297 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU a 302 " --> pdb=" O LYS a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 323 removed outlier: 3.764A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 381 through 405 removed outlier: 3.612A pdb=" N GLU a 387 " --> pdb=" O PHE a 383 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG a 390 " --> pdb=" O ASP a 386 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL a 398 " --> pdb=" O ASP a 394 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL a 399 " --> pdb=" O ALA a 395 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL a 402 " --> pdb=" O VAL a 398 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER a 405 " --> pdb=" O ARG a 401 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 431 removed outlier: 3.564A pdb=" N ALA a 418 " --> pdb=" O ALA a 414 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR a 422 " --> pdb=" O ALA a 418 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 445 Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 472 removed outlier: 3.667A pdb=" N VAL a 464 " --> pdb=" O SER a 460 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU a 467 " --> pdb=" O LEU a 463 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE a 470 " --> pdb=" O LYS a 466 " (cutoff:3.500A) Processing helix chain 'a' and resid 472 through 477 removed outlier: 3.633A 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 removed outlier: 3.647A pdb=" N SER a 513 " --> pdb=" O VAL a 509 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU a 514 " --> pdb=" O LYS a 510 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR a 518 " --> pdb=" O LEU a 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.563A pdb=" N SER A 12 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP d 58 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP A 529 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET d 60 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE d 61 " --> pdb=" O THR d 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR d 69 " --> pdb=" O ILE d 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.601A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 137 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 200 removed outlier: 6.595A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 376 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET A 209 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.640A pdb=" N LEU A 361 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 354 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 363 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 352 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 237 removed outlier: 3.605A pdb=" N LEU A 237 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.724A pdb=" N ASP A 489 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 64 removed outlier: 6.553A pdb=" N SER B 60 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER B 54 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASP B 49 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL D 535 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 51 " --> pdb=" O VAL D 535 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 200 through 205 removed outlier: 5.949A pdb=" N HIS B 200 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 375 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY B 377 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 235 removed outlier: 8.011A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 348 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 239 through 240 Processing sheet with id=AB3, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AB4, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.530A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 520 through 521 removed outlier: 7.129A pdb=" N ILE B 521 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 68 through 71 removed outlier: 3.801A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 59 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP D 58 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP a 529 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER a 12 " --> pdb=" O LEU a 530 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 removed outlier: 3.568A pdb=" N ILE D 388 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 211 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 222 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 227 through 229 removed outlier: 3.689A pdb=" N LEU D 229 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 373 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR D 377 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 361 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 361 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 242 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU D 363 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG D 240 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 246 through 248 removed outlier: 3.659A pdb=" N LEU D 299 " --> pdb=" O GLY D 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 491 through 494 Processing sheet with id=AC3, first strand: chain 'E' and resid 207 through 211 removed outlier: 3.609A pdb=" N ILE E 385 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR E 382 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 223 " --> pdb=" O THR E 382 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE E 384 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 221 " --> pdb=" O PHE E 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 225 through 228 removed outlier: 3.652A pdb=" N VAL E 226 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 372 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP E 367 " --> pdb=" O PHE E 362 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE E 362 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET E 369 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE E 360 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 246 through 248 removed outlier: 6.611A pdb=" N ALA E 298 " --> pdb=" O VAL E 320 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AC7, first strand: chain 'E' and resid 528 through 532 removed outlier: 4.436A pdb=" N ILE E 528 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU H 48 " --> pdb=" O ILE E 528 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASP E 530 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL H 50 " --> pdb=" O ASP E 530 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG E 532 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 17 through 18 removed outlier: 3.520A pdb=" N GLU G 17 " --> pdb=" O ILE G 522 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP G 521 " --> pdb=" O MET a 44 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL a 46 " --> pdb=" O ASP G 521 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL G 523 " --> pdb=" O VAL a 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR a 55 " --> pdb=" O LYS a 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 57 through 58 removed outlier: 3.708A pdb=" N VAL G 58 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET G 49 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AD2, first strand: chain 'G' and resid 199 through 203 removed outlier: 3.857A pdb=" N ARG G 200 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU G 215 " --> pdb=" O THR G 373 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD4, first strand: chain 'G' and resid 232 through 233 Processing sheet with id=AD5, first strand: chain 'G' and resid 310 through 312 removed outlier: 3.746A pdb=" N VAL G 239 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N VAL G 332 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU G 240 " --> pdb=" O VAL G 332 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 479 through 480 Processing sheet with id=AD7, first strand: chain 'H' and resid 141 through 142 removed outlier: 3.652A pdb=" N VAL H 141 " --> pdb=" O VAL H 405 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 195 through 199 removed outlier: 6.447A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.032A pdb=" N VAL H 289 " --> pdb=" O ALA H 311 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 347 through 351 removed outlier: 4.001A pdb=" N GLU H 349 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE H 360 " --> pdb=" O GLU H 349 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 351 " --> pdb=" O TYR H 358 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR H 358 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 475 through 477 removed outlier: 3.683A pdb=" N ALA H 485 " --> pdb=" O GLY H 476 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 516 through 521 removed outlier: 4.475A pdb=" N VAL H 516 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET Q 55 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU H 518 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE Q 57 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE H 520 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 202 through 208 removed outlier: 3.563A pdb=" N CYS Q 205 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY Q 379 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER Q 216 " --> pdb=" O VAL Q 376 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 221 through 223 removed outlier: 3.559A pdb=" N MET Q 221 " --> pdb=" O PHE Q 363 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL Q 361 " --> pdb=" O PHE Q 223 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 311 through 314 removed outlier: 6.692A pdb=" N ASN Q 289 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL Q 313 " --> pdb=" O ASN Q 289 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL Q 291 " --> pdb=" O VAL Q 313 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS Q 238 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL Q 290 " --> pdb=" O LYS Q 238 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N LEU Q 333 " --> pdb=" O ILE Q 239 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL Q 241 " --> pdb=" O LEU Q 333 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 311 through 314 removed outlier: 6.692A pdb=" N ASN Q 289 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL Q 313 " --> pdb=" O ASN Q 289 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL Q 291 " --> pdb=" O VAL Q 313 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS Q 238 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL Q 290 " --> pdb=" O LYS Q 238 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE Q 239 " --> pdb=" O GLY Q 345 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 408 through 409 Processing sheet with id=AE9, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF1, first strand: chain 'Q' and resid 521 through 526 removed outlier: 7.862A pdb=" N MET Z 46 " --> pdb=" O ASP Q 522 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE Q 524 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL Z 48 " --> pdb=" O ILE Q 524 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N MET Q 526 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.466A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 211 through 212 removed outlier: 3.542A pdb=" N LEU Z 212 " --> pdb=" O THR Z 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR Z 361 " --> pdb=" O LEU Z 212 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 229 through 231 Processing sheet with id=AF5, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id=AF6, first strand: chain 'b' and resid 17 through 19 removed outlier: 3.835A pdb=" N ASP b 17 " --> pdb=" O LYS b 522 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS b 522 " --> pdb=" O ASP b 17 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE b 520 " --> pdb=" O GLU b 19 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP e 56 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN b 519 " --> pdb=" O ASP e 56 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR e 67 " --> pdb=" O MET e 59 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 62 through 63 removed outlier: 7.581A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR d 538 " --> pdb=" O ILE b 51 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU b 53 " --> pdb=" O THR d 538 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.421A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU b 375 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE b 202 " --> pdb=" O LEU b 375 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY b 377 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS b 204 " --> pdb=" O GLY b 377 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 231 through 235 removed outlier: 4.005A pdb=" N ILE b 232 " --> pdb=" O ILE b 349 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE b 349 " --> pdb=" O ILE b 232 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 237 through 240 removed outlier: 6.476A pdb=" N LEU b 238 " --> pdb=" O ILE b 291 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE b 290 " --> pdb=" O ILE b 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'b' and resid 406 through 407 Processing sheet with id=AG3, first strand: chain 'b' and resid 476 through 479 removed outlier: 3.541A pdb=" N ASP b 479 " --> pdb=" O THR b 484 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR b 484 " --> pdb=" O ASP b 479 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.622A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.830A pdb=" N GLY d 371 " --> pdb=" O LEU d 367 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU d 367 " --> pdb=" O GLY d 371 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU d 360 " --> pdb=" O LYS d 243 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'd' and resid 246 through 249 removed outlier: 3.686A pdb=" N GLN d 301 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP d 327 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'd' and resid 421 through 423 Processing sheet with id=AG8, first strand: chain 'd' and resid 491 through 494 removed outlier: 3.587A pdb=" N GLY d 492 " --> pdb=" O SER d 501 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER d 501 " --> pdb=" O GLY d 492 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'e' and resid 23 through 26 removed outlier: 3.630A pdb=" N ILE e 531 " --> pdb=" O LEU e 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG e 532 " --> pdb=" O VAL h 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER h 59 " --> pdb=" O LYS h 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 207 through 213 removed outlier: 3.684A pdb=" N LYS e 212 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY e 387 " --> pdb=" O LYS e 212 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE e 384 " --> pdb=" O LYS e 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS e 221 " --> pdb=" O PHE e 384 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'e' and resid 225 through 228 removed outlier: 6.664A pdb=" N ASP e 367 " --> pdb=" O PHE e 362 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE e 362 " --> pdb=" O ASP e 367 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET e 369 " --> pdb=" O ILE e 360 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'e' and resid 246 through 248 removed outlier: 6.712A pdb=" N ALA e 298 " --> pdb=" O VAL e 320 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'e' and resid 416 through 417 Processing sheet with id=AH5, first strand: chain 'g' and resid 57 through 58 removed outlier: 7.788A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AH7, first strand: chain 'g' and resid 201 through 205 removed outlier: 4.024A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'g' and resid 219 through 220 Processing sheet with id=AH9, first strand: chain 'g' and resid 232 through 233 Processing sheet with id=AI1, first strand: chain 'g' and resid 238 through 241 removed outlier: 5.701A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL g 290 " --> pdb=" O ILE g 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'g' and resid 479 through 480 removed outlier: 3.761A pdb=" N VAL g 488 " --> pdb=" O GLY g 479 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'h' and resid 141 through 142 removed outlier: 3.556A pdb=" N VAL h 141 " --> pdb=" O VAL h 405 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.900A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'h' and resid 309 through 311 removed outlier: 5.970A pdb=" N VAL h 289 " --> pdb=" O ALA h 311 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL h 288 " --> pdb=" O LYS h 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA h 238 " --> pdb=" O VAL h 288 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'h' and resid 347 through 351 removed outlier: 3.603A pdb=" N GLU h 349 " --> pdb=" O PHE h 360 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE h 360 " --> pdb=" O GLU h 349 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'h' and resid 475 through 477 Processing sheet with id=AI8, first strand: chain 'h' and resid 516 through 521 removed outlier: 6.320A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'q' and resid 202 through 208 removed outlier: 3.615A pdb=" N CYS q 205 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY q 379 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'q' and resid 221 through 223 Processing sheet with id=AJ2, first strand: chain 'q' and resid 239 through 242 Processing sheet with id=AJ3, first strand: chain 'q' and resid 408 through 410 Processing sheet with id=AJ4, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AJ5, first strand: chain 'q' and resid 521 through 526 removed outlier: 4.430A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS z 45 " --> pdb=" O THR z 57 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR z 57 " --> pdb=" O LYS z 45 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.353A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'z' and resid 224 through 225 Processing sheet with id=AJ8, first strand: chain 'z' and resid 310 through 312 removed outlier: 6.900A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA z 228 " --> pdb=" O ALA z 347 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'z' and resid 407 through 409 Processing sheet with id=AK1, first strand: chain 'z' and resid 477 through 478 Processing sheet with id=AK2, first strand: chain 'a' and resid 137 through 138 Processing sheet with id=AK3, first strand: chain 'a' and resid 196 through 200 removed outlier: 6.594A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE a 376 " --> pdb=" O MET a 209 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET a 209 " --> pdb=" O ILE a 376 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'a' and resid 215 through 216 removed outlier: 3.641A pdb=" N LEU a 361 " --> pdb=" O GLU a 354 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU a 354 " --> pdb=" O LEU a 361 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL a 352 " --> pdb=" O LEU a 363 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'a' and resid 234 through 237 removed outlier: 3.606A pdb=" N LEU a 237 " --> pdb=" O LEU a 287 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.724A pdb=" N ASP a 489 " --> pdb=" O LYS a 494 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) 2611 hydrogen bonds defined for protein. 7617 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: 23.14 Time building geometry restraints manager: 13.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 21308 1.35 - 1.47: 12084 1.47 - 1.59: 29812 1.59 - 1.71: 80 1.71 - 1.83: 642 Bond restraints: 63926 Sorted by residual: bond pdb=" C4 ATP q 601 " pdb=" C5 ATP q 601 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.32e+01 bond pdb=" C4 ATP Q 601 " pdb=" C5 ATP Q 601 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.97e+01 bond pdb=" C4 ATP a 601 " pdb=" C5 ATP a 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 ... (remaining 63921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 86005 4.47 - 8.93: 302 8.93 - 13.40: 22 13.40 - 17.86: 15 17.86 - 22.33: 16 Bond angle restraints: 86360 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.54 22.33 1.00e+00 1.00e+00 4.98e+02 angle pdb=" PB ATP a 601 " pdb=" O3B ATP a 601 " pdb=" PG ATP a 601 " ideal model delta sigma weight residual 139.87 117.56 22.31 1.00e+00 1.00e+00 4.98e+02 angle pdb=" PA ATP Q 601 " pdb=" O3A ATP Q 601 " pdb=" PB ATP Q 601 " ideal model delta sigma weight residual 136.83 115.32 21.51 1.00e+00 1.00e+00 4.63e+02 angle pdb=" PA ATP q 601 " pdb=" O3A ATP q 601 " pdb=" PB ATP q 601 " ideal model delta sigma weight residual 136.83 115.33 21.50 1.00e+00 1.00e+00 4.62e+02 angle pdb=" PB ATP q 601 " pdb=" O3B ATP q 601 " pdb=" PG ATP q 601 " ideal model delta sigma weight residual 139.87 118.42 21.45 1.00e+00 1.00e+00 4.60e+02 ... (remaining 86355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 36023 17.99 - 35.99: 3063 35.99 - 53.98: 586 53.98 - 71.97: 147 71.97 - 89.96: 75 Dihedral angle restraints: 39894 sinusoidal: 16276 harmonic: 23618 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 -120.59 -59.41 0 5.00e+00 4.00e-02 1.41e+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 -120.76 -59.24 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA ASP a 146 " pdb=" C ASP a 146 " pdb=" N CYS a 147 " pdb=" CA CYS a 147 " ideal model delta harmonic sigma weight residual 180.00 129.18 50.82 0 5.00e+00 4.00e-02 1.03e+02 ... (remaining 39891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 8751 0.061 - 0.123: 1398 0.123 - 0.184: 158 0.184 - 0.245: 7 0.245 - 0.307: 8 Chirality restraints: 10322 Sorted by residual: chirality pdb=" CB ILE D 70 " pdb=" CA ILE D 70 " pdb=" CG1 ILE D 70 " pdb=" CG2 ILE D 70 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE b 331 " pdb=" CA ILE b 331 " pdb=" CG1 ILE b 331 " pdb=" CG2 ILE b 331 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR a 90 " pdb=" N THR a 90 " pdb=" C THR a 90 " pdb=" CB THR a 90 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 10319 not shown) Planarity restraints: 10999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 187 " 0.066 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO a 188 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO a 188 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO a 188 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 187 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 188 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Q 191 " 0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO Q 192 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO Q 192 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Q 192 " 0.039 5.00e-02 4.00e+02 ... (remaining 10996 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 10 1.89 - 2.64: 640 2.64 - 3.39: 80672 3.39 - 4.15: 144480 4.15 - 4.90: 260585 Nonbonded interactions: 486387 Sorted by model distance: nonbonded pdb=" CD2 LEU D 84 " pdb=" CB SER a 6 " model vdw 1.136 3.860 nonbonded pdb=" NH2 ARG G 330 " pdb=" NZ LYS a 243 " model vdw 1.240 3.200 nonbonded pdb=" NE ARG G 334 " pdb=" O GLY a 249 " model vdw 1.316 3.120 nonbonded pdb=" CD2 LEU D 84 " pdb=" CA SER a 6 " model vdw 1.317 3.890 nonbonded pdb=" CG ARG G 334 " pdb=" OE1 GLN a 251 " model vdw 1.436 3.440 ... (remaining 486382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = (chain 'b' and (resid 19 through 522 or resid 601)) } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 30 through 254 or resid 286 through 300 or resid 311 throu \ gh 539 or resid 601)) } ncs_group { reference = chain 'E' selection = (chain 'e' and (resid 25 through 533 or resid 601)) } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = (chain 'h' and (resid 16 through 524 or resid 601)) } ncs_group { reference = chain 'Q' selection = (chain 'q' and (resid 24 through 529 or resid 601)) } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 13 through 526 or resid 601)) } 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: 0.830 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: 0.080 Extract box with map and model: 1.830 Check model and map are aligned: 0.380 Set scattering table: 0.430 Process input model: 109.820 Find NCS groups from input model: 5.280 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 63926 Z= 0.254 Angle : 0.860 22.325 86360 Z= 0.601 Chirality : 0.045 0.307 10322 Planarity : 0.005 0.102 10999 Dihedral : 14.405 89.963 24594 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.90 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.05 % 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: -5.53 (0.06), residues: 8173 helix: -4.97 (0.02), residues: 3922 sheet: -1.51 (0.18), residues: 684 loop : -2.30 (0.08), residues: 3567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP h 493 HIS 0.006 0.001 HIS q 21 PHE 0.022 0.001 PHE E 204 TYR 0.018 0.001 TYR Q 47 ARG 0.008 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1633 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1626 time to evaluate : 5.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ILE cc_start: 0.5753 (mm) cc_final: 0.5411 (mm) REVERT: A 295 MET cc_start: -0.1963 (ppp) cc_final: -0.3366 (mpp) REVERT: A 459 ASP cc_start: 0.5996 (t0) cc_final: 0.5414 (p0) REVERT: B 76 VAL cc_start: 0.6102 (t) cc_final: 0.5769 (t) REVERT: B 97 ASP cc_start: 0.8276 (t70) cc_final: 0.7999 (t0) REVERT: B 131 ARG cc_start: 0.7070 (mtt180) cc_final: 0.6262 (mtp85) REVERT: B 159 LEU cc_start: 0.5105 (mt) cc_final: 0.4607 (mt) REVERT: B 182 LEU cc_start: 0.7060 (mt) cc_final: 0.6791 (mt) REVERT: B 488 MET cc_start: 0.7621 (mmp) cc_final: 0.6872 (mmt) REVERT: B 512 GLU cc_start: 0.5897 (tt0) cc_final: 0.5328 (tt0) REVERT: B 518 ASP cc_start: 0.4973 (p0) cc_final: 0.4520 (p0) REVERT: D 139 LYS cc_start: 0.8001 (mttt) cc_final: 0.7597 (ttmm) REVERT: D 192 MET cc_start: 0.6270 (ptm) cc_final: 0.5939 (ptm) REVERT: D 208 ILE cc_start: 0.4517 (tp) cc_final: 0.4090 (mm) REVERT: D 349 ASP cc_start: 0.3326 (p0) cc_final: 0.2764 (t0) REVERT: E 78 MET cc_start: 0.6042 (mmt) cc_final: 0.5473 (mmt) REVERT: E 197 MET cc_start: 0.1224 (ttt) cc_final: 0.0948 (ttt) REVERT: E 321 ARG cc_start: 0.3071 (ptt180) cc_final: 0.1967 (mtp180) REVERT: E 436 ASP cc_start: 0.4825 (m-30) cc_final: 0.4502 (t0) REVERT: E 529 ASP cc_start: 0.5170 (p0) cc_final: 0.3996 (t0) REVERT: G 46 MET cc_start: 0.8435 (mmm) cc_final: 0.8195 (mtt) REVERT: G 83 ILE cc_start: 0.7321 (tp) cc_final: 0.7070 (tp) REVERT: G 229 MET cc_start: 0.0632 (mtt) cc_final: 0.0390 (mtt) REVERT: H 39 THR cc_start: 0.8125 (p) cc_final: 0.7805 (p) REVERT: H 95 THR cc_start: 0.7918 (t) cc_final: 0.7608 (m) REVERT: H 357 ARG cc_start: 0.3384 (mmt90) cc_final: 0.3089 (ptt-90) REVERT: Q 276 MET cc_start: 0.2169 (mtm) cc_final: 0.1714 (ttp) REVERT: Q 326 LYS cc_start: 0.4863 (mmtt) cc_final: 0.4658 (tttm) REVERT: Q 461 ASN cc_start: 0.7973 (m-40) cc_final: 0.7736 (m-40) REVERT: Z 95 ASN cc_start: 0.7912 (t0) cc_final: 0.7693 (t0) REVERT: Z 131 LEU cc_start: 0.8161 (mt) cc_final: 0.7804 (tt) REVERT: Z 221 MET cc_start: 0.3940 (mmt) cc_final: 0.1471 (ptm) REVERT: Z 321 MET cc_start: 0.3775 (ttp) cc_final: 0.3197 (ttm) REVERT: b 90 VAL cc_start: 0.8091 (m) cc_final: 0.7881 (p) REVERT: b 112 GLU cc_start: 0.4813 (tp30) cc_final: 0.4603 (mm-30) REVERT: b 272 LYS cc_start: 0.2684 (mmtt) cc_final: 0.2080 (tttt) REVERT: b 353 MET cc_start: 0.4121 (mmp) cc_final: 0.3643 (mmp) REVERT: b 488 MET cc_start: 0.6909 (mmp) cc_final: 0.6618 (mmm) REVERT: d 133 ILE cc_start: 0.8517 (mt) cc_final: 0.8283 (mm) REVERT: d 260 MET cc_start: -0.1376 (mtt) cc_final: -0.2090 (mtt) REVERT: d 302 LYS cc_start: 0.3207 (tttt) cc_final: 0.2693 (mttt) REVERT: e 104 THR cc_start: 0.7898 (m) cc_final: 0.7658 (m) REVERT: e 197 MET cc_start: 0.4007 (ttm) cc_final: 0.3601 (tpt) REVERT: e 288 GLN cc_start: 0.5421 (mm110) cc_final: 0.4390 (mt0) REVERT: e 411 ILE cc_start: 0.3510 (mt) cc_final: 0.3252 (mt) REVERT: e 472 MET cc_start: 0.7288 (mmm) cc_final: 0.6925 (tpp) REVERT: g 54 MET cc_start: 0.4933 (mpp) cc_final: 0.4322 (mmt) REVERT: g 145 ASP cc_start: 0.7648 (p0) cc_final: 0.7160 (p0) REVERT: g 330 ARG cc_start: 0.2456 (ttt180) cc_final: 0.1401 (tpt170) REVERT: g 362 PHE cc_start: 0.2921 (m-80) cc_final: 0.2474 (m-80) REVERT: g 516 LEU cc_start: 0.8752 (mp) cc_final: 0.8496 (mt) REVERT: h 319 LEU cc_start: 0.5586 (mt) cc_final: 0.4994 (tp) REVERT: h 500 ILE cc_start: 0.8616 (mt) cc_final: 0.8395 (pt) REVERT: q 129 ILE cc_start: 0.8661 (tt) cc_final: 0.8403 (tp) REVERT: q 164 LEU cc_start: 0.8422 (mt) cc_final: 0.8053 (mm) REVERT: q 401 VAL cc_start: 0.6587 (p) cc_final: 0.6218 (p) REVERT: q 404 ARG cc_start: 0.2440 (mtt180) cc_final: 0.2098 (mmp80) REVERT: z 68 GLN cc_start: 0.3924 (mm-40) cc_final: 0.3701 (mm110) REVERT: z 87 ILE cc_start: 0.3929 (tp) cc_final: 0.3563 (tp) REVERT: z 101 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6255 (tm-30) REVERT: z 206 LEU cc_start: 0.7842 (mt) cc_final: 0.7344 (tt) REVERT: z 295 LYS cc_start: 0.5472 (mmtt) cc_final: 0.4466 (mtmt) REVERT: a 28 ILE cc_start: 0.8843 (mm) cc_final: 0.8585 (mm) REVERT: a 36 LEU cc_start: 0.7765 (tp) cc_final: 0.7522 (tp) REVERT: a 108 VAL cc_start: 0.6226 (t) cc_final: 0.5677 (p) REVERT: a 156 MET cc_start: 0.1490 (mmt) cc_final: 0.0803 (mmp) REVERT: a 306 MET cc_start: -0.0948 (ttt) cc_final: -0.1858 (mmm) outliers start: 7 outliers final: 4 residues processed: 1632 average time/residue: 0.6268 time to fit residues: 1668.1771 Evaluate side-chains 973 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 969 time to evaluate : 5.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 685 optimal weight: 8.9990 chunk 615 optimal weight: 4.9990 chunk 341 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 415 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 chunk 636 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 386 optimal weight: 5.9990 chunk 473 optimal weight: 10.0000 chunk 737 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 223 GLN A 475 GLN B 148 HIS ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN D 406 HIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 ASN E 234 HIS E 310 HIS ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS G 184 GLN G 226 HIS G 276 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 GLN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN Q 34 GLN Q 41 GLN Q 153 ASN Q 175 ASN Z 161 HIS Z 182 GLN ** Z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 382 HIS ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 285 HIS b 288 ASN d 62 GLN d 129 HIS d 262 ASN d 366 ASN ** d 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN e 35 HIS ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 HIS g 235 ASN g 392 GLN ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 448 GLN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 289 ASN q 346 HIS z 105 GLN z 245 ASN z 346 HIS a 20 GLN a 242 GLN ** a 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 63926 Z= 0.323 Angle : 0.756 12.823 86360 Z= 0.395 Chirality : 0.048 0.378 10322 Planarity : 0.006 0.128 10999 Dihedral : 7.922 89.677 9257 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % 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: -3.60 (0.08), residues: 8173 helix: -2.85 (0.06), residues: 4002 sheet: -1.31 (0.18), residues: 720 loop : -1.82 (0.09), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 496 HIS 0.009 0.002 HIS e 493 PHE 0.025 0.002 PHE A 470 TYR 0.026 0.002 TYR q 47 ARG 0.036 0.001 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1212 time to evaluate : 5.345 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 54 ILE cc_start: 0.7487 (mm) cc_final: 0.7223 (mt) REVERT: A 156 MET cc_start: 0.3446 (mmp) cc_final: 0.3131 (mmt) REVERT: A 355 ARG cc_start: 0.5331 (tmt-80) cc_final: 0.4868 (pmt-80) REVERT: A 401 ARG cc_start: 0.4366 (mmt180) cc_final: 0.4097 (mmt180) REVERT: A 459 ASP cc_start: 0.6320 (t0) cc_final: 0.5643 (p0) REVERT: B 50 LYS cc_start: 0.6737 (mtmt) cc_final: 0.6440 (mtmt) REVERT: B 182 LEU cc_start: 0.6253 (mt) cc_final: 0.5995 (tt) REVERT: B 190 LEU cc_start: 0.5558 (tp) cc_final: 0.5329 (tp) REVERT: B 488 MET cc_start: 0.7844 (mmp) cc_final: 0.6824 (mmt) REVERT: B 512 GLU cc_start: 0.5989 (tt0) cc_final: 0.5676 (tt0) REVERT: D 46 ASP cc_start: 0.6688 (m-30) cc_final: 0.6430 (m-30) REVERT: D 161 GLU cc_start: 0.6189 (mm-30) cc_final: 0.4549 (tm-30) REVERT: E 35 HIS cc_start: 0.7329 (m-70) cc_final: 0.6858 (m-70) REVERT: E 197 MET cc_start: 0.0489 (ttt) cc_final: -0.0846 (mmp) REVERT: E 321 ARG cc_start: 0.2979 (ptt180) cc_final: 0.1783 (mtp180) REVERT: E 521 MET cc_start: 0.7136 (mmm) cc_final: 0.6850 (mmt) REVERT: E 529 ASP cc_start: 0.5686 (p0) cc_final: 0.4186 (t0) REVERT: E 530 ASP cc_start: 0.6051 (t0) cc_final: 0.5308 (t0) REVERT: G 35 ASP cc_start: 0.7442 (m-30) cc_final: 0.7127 (m-30) REVERT: G 286 LYS cc_start: 0.3649 (mttt) cc_final: 0.2835 (ptpp) REVERT: G 432 VAL cc_start: 0.8354 (t) cc_final: 0.8015 (t) REVERT: H 134 ASN cc_start: 0.7073 (m-40) cc_final: 0.6254 (m-40) REVERT: H 218 LYS cc_start: 0.5359 (tttt) cc_final: 0.4692 (tppt) REVERT: H 227 MET cc_start: 0.2771 (tpt) cc_final: 0.0391 (mtt) REVERT: H 252 ASN cc_start: 0.4632 (m-40) cc_final: 0.4002 (m-40) REVERT: H 357 ARG cc_start: 0.4137 (mmt90) cc_final: 0.3218 (ptp90) REVERT: H 382 MET cc_start: 0.4202 (ttm) cc_final: 0.3739 (ttm) REVERT: Q 54 LYS cc_start: 0.8098 (mmtp) cc_final: 0.7832 (mmtp) REVERT: Q 393 ASP cc_start: 0.6722 (m-30) cc_final: 0.6354 (m-30) REVERT: Q 418 GLU cc_start: 0.6229 (tm-30) cc_final: 0.5550 (tp30) REVERT: Q 434 GLU cc_start: 0.6522 (pm20) cc_final: 0.6272 (mp0) REVERT: Z 24 ILE cc_start: 0.8920 (pt) cc_final: 0.8539 (pt) REVERT: Z 221 MET cc_start: 0.4585 (mmt) cc_final: 0.0978 (ptt) REVERT: Z 321 MET cc_start: 0.4763 (ttp) cc_final: 0.4451 (tpp) REVERT: b 25 ARG cc_start: 0.6812 (tpp-160) cc_final: 0.6605 (tpp-160) REVERT: b 108 GLU cc_start: 0.7295 (tp30) cc_final: 0.6278 (tp30) REVERT: b 141 LEU cc_start: 0.7252 (mp) cc_final: 0.7015 (mp) REVERT: b 353 MET cc_start: 0.4308 (mmp) cc_final: 0.3871 (mmp) REVERT: b 445 MET cc_start: 0.7430 (tpp) cc_final: 0.7124 (mtt) REVERT: b 485 ILE cc_start: 0.5540 (mt) cc_final: 0.5315 (mt) REVERT: d 135 GLU cc_start: 0.6524 (pp20) cc_final: 0.6276 (pp20) REVERT: d 355 MET cc_start: 0.3494 (tmm) cc_final: 0.3232 (tmm) REVERT: e 79 MET cc_start: 0.6835 (mtp) cc_final: 0.6418 (mtp) REVERT: e 168 LYS cc_start: 0.5774 (mmtp) cc_final: 0.4956 (mmtt) REVERT: e 197 MET cc_start: 0.4641 (ttm) cc_final: 0.4028 (tpt) REVERT: g 131 ASP cc_start: 0.8104 (p0) cc_final: 0.7460 (p0) REVERT: g 156 ILE cc_start: 0.7066 (mt) cc_final: 0.6855 (mt) REVERT: g 322 ARG cc_start: 0.6614 (mtm180) cc_final: 0.6349 (mtm110) REVERT: g 330 ARG cc_start: 0.3013 (ttt180) cc_final: 0.1385 (tpt170) REVERT: g 362 PHE cc_start: 0.3943 (m-80) cc_final: 0.2701 (m-80) REVERT: g 382 GLU cc_start: 0.3870 (mp0) cc_final: 0.3607 (pp20) REVERT: g 477 THR cc_start: 0.4964 (m) cc_final: 0.4509 (m) REVERT: g 516 LEU cc_start: 0.8866 (mp) cc_final: 0.8602 (mt) REVERT: h 103 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6345 (mm-30) REVERT: h 138 GLU cc_start: 0.7870 (tt0) cc_final: 0.7484 (tm-30) REVERT: h 160 MET cc_start: 0.5567 (ptt) cc_final: 0.5189 (ptt) REVERT: h 319 LEU cc_start: 0.5652 (mt) cc_final: 0.5204 (tp) REVERT: q 92 MET cc_start: 0.7106 (mmm) cc_final: 0.6662 (mmm) REVERT: q 129 ILE cc_start: 0.8712 (tt) cc_final: 0.8232 (tp) REVERT: q 179 LEU cc_start: 0.7738 (mt) cc_final: 0.7530 (mt) REVERT: q 404 ARG cc_start: 0.3862 (mtt180) cc_final: 0.2530 (mmp80) REVERT: q 492 MET cc_start: 0.7388 (tpp) cc_final: 0.7095 (tpp) REVERT: z 44 MET cc_start: 0.6692 (mtt) cc_final: 0.6237 (mtt) REVERT: z 63 LEU cc_start: 0.7851 (mt) cc_final: 0.7354 (mt) REVERT: z 64 LEU cc_start: 0.8843 (mt) cc_final: 0.8591 (mt) REVERT: z 138 LYS cc_start: 0.7790 (pttt) cc_final: 0.7415 (ttpt) REVERT: z 206 LEU cc_start: 0.7869 (mt) cc_final: 0.7214 (tt) REVERT: z 295 LYS cc_start: 0.5666 (mmtt) cc_final: 0.4233 (mtmt) REVERT: z 487 MET cc_start: 0.6806 (ptm) cc_final: 0.6421 (ptm) REVERT: a 103 ASN cc_start: 0.6766 (m-40) cc_final: 0.5730 (m110) REVERT: a 206 MET cc_start: 0.5110 (ttm) cc_final: 0.4681 (ttm) REVERT: a 306 MET cc_start: -0.0541 (ttt) cc_final: -0.2551 (mmm) REVERT: a 344 MET cc_start: 0.1649 (ppp) cc_final: 0.0772 (ppp) REVERT: a 528 ASP cc_start: 0.6761 (m-30) cc_final: 0.6290 (m-30) REVERT: a 530 LEU cc_start: 0.7998 (tp) cc_final: 0.7680 (tt) REVERT: a 532 LYS cc_start: 0.6834 (ptpp) cc_final: 0.6502 (tmtt) outliers start: 11 outliers final: 2 residues processed: 1221 average time/residue: 0.5922 time to fit residues: 1226.2463 Evaluate side-chains 859 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 857 time to evaluate : 5.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 409 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 613 optimal weight: 0.8980 chunk 502 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 738 optimal weight: 0.0870 chunk 798 optimal weight: 0.9990 chunk 657 optimal weight: 0.0060 chunk 732 optimal weight: 5.9990 chunk 251 optimal weight: 0.0470 chunk 592 optimal weight: 2.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS D 37 ASN E 236 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 513 GLN G 308 ASN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 422 GLN Z 31 GLN Z 346 HIS ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 503 GLN d 37 ASN d 129 HIS ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 288 GLN e 315 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 GLN h 151 GLN h 234 ASN h 282 HIS ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS z 68 GLN a 113 HIS a 223 GLN a 353 GLN a 482 ASN a 498 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 63926 Z= 0.157 Angle : 0.545 10.468 86360 Z= 0.282 Chirality : 0.043 0.290 10322 Planarity : 0.004 0.097 10999 Dihedral : 7.348 88.567 9257 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.07 % Allowed : 2.64 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.08), residues: 8173 helix: -1.44 (0.07), residues: 4006 sheet: -1.09 (0.18), residues: 788 loop : -1.50 (0.10), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 435 HIS 0.010 0.001 HIS d 406 PHE 0.014 0.001 PHE q 399 TYR 0.026 0.001 TYR a 422 ARG 0.021 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1163 time to evaluate : 5.432 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 44 MET cc_start: 0.7441 (ttm) cc_final: 0.7042 (ttt) REVERT: A 156 MET cc_start: 0.2996 (mmp) cc_final: 0.2597 (mmt) REVERT: A 161 ILE cc_start: 0.4059 (tt) cc_final: 0.2865 (tt) REVERT: A 275 ILE cc_start: 0.4571 (pt) cc_final: 0.4325 (pt) REVERT: A 388 MET cc_start: 0.1621 (mmp) cc_final: 0.1004 (tpp) REVERT: A 390 ARG cc_start: 0.4954 (ptm-80) cc_final: 0.3258 (mmm-85) REVERT: A 459 ASP cc_start: 0.6214 (t0) cc_final: 0.5501 (p0) REVERT: A 485 TRP cc_start: 0.4372 (m-10) cc_final: 0.3930 (m-10) REVERT: A 514 LEU cc_start: 0.7882 (mt) cc_final: 0.7568 (mt) REVERT: B 62 MET cc_start: 0.5878 (tpp) cc_final: 0.5619 (tpt) REVERT: B 488 MET cc_start: 0.7685 (mmp) cc_final: 0.6602 (mmt) REVERT: B 520 ILE cc_start: 0.7312 (mm) cc_final: 0.7082 (mm) REVERT: D 95 SER cc_start: 0.8316 (t) cc_final: 0.8054 (t) REVERT: D 161 GLU cc_start: 0.6383 (mm-30) cc_final: 0.4461 (tm-30) REVERT: D 203 VAL cc_start: 0.2267 (t) cc_final: 0.1945 (t) REVERT: E 58 MET cc_start: 0.6013 (ttt) cc_final: 0.5703 (ttt) REVERT: E 78 MET cc_start: 0.6136 (mmt) cc_final: 0.5617 (mmt) REVERT: E 197 MET cc_start: 0.1039 (ttt) cc_final: -0.0463 (mmp) REVERT: E 321 ARG cc_start: 0.2363 (ptt180) cc_final: 0.1598 (mtp180) REVERT: E 529 ASP cc_start: 0.5194 (p0) cc_final: 0.3919 (t0) REVERT: G 35 ASP cc_start: 0.7447 (m-30) cc_final: 0.7206 (m-30) REVERT: G 181 LYS cc_start: 0.5822 (tptt) cc_final: 0.4854 (pttm) REVERT: G 286 LYS cc_start: 0.3510 (mttt) cc_final: 0.2765 (ptpp) REVERT: G 519 ILE cc_start: 0.8368 (mm) cc_final: 0.8140 (mt) REVERT: H 107 GLN cc_start: 0.7218 (mm110) cc_final: 0.7014 (mm110) REVERT: H 227 MET cc_start: 0.2394 (tpt) cc_final: -0.0102 (mtt) REVERT: H 357 ARG cc_start: 0.3914 (mmt90) cc_final: 0.3075 (ptp90) REVERT: Q 123 LEU cc_start: 0.8698 (tp) cc_final: 0.8311 (mt) REVERT: Z 131 LEU cc_start: 0.7981 (mt) cc_final: 0.7528 (tt) REVERT: Z 221 MET cc_start: 0.4682 (mmt) cc_final: 0.1160 (ptt) REVERT: Z 234 ASN cc_start: 0.2364 (t0) cc_final: 0.0541 (p0) REVERT: Z 305 LEU cc_start: 0.3740 (mt) cc_final: 0.3537 (tt) REVERT: b 117 ILE cc_start: 0.8785 (pt) cc_final: 0.8548 (tt) REVERT: b 141 LEU cc_start: 0.7336 (mp) cc_final: 0.7013 (mp) REVERT: b 353 MET cc_start: 0.4539 (mmp) cc_final: 0.4130 (mmp) REVERT: b 480 MET cc_start: 0.6243 (ppp) cc_final: 0.5583 (ppp) REVERT: d 90 MET cc_start: 0.6974 (mtp) cc_final: 0.6747 (mtm) REVERT: d 300 ILE cc_start: 0.3173 (mt) cc_final: 0.2925 (mm) REVERT: d 432 LEU cc_start: 0.8222 (mt) cc_final: 0.7970 (mt) REVERT: e 27 MET cc_start: 0.4198 (mpp) cc_final: 0.3928 (mpp) REVERT: e 79 MET cc_start: 0.6306 (mtp) cc_final: 0.5907 (mtp) REVERT: e 197 MET cc_start: 0.4246 (ttm) cc_final: 0.3800 (tpt) REVERT: e 391 MET cc_start: 0.4926 (ptp) cc_final: 0.3887 (ptp) REVERT: g 131 ASP cc_start: 0.7903 (p0) cc_final: 0.7431 (p0) REVERT: g 132 ASP cc_start: 0.7578 (m-30) cc_final: 0.6708 (m-30) REVERT: g 362 PHE cc_start: 0.3420 (m-80) cc_final: 0.2141 (m-80) REVERT: g 516 LEU cc_start: 0.8835 (mp) cc_final: 0.8588 (mt) REVERT: g 522 ILE cc_start: 0.7799 (mm) cc_final: 0.7578 (mm) REVERT: g 523 VAL cc_start: 0.8789 (t) cc_final: 0.8504 (m) REVERT: h 45 MET cc_start: 0.8677 (mpp) cc_final: 0.8056 (mmt) REVERT: h 138 GLU cc_start: 0.7692 (tt0) cc_final: 0.7448 (tm-30) REVERT: h 183 VAL cc_start: 0.8019 (t) cc_final: 0.7784 (p) REVERT: h 482 GLU cc_start: 0.7182 (mp0) cc_final: 0.6588 (tm-30) REVERT: q 16 LYS cc_start: 0.5501 (mttt) cc_final: 0.5290 (tttt) REVERT: q 37 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7963 (ttpp) REVERT: q 346 HIS cc_start: 0.6861 (t70) cc_final: 0.6615 (t-170) REVERT: q 401 VAL cc_start: 0.7095 (p) cc_final: 0.6657 (p) REVERT: q 404 ARG cc_start: 0.3382 (mtt180) cc_final: 0.2421 (mmp80) REVERT: q 492 MET cc_start: 0.7147 (tpp) cc_final: 0.6916 (tpp) REVERT: z 63 LEU cc_start: 0.7417 (mt) cc_final: 0.6979 (mt) REVERT: z 138 LYS cc_start: 0.7897 (pttt) cc_final: 0.7465 (ttpt) REVERT: z 143 MET cc_start: 0.2863 (ppp) cc_final: 0.2454 (ppp) REVERT: z 190 MET cc_start: 0.4980 (tpp) cc_final: 0.4705 (tpp) REVERT: z 206 LEU cc_start: 0.7614 (mt) cc_final: 0.7178 (tt) REVERT: z 295 LYS cc_start: 0.5492 (mmtt) cc_final: 0.4215 (mtmt) REVERT: a 103 ASN cc_start: 0.6337 (m-40) cc_final: 0.5908 (m-40) REVERT: a 306 MET cc_start: -0.0496 (ttt) cc_final: -0.2675 (mmm) outliers start: 5 outliers final: 0 residues processed: 1167 average time/residue: 0.5817 time to fit residues: 1153.0582 Evaluate side-chains 846 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 846 time to evaluate : 5.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 729 optimal weight: 4.9990 chunk 555 optimal weight: 6.9990 chunk 383 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 352 optimal weight: 9.9990 chunk 496 optimal weight: 0.9990 chunk 741 optimal weight: 0.4980 chunk 784 optimal weight: 3.9990 chunk 387 optimal weight: 0.9980 chunk 702 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS D 406 HIS ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN G 308 ASN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 ASN d 129 HIS e 262 HIS e 497 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 GLN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 282 HIS ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 140 HIS ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 GLN a 435 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 63926 Z= 0.185 Angle : 0.570 9.865 86360 Z= 0.294 Chirality : 0.044 0.356 10322 Planarity : 0.004 0.147 10999 Dihedral : 7.858 161.329 9257 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % 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: -1.66 (0.09), residues: 8173 helix: -0.76 (0.08), residues: 4005 sheet: -0.96 (0.18), residues: 796 loop : -1.41 (0.10), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 496 HIS 0.015 0.001 HIS E 35 PHE 0.025 0.001 PHE e 343 TYR 0.028 0.001 TYR H 423 ARG 0.016 0.000 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1103 time to evaluate : 5.280 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: A 156 MET cc_start: 0.2844 (mmp) cc_final: 0.2488 (mmt) REVERT: A 161 ILE cc_start: 0.3943 (tt) cc_final: 0.3264 (tt) REVERT: A 275 ILE cc_start: 0.4708 (pt) cc_final: 0.4451 (pt) REVERT: A 388 MET cc_start: 0.1336 (mmp) cc_final: 0.0818 (tpp) REVERT: A 390 ARG cc_start: 0.5231 (ptm-80) cc_final: 0.3537 (mmm-85) REVERT: A 459 ASP cc_start: 0.6431 (t0) cc_final: 0.5541 (p0) REVERT: B 50 LYS cc_start: 0.6763 (mtmt) cc_final: 0.6247 (mtmt) REVERT: B 62 MET cc_start: 0.6060 (tpp) cc_final: 0.5760 (tpt) REVERT: B 159 LEU cc_start: 0.6318 (mt) cc_final: 0.5988 (mt) REVERT: B 182 LEU cc_start: 0.6635 (mm) cc_final: 0.5838 (pp) REVERT: B 438 SER cc_start: 0.7603 (p) cc_final: 0.6327 (p) REVERT: B 488 MET cc_start: 0.7824 (mmp) cc_final: 0.6618 (mmt) REVERT: B 520 ILE cc_start: 0.7220 (mm) cc_final: 0.6851 (mm) REVERT: D 161 GLU cc_start: 0.6111 (mm-30) cc_final: 0.4729 (tm-30) REVERT: D 203 VAL cc_start: 0.2348 (t) cc_final: 0.2058 (t) REVERT: E 78 MET cc_start: 0.6218 (mmt) cc_final: 0.5882 (mmt) REVERT: E 197 MET cc_start: 0.0814 (ttt) cc_final: -0.0106 (ptm) REVERT: E 321 ARG cc_start: 0.2454 (ptt180) cc_final: 0.1869 (mtp180) REVERT: E 436 ASP cc_start: 0.5689 (m-30) cc_final: 0.4467 (t0) REVERT: E 473 THR cc_start: 0.6645 (p) cc_final: 0.6424 (p) REVERT: E 489 ILE cc_start: 0.8745 (mt) cc_final: 0.8478 (tt) REVERT: E 529 ASP cc_start: 0.5566 (p0) cc_final: 0.3977 (t0) REVERT: G 219 MET cc_start: 0.3411 (ptp) cc_final: 0.2261 (mtp) REVERT: G 222 LYS cc_start: 0.1670 (tttm) cc_final: 0.0889 (tptp) REVERT: G 286 LYS cc_start: 0.3305 (mttt) cc_final: 0.2638 (ptpp) REVERT: H 218 LYS cc_start: 0.5282 (tttt) cc_final: 0.4600 (tppt) REVERT: H 227 MET cc_start: 0.1997 (tpt) cc_final: -0.0174 (mtt) REVERT: H 357 ARG cc_start: 0.4198 (mmt90) cc_final: 0.3061 (ptp90) REVERT: Q 88 MET cc_start: 0.7321 (tpp) cc_final: 0.7095 (tpp) REVERT: Q 123 LEU cc_start: 0.8817 (tp) cc_final: 0.8384 (mt) REVERT: Z 98 ILE cc_start: 0.8840 (mm) cc_final: 0.8447 (tp) REVERT: Z 131 LEU cc_start: 0.7950 (mt) cc_final: 0.7545 (tt) REVERT: Z 143 MET cc_start: 0.5646 (mpp) cc_final: 0.5312 (mpp) REVERT: Z 305 LEU cc_start: 0.3965 (mt) cc_final: 0.3688 (tt) REVERT: b 25 ARG cc_start: 0.6208 (tmt170) cc_final: 0.5908 (tmm-80) REVERT: b 353 MET cc_start: 0.4613 (mmp) cc_final: 0.4322 (mmp) REVERT: b 488 MET cc_start: 0.6652 (mmm) cc_final: 0.6234 (mmm) REVERT: d 80 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7112 (mt0) REVERT: d 300 ILE cc_start: 0.3740 (mt) cc_final: 0.3429 (mm) REVERT: d 432 LEU cc_start: 0.8620 (mt) cc_final: 0.7973 (mt) REVERT: d 446 MET cc_start: 0.4317 (mmp) cc_final: 0.3723 (mmt) REVERT: d 459 GLU cc_start: 0.7269 (pp20) cc_final: 0.6954 (pt0) REVERT: d 528 SER cc_start: 0.9004 (p) cc_final: 0.8759 (m) REVERT: e 68 VAL cc_start: 0.8048 (p) cc_final: 0.7666 (t) REVERT: e 197 MET cc_start: 0.4518 (ttm) cc_final: 0.3928 (tpt) REVERT: e 283 PHE cc_start: -0.1037 (m-80) cc_final: -0.1659 (m-80) REVERT: g 131 ASP cc_start: 0.7978 (p0) cc_final: 0.7381 (p0) REVERT: g 132 ASP cc_start: 0.6746 (m-30) cc_final: 0.6216 (m-30) REVERT: g 145 ASP cc_start: 0.7602 (p0) cc_final: 0.7306 (p0) REVERT: g 182 MET cc_start: 0.3990 (ttm) cc_final: 0.3509 (ttp) REVERT: g 270 MET cc_start: 0.4034 (ppp) cc_final: 0.3469 (ppp) REVERT: g 322 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6610 (mtm110) REVERT: g 516 LEU cc_start: 0.8916 (mp) cc_final: 0.8447 (mt) REVERT: h 47 LYS cc_start: 0.7813 (mttp) cc_final: 0.7609 (mttp) REVERT: h 64 THR cc_start: 0.7751 (p) cc_final: 0.7475 (p) REVERT: h 138 GLU cc_start: 0.7699 (tt0) cc_final: 0.7441 (tm-30) REVERT: h 139 ILE cc_start: 0.9091 (mt) cc_final: 0.8666 (mm) REVERT: h 183 VAL cc_start: 0.8087 (t) cc_final: 0.7818 (p) REVERT: q 129 ILE cc_start: 0.8577 (tt) cc_final: 0.8289 (tp) REVERT: q 346 HIS cc_start: 0.6817 (t70) cc_final: 0.6573 (t-170) REVERT: q 401 VAL cc_start: 0.7052 (p) cc_final: 0.6814 (p) REVERT: q 404 ARG cc_start: 0.3591 (mtt180) cc_final: 0.2577 (mmp80) REVERT: z 63 LEU cc_start: 0.7685 (mt) cc_final: 0.7210 (mt) REVERT: z 138 LYS cc_start: 0.7866 (pttt) cc_final: 0.7461 (ttpt) REVERT: z 190 MET cc_start: 0.5094 (tpp) cc_final: 0.4885 (tpp) REVERT: z 206 LEU cc_start: 0.7697 (mt) cc_final: 0.7225 (tt) REVERT: z 268 GLU cc_start: 0.4888 (OUTLIER) cc_final: 0.4542 (mp0) REVERT: z 295 LYS cc_start: 0.5391 (mmtt) cc_final: 0.3986 (mtmt) REVERT: a 244 THR cc_start: 0.5017 (t) cc_final: 0.4657 (m) REVERT: a 306 MET cc_start: -0.0220 (ttt) cc_final: -0.2028 (mmm) outliers start: 4 outliers final: 0 residues processed: 1105 average time/residue: 0.5543 time to fit residues: 1050.4804 Evaluate side-chains 840 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 839 time to evaluate : 5.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 653 optimal weight: 4.9990 chunk 445 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 584 optimal weight: 7.9990 chunk 323 optimal weight: 6.9990 chunk 669 optimal weight: 8.9990 chunk 542 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 400 optimal weight: 0.5980 chunk 704 optimal weight: 0.6980 chunk 198 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS D 406 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 GLN G 308 ASN H 17 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 HIS Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 78 ASN b 391 HIS d 129 HIS ** e 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 180 HIS e 262 HIS e 497 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 392 GLN h 234 ASN ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 432 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 475 GLN a 498 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 63926 Z= 0.232 Angle : 0.616 11.129 86360 Z= 0.318 Chirality : 0.045 0.345 10322 Planarity : 0.004 0.101 10999 Dihedral : 7.621 87.945 9257 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % 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: -1.49 (0.09), residues: 8173 helix: -0.52 (0.08), residues: 4001 sheet: -1.06 (0.19), residues: 715 loop : -1.41 (0.10), residues: 3457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 493 HIS 0.007 0.001 HIS H 468 PHE 0.031 0.002 PHE H 303 TYR 0.016 0.002 TYR q 47 ARG 0.045 0.001 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1103 time to evaluate : 5.362 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 127 GLU cc_start: 0.4542 (tp30) cc_final: 0.4246 (tp30) REVERT: A 388 MET cc_start: 0.1854 (mmp) cc_final: 0.1256 (tpp) REVERT: A 390 ARG cc_start: 0.5135 (ptm-80) cc_final: 0.3503 (mmm160) REVERT: A 459 ASP cc_start: 0.6632 (t0) cc_final: 0.5676 (p0) REVERT: B 62 MET cc_start: 0.6093 (tpp) cc_final: 0.5872 (tpt) REVERT: B 159 LEU cc_start: 0.6032 (mt) cc_final: 0.5819 (mt) REVERT: B 182 LEU cc_start: 0.6738 (mm) cc_final: 0.6290 (pp) REVERT: B 488 MET cc_start: 0.7683 (mmp) cc_final: 0.6757 (mmt) REVERT: D 42 LYS cc_start: 0.7356 (ttmt) cc_final: 0.7150 (ttmt) REVERT: D 57 MET cc_start: 0.8489 (mmm) cc_final: 0.8251 (mtt) REVERT: D 161 GLU cc_start: 0.6035 (mm-30) cc_final: 0.4697 (tm-30) REVERT: D 192 MET cc_start: 0.6787 (ptm) cc_final: 0.5905 (tmm) REVERT: D 203 VAL cc_start: 0.2430 (t) cc_final: 0.2197 (t) REVERT: E 197 MET cc_start: 0.0949 (ttt) cc_final: -0.0025 (ptm) REVERT: E 321 ARG cc_start: 0.2506 (ptt180) cc_final: 0.2063 (mtp180) REVERT: E 436 ASP cc_start: 0.5839 (m-30) cc_final: 0.4311 (t0) REVERT: E 530 ASP cc_start: 0.5461 (t0) cc_final: 0.4776 (t0) REVERT: G 127 ARG cc_start: 0.6870 (mmt-90) cc_final: 0.6354 (mpt180) REVERT: G 219 MET cc_start: 0.3938 (ptp) cc_final: 0.2637 (mtp) REVERT: G 222 LYS cc_start: 0.1720 (tttm) cc_final: 0.1218 (tptp) REVERT: G 286 LYS cc_start: 0.3730 (mttt) cc_final: 0.2880 (ptpp) REVERT: G 432 VAL cc_start: 0.8273 (t) cc_final: 0.8058 (t) REVERT: H 139 ILE cc_start: 0.8410 (tp) cc_final: 0.8171 (tp) REVERT: H 218 LYS cc_start: 0.5345 (tttt) cc_final: 0.4780 (tppt) REVERT: H 227 MET cc_start: 0.1915 (tpt) cc_final: -0.0351 (mtt) REVERT: H 357 ARG cc_start: 0.4716 (mmt90) cc_final: 0.3533 (ptp90) REVERT: H 394 MET cc_start: 0.6244 (tpt) cc_final: 0.5728 (mmt) REVERT: Z 98 ILE cc_start: 0.8821 (mm) cc_final: 0.8227 (mt) REVERT: Z 131 LEU cc_start: 0.7913 (mt) cc_final: 0.7670 (tt) REVERT: Z 143 MET cc_start: 0.5694 (mpp) cc_final: 0.5204 (mpp) REVERT: Z 221 MET cc_start: 0.2687 (mmp) cc_final: 0.0970 (ptm) REVERT: Z 305 LEU cc_start: 0.3802 (mt) cc_final: 0.3545 (tt) REVERT: b 78 ASN cc_start: 0.6693 (OUTLIER) cc_final: 0.5878 (t0) REVERT: b 268 GLU cc_start: 0.1778 (mm-30) cc_final: 0.1090 (tp30) REVERT: b 488 MET cc_start: 0.6791 (mmm) cc_final: 0.6572 (tpp) REVERT: d 80 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7217 (mt0) REVERT: d 134 SER cc_start: 0.8257 (t) cc_final: 0.7190 (t) REVERT: d 260 MET cc_start: 0.3354 (mtm) cc_final: 0.3040 (mtt) REVERT: d 459 GLU cc_start: 0.7244 (pp20) cc_final: 0.6872 (pt0) REVERT: e 79 MET cc_start: 0.6748 (mtp) cc_final: 0.6379 (mtp) REVERT: e 168 LYS cc_start: 0.5759 (mmtt) cc_final: 0.4584 (mmtt) REVERT: e 197 MET cc_start: 0.4571 (ttm) cc_final: 0.4040 (tpt) REVERT: e 283 PHE cc_start: -0.1110 (m-80) cc_final: -0.2035 (m-80) REVERT: e 391 MET cc_start: 0.5023 (ptp) cc_final: 0.4417 (ptp) REVERT: g 54 MET cc_start: 0.5586 (mpp) cc_final: 0.4701 (mpp) REVERT: g 90 GLU cc_start: 0.6358 (pp20) cc_final: 0.5913 (mt-10) REVERT: g 131 ASP cc_start: 0.7842 (p0) cc_final: 0.7349 (p0) REVERT: g 132 ASP cc_start: 0.7281 (m-30) cc_final: 0.6502 (m-30) REVERT: g 145 ASP cc_start: 0.7826 (p0) cc_final: 0.7384 (p0) REVERT: g 182 MET cc_start: 0.3582 (ttm) cc_final: 0.3137 (ttp) REVERT: g 228 ARG cc_start: 0.3611 (mtt-85) cc_final: 0.1835 (mmp80) REVERT: h 45 MET cc_start: 0.8838 (mpp) cc_final: 0.8348 (mmt) REVERT: h 138 GLU cc_start: 0.7843 (tt0) cc_final: 0.7632 (tm-30) REVERT: h 139 ILE cc_start: 0.9101 (mt) cc_final: 0.8837 (mt) REVERT: h 194 MET cc_start: 0.4345 (mtt) cc_final: 0.4037 (mtt) REVERT: q 33 ILE cc_start: 0.8388 (mt) cc_final: 0.8013 (mt) REVERT: q 37 LYS cc_start: 0.8340 (ttpp) cc_final: 0.8032 (ttpp) REVERT: q 129 ILE cc_start: 0.8769 (tt) cc_final: 0.8531 (tp) REVERT: q 179 LEU cc_start: 0.7708 (mt) cc_final: 0.7495 (mt) REVERT: q 401 VAL cc_start: 0.7266 (p) cc_final: 0.7063 (p) REVERT: q 404 ARG cc_start: 0.4126 (mtt180) cc_final: 0.2766 (mmp80) REVERT: q 492 MET cc_start: 0.7203 (tpp) cc_final: 0.7000 (tpp) REVERT: z 63 LEU cc_start: 0.7806 (mt) cc_final: 0.7192 (mt) REVERT: z 138 LYS cc_start: 0.7849 (pttt) cc_final: 0.7170 (ttpt) REVERT: z 143 MET cc_start: 0.3365 (ppp) cc_final: 0.3133 (ppp) REVERT: z 206 LEU cc_start: 0.7653 (mt) cc_final: 0.7096 (tt) REVERT: z 272 LYS cc_start: 0.3366 (mmtt) cc_final: 0.3141 (mmtp) REVERT: z 295 LYS cc_start: 0.5696 (mmtt) cc_final: 0.4225 (mtmt) REVERT: z 526 MET cc_start: 0.1505 (mmm) cc_final: 0.1159 (mmm) REVERT: a 244 THR cc_start: 0.4886 (t) cc_final: 0.4602 (m) REVERT: a 306 MET cc_start: 0.0221 (ttt) cc_final: -0.2279 (mmm) REVERT: a 528 ASP cc_start: 0.6355 (m-30) cc_final: 0.5903 (m-30) outliers start: 5 outliers final: 1 residues processed: 1106 average time/residue: 0.5771 time to fit residues: 1093.5282 Evaluate side-chains 823 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 821 time to evaluate : 5.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 264 optimal weight: 0.9990 chunk 706 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 460 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 785 optimal weight: 3.9990 chunk 652 optimal weight: 6.9990 chunk 363 optimal weight: 0.0370 chunk 65 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 412 optimal weight: 5.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS G 111 HIS H 17 GLN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS d 482 ASN e 182 GLN e 497 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 316 ASN q 346 HIS q 422 GLN ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 GLN z 386 GLN a 82 GLN a 472 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 63926 Z= 0.159 Angle : 0.555 19.586 86360 Z= 0.286 Chirality : 0.043 0.340 10322 Planarity : 0.004 0.132 10999 Dihedral : 7.552 89.276 9257 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.03 % Allowed : 1.96 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % 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: -1.14 (0.09), residues: 8173 helix: -0.17 (0.08), residues: 3988 sheet: -1.00 (0.19), residues: 727 loop : -1.29 (0.10), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP h 493 HIS 0.007 0.001 HIS H 468 PHE 0.022 0.001 PHE A 167 TYR 0.022 0.001 TYR h 423 ARG 0.031 0.001 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1088 time to evaluate : 5.363 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 127 GLU cc_start: 0.4677 (tp30) cc_final: 0.4308 (tp30) REVERT: A 388 MET cc_start: 0.1558 (mmp) cc_final: 0.1028 (tpp) REVERT: A 390 ARG cc_start: 0.4720 (ptm-80) cc_final: 0.3329 (mmm160) REVERT: B 50 LYS cc_start: 0.6254 (mtmt) cc_final: 0.5982 (mtpt) REVERT: B 159 LEU cc_start: 0.6030 (mt) cc_final: 0.5736 (mt) REVERT: B 182 LEU cc_start: 0.6817 (mm) cc_final: 0.6355 (pp) REVERT: B 488 MET cc_start: 0.7585 (mmp) cc_final: 0.6713 (mmt) REVERT: D 42 LYS cc_start: 0.7469 (ttmt) cc_final: 0.7138 (ttmt) REVERT: D 46 ASP cc_start: 0.6932 (m-30) cc_final: 0.6648 (m-30) REVERT: D 124 LEU cc_start: 0.7758 (mp) cc_final: 0.7551 (mp) REVERT: D 161 GLU cc_start: 0.6051 (mm-30) cc_final: 0.4415 (tm-30) REVERT: D 192 MET cc_start: 0.6604 (ptm) cc_final: 0.5896 (tmm) REVERT: D 203 VAL cc_start: 0.2262 (t) cc_final: 0.1974 (t) REVERT: E 35 HIS cc_start: 0.6791 (m90) cc_final: 0.6283 (m-70) REVERT: E 197 MET cc_start: 0.0876 (ttt) cc_final: -0.0232 (ptm) REVERT: E 321 ARG cc_start: 0.2288 (ptt180) cc_final: 0.1939 (mtp180) REVERT: E 436 ASP cc_start: 0.5860 (m-30) cc_final: 0.4533 (t0) REVERT: E 529 ASP cc_start: 0.5799 (p0) cc_final: 0.3645 (t0) REVERT: G 219 MET cc_start: 0.3832 (ptp) cc_final: 0.2540 (mtp) REVERT: G 222 LYS cc_start: 0.1641 (tttm) cc_final: 0.1192 (tptp) REVERT: G 286 LYS cc_start: 0.3679 (mttt) cc_final: 0.2851 (ptpp) REVERT: H 139 ILE cc_start: 0.8384 (tp) cc_final: 0.8132 (tp) REVERT: H 194 MET cc_start: 0.3075 (mmm) cc_final: 0.2049 (mmt) REVERT: H 357 ARG cc_start: 0.4534 (mmt90) cc_final: 0.3307 (ptp90) REVERT: H 394 MET cc_start: 0.6142 (tpt) cc_final: 0.5664 (mmt) REVERT: H 493 TRP cc_start: 0.5326 (m-10) cc_final: 0.4782 (m-10) REVERT: H 500 ILE cc_start: 0.8168 (mp) cc_final: 0.7912 (mp) REVERT: Q 378 ARG cc_start: 0.6103 (ttm-80) cc_final: 0.4969 (ttt180) REVERT: Z 98 ILE cc_start: 0.8787 (mm) cc_final: 0.8249 (mt) REVERT: Z 131 LEU cc_start: 0.7985 (mt) cc_final: 0.7715 (tt) REVERT: Z 143 MET cc_start: 0.5376 (mpp) cc_final: 0.5157 (mpp) REVERT: Z 221 MET cc_start: 0.2679 (mmp) cc_final: 0.1043 (ptm) REVERT: b 213 TYR cc_start: 0.6414 (t80) cc_final: 0.6129 (t80) REVERT: b 443 LEU cc_start: 0.8814 (mt) cc_final: 0.8519 (mt) REVERT: b 478 LEU cc_start: 0.6363 (mm) cc_final: 0.5969 (mp) REVERT: d 80 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7198 (mt0) REVERT: d 352 THR cc_start: 0.4541 (p) cc_final: 0.4336 (p) REVERT: d 459 GLU cc_start: 0.7357 (pp20) cc_final: 0.6772 (pt0) REVERT: d 462 PRO cc_start: 0.8654 (Cg_exo) cc_final: 0.8416 (Cg_endo) REVERT: e 79 MET cc_start: 0.6746 (mtp) cc_final: 0.6227 (mtp) REVERT: e 182 GLN cc_start: 0.4078 (OUTLIER) cc_final: 0.3862 (pp30) REVERT: e 197 MET cc_start: 0.4492 (ttm) cc_final: 0.3937 (tpt) REVERT: e 283 PHE cc_start: -0.1017 (m-80) cc_final: -0.1906 (m-80) REVERT: e 391 MET cc_start: 0.4703 (ptp) cc_final: 0.4063 (ptp) REVERT: e 531 ILE cc_start: 0.6763 (pt) cc_final: 0.6542 (pt) REVERT: g 54 MET cc_start: 0.5378 (mpp) cc_final: 0.4918 (mpp) REVERT: g 71 GLN cc_start: 0.7349 (pp30) cc_final: 0.7044 (pt0) REVERT: g 90 GLU cc_start: 0.6485 (pp20) cc_final: 0.6088 (mt-10) REVERT: g 111 HIS cc_start: 0.5974 (m90) cc_final: 0.5770 (m-70) REVERT: g 145 ASP cc_start: 0.7848 (p0) cc_final: 0.7475 (p0) REVERT: g 156 ILE cc_start: 0.6969 (mt) cc_final: 0.6761 (mt) REVERT: g 182 MET cc_start: 0.4221 (ttm) cc_final: 0.3890 (ttp) REVERT: g 228 ARG cc_start: 0.3375 (mtt-85) cc_final: 0.1601 (mmp80) REVERT: g 490 MET cc_start: 0.7200 (tpp) cc_final: 0.6677 (tpp) REVERT: h 45 MET cc_start: 0.8740 (mpp) cc_final: 0.8284 (mmt) REVERT: h 46 ASP cc_start: 0.5869 (p0) cc_final: 0.5374 (p0) REVERT: h 138 GLU cc_start: 0.7847 (tt0) cc_final: 0.7637 (tm-30) REVERT: q 37 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7891 (ttpp) REVERT: q 129 ILE cc_start: 0.8746 (tt) cc_final: 0.8399 (tp) REVERT: q 223 PHE cc_start: 0.4550 (m-80) cc_final: 0.4189 (m-80) REVERT: q 317 SER cc_start: 0.3533 (p) cc_final: 0.3003 (m) REVERT: q 385 MET cc_start: 0.5968 (ttm) cc_final: 0.4911 (tpp) REVERT: q 401 VAL cc_start: 0.6986 (p) cc_final: 0.6683 (p) REVERT: q 404 ARG cc_start: 0.3960 (mtt180) cc_final: 0.2704 (mmp80) REVERT: z 59 ASP cc_start: 0.4783 (t0) cc_final: 0.4552 (t0) REVERT: z 63 LEU cc_start: 0.7728 (mt) cc_final: 0.7338 (mt) REVERT: z 68 GLN cc_start: 0.4909 (mm-40) cc_final: 0.4636 (mm110) REVERT: z 137 VAL cc_start: 0.8237 (t) cc_final: 0.7968 (p) REVERT: z 138 LYS cc_start: 0.7803 (pttt) cc_final: 0.7205 (ttpt) REVERT: z 206 LEU cc_start: 0.7507 (mt) cc_final: 0.7000 (tt) REVERT: z 272 LYS cc_start: 0.3349 (mmtt) cc_final: 0.3127 (mmtp) REVERT: z 295 LYS cc_start: 0.5438 (mmtt) cc_final: 0.3996 (mtmt) REVERT: a 244 THR cc_start: 0.4741 (t) cc_final: 0.4498 (m) REVERT: a 306 MET cc_start: -0.0179 (ttt) cc_final: -0.2198 (mmm) outliers start: 2 outliers final: 0 residues processed: 1089 average time/residue: 0.5599 time to fit residues: 1055.4488 Evaluate side-chains 828 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 827 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 757 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 447 optimal weight: 0.0470 chunk 573 optimal weight: 0.0870 chunk 444 optimal weight: 5.9990 chunk 661 optimal weight: 0.9980 chunk 438 optimal weight: 1.9990 chunk 782 optimal weight: 0.9990 chunk 489 optimal weight: 2.9990 chunk 477 optimal weight: 3.9990 chunk 361 optimal weight: 0.0060 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS G 111 HIS ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 361 HIS d 129 HIS e 84 GLN e 497 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN q 346 HIS ** q 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 503 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5661 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 63926 Z= 0.145 Angle : 0.548 14.797 86360 Z= 0.280 Chirality : 0.043 0.364 10322 Planarity : 0.005 0.316 10999 Dihedral : 7.490 137.979 9257 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.01 % Allowed : 1.12 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % 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: -0.88 (0.09), residues: 8173 helix: 0.09 (0.08), residues: 3999 sheet: -0.97 (0.19), residues: 711 loop : -1.21 (0.10), residues: 3463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 485 HIS 0.005 0.001 HIS E 35 PHE 0.025 0.001 PHE A 167 TYR 0.019 0.001 TYR B 213 ARG 0.038 0.000 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1080 time to evaluate : 5.441 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: A 127 GLU cc_start: 0.4609 (tp30) cc_final: 0.4387 (tp30) REVERT: A 275 ILE cc_start: 0.4913 (pt) cc_final: 0.4656 (pt) REVERT: A 388 MET cc_start: 0.1625 (mmp) cc_final: 0.1093 (tpp) REVERT: A 390 ARG cc_start: 0.5035 (ptm-80) cc_final: 0.3643 (mmm160) REVERT: A 485 TRP cc_start: 0.4862 (m-10) cc_final: 0.4503 (m-10) REVERT: B 159 LEU cc_start: 0.5673 (mt) cc_final: 0.5455 (mt) REVERT: B 182 LEU cc_start: 0.6816 (mm) cc_final: 0.6329 (pp) REVERT: B 480 MET cc_start: 0.6863 (ppp) cc_final: 0.6600 (ppp) REVERT: B 488 MET cc_start: 0.7538 (mmp) cc_final: 0.6467 (mmt) REVERT: D 42 LYS cc_start: 0.7499 (ttmt) cc_final: 0.7090 (ttmt) REVERT: D 46 ASP cc_start: 0.6894 (m-30) cc_final: 0.6647 (m-30) REVERT: D 95 SER cc_start: 0.8431 (t) cc_final: 0.8224 (t) REVERT: D 161 GLU cc_start: 0.5942 (mm-30) cc_final: 0.4277 (tm-30) REVERT: D 192 MET cc_start: 0.6596 (ptm) cc_final: 0.6015 (tmm) REVERT: D 203 VAL cc_start: 0.2281 (t) cc_final: 0.2036 (t) REVERT: D 323 MET cc_start: 0.2751 (mpp) cc_final: 0.2534 (mtt) REVERT: E 35 HIS cc_start: 0.6762 (m90) cc_final: 0.6223 (m-70) REVERT: E 197 MET cc_start: 0.0764 (ttt) cc_final: -0.0301 (ptm) REVERT: E 286 MET cc_start: 0.2585 (mmm) cc_final: 0.2248 (mmp) REVERT: E 321 ARG cc_start: 0.2244 (ptt180) cc_final: 0.1316 (mtp180) REVERT: E 382 THR cc_start: 0.2321 (p) cc_final: 0.2087 (p) REVERT: E 436 ASP cc_start: 0.5971 (m-30) cc_final: 0.4445 (t0) REVERT: E 529 ASP cc_start: 0.5683 (p0) cc_final: 0.3604 (t0) REVERT: G 219 MET cc_start: 0.3774 (ptp) cc_final: 0.2450 (mtp) REVERT: G 222 LYS cc_start: 0.1661 (tttm) cc_final: 0.1217 (tptp) REVERT: G 286 LYS cc_start: 0.3558 (mttt) cc_final: 0.2842 (ptpp) REVERT: H 19 ILE cc_start: 0.9046 (mm) cc_final: 0.8837 (mt) REVERT: H 46 ASP cc_start: 0.7175 (m-30) cc_final: 0.6564 (m-30) REVERT: H 139 ILE cc_start: 0.8277 (tp) cc_final: 0.8000 (tp) REVERT: H 194 MET cc_start: 0.3022 (mmm) cc_final: 0.2042 (mmt) REVERT: H 218 LYS cc_start: 0.5518 (tttt) cc_final: 0.4821 (tppt) REVERT: H 227 MET cc_start: 0.2598 (tpt) cc_final: 0.0277 (mtt) REVERT: H 357 ARG cc_start: 0.4507 (mmt90) cc_final: 0.3274 (ptp90) REVERT: H 493 TRP cc_start: 0.5187 (m-10) cc_final: 0.4636 (m-10) REVERT: H 517 ASP cc_start: 0.7050 (t0) cc_final: 0.6589 (t0) REVERT: Q 378 ARG cc_start: 0.5945 (ttm-80) cc_final: 0.5013 (ttt-90) REVERT: Q 393 ASP cc_start: 0.5665 (m-30) cc_final: 0.5254 (m-30) REVERT: Z 98 ILE cc_start: 0.8668 (mm) cc_final: 0.8195 (mt) REVERT: Z 143 MET cc_start: 0.5516 (mpp) cc_final: 0.5274 (mpp) REVERT: Z 221 MET cc_start: 0.2663 (mmp) cc_final: 0.1566 (ptm) REVERT: Z 305 LEU cc_start: 0.4565 (tt) cc_final: 0.3032 (mt) REVERT: b 213 TYR cc_start: 0.6505 (t80) cc_final: 0.6286 (t80) REVERT: b 290 PHE cc_start: 0.4450 (t80) cc_final: 0.3905 (t80) REVERT: d 446 MET cc_start: 0.4010 (mmp) cc_final: 0.3326 (mmp) REVERT: d 452 ARG cc_start: 0.6487 (ptm160) cc_final: 0.6195 (ptm160) REVERT: d 462 PRO cc_start: 0.8701 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: d 481 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7507 (ttm170) REVERT: e 79 MET cc_start: 0.6337 (mtp) cc_final: 0.5935 (mtp) REVERT: e 197 MET cc_start: 0.4458 (ttm) cc_final: 0.3876 (tpt) REVERT: e 283 PHE cc_start: -0.1092 (m-80) cc_final: -0.1721 (m-80) REVERT: e 391 MET cc_start: 0.4640 (ptp) cc_final: 0.4069 (ptp) REVERT: e 449 PHE cc_start: 0.7240 (t80) cc_final: 0.7028 (t80) REVERT: g 54 MET cc_start: 0.5489 (mpp) cc_final: 0.5021 (mpp) REVERT: g 71 GLN cc_start: 0.7472 (pp30) cc_final: 0.7039 (pt0) REVERT: g 90 GLU cc_start: 0.6449 (pp20) cc_final: 0.6204 (mt-10) REVERT: g 133 MET cc_start: 0.7362 (mtm) cc_final: 0.7129 (mtm) REVERT: g 145 ASP cc_start: 0.7816 (p0) cc_final: 0.7506 (p0) REVERT: g 156 ILE cc_start: 0.6772 (mt) cc_final: 0.6513 (mt) REVERT: g 182 MET cc_start: 0.4178 (ttm) cc_final: 0.3765 (ttp) REVERT: g 270 MET cc_start: 0.4289 (ppp) cc_final: 0.3681 (ppp) REVERT: g 362 PHE cc_start: 0.4535 (m-10) cc_final: 0.4005 (m-80) REVERT: h 45 MET cc_start: 0.8676 (mpp) cc_final: 0.8284 (mmt) REVERT: q 129 ILE cc_start: 0.8684 (tt) cc_final: 0.8320 (tp) REVERT: q 223 PHE cc_start: 0.4441 (m-80) cc_final: 0.4181 (m-80) REVERT: q 401 VAL cc_start: 0.6842 (p) cc_final: 0.6475 (p) REVERT: q 404 ARG cc_start: 0.3575 (mtt180) cc_final: 0.2458 (mmp80) REVERT: z 59 ASP cc_start: 0.4819 (t0) cc_final: 0.4286 (t0) REVERT: z 63 LEU cc_start: 0.7634 (mt) cc_final: 0.6544 (mt) REVERT: z 137 VAL cc_start: 0.7862 (t) cc_final: 0.7538 (p) REVERT: z 138 LYS cc_start: 0.7799 (pttt) cc_final: 0.7077 (ttpt) REVERT: z 143 MET cc_start: 0.2818 (ppp) cc_final: 0.1834 (ppp) REVERT: z 206 LEU cc_start: 0.7245 (mt) cc_final: 0.6889 (tt) REVERT: z 295 LYS cc_start: 0.4777 (mmtt) cc_final: 0.3482 (mtmt) REVERT: a 244 THR cc_start: 0.4762 (t) cc_final: 0.4527 (m) REVERT: a 306 MET cc_start: -0.0390 (ttt) cc_final: -0.2391 (mmm) outliers start: 1 outliers final: 0 residues processed: 1081 average time/residue: 0.5692 time to fit residues: 1066.4738 Evaluate side-chains 844 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 844 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 484 optimal weight: 7.9990 chunk 312 optimal weight: 3.9990 chunk 467 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 497 optimal weight: 7.9990 chunk 533 optimal weight: 0.9990 chunk 386 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 615 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS B 391 HIS E 315 ASN E 409 ASN E 443 GLN ** E 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS H 17 GLN H 252 ASN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 GLN Q 50 ASN Q 175 ASN Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 453 ASN d 129 HIS ** d 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 497 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 380 GLN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS ** q 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 68 GLN ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 135 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 63926 Z= 0.268 Angle : 0.685 16.804 86360 Z= 0.351 Chirality : 0.047 0.301 10322 Planarity : 0.004 0.101 10999 Dihedral : 7.751 89.780 9257 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.06 % Allowed : 1.39 % Favored : 98.55 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % 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: -1.19 (0.09), residues: 8173 helix: -0.16 (0.08), residues: 3970 sheet: -1.05 (0.19), residues: 740 loop : -1.37 (0.10), residues: 3463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 168 HIS 0.010 0.001 HIS H 468 PHE 0.033 0.002 PHE E 449 TYR 0.025 0.002 TYR h 423 ARG 0.016 0.001 ARG Z 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1030 time to evaluate : 5.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.3705 (m-80) cc_final: 0.3458 (m-10) REVERT: A 390 ARG cc_start: 0.4772 (ptm-80) cc_final: 0.3349 (mmm160) REVERT: B 50 LYS cc_start: 0.6268 (mtmt) cc_final: 0.5922 (mtmt) REVERT: B 62 MET cc_start: 0.6591 (tmm) cc_final: 0.5889 (tpp) REVERT: B 159 LEU cc_start: 0.5960 (mt) cc_final: 0.5721 (mt) REVERT: B 182 LEU cc_start: 0.7031 (mm) cc_final: 0.6259 (pp) REVERT: B 488 MET cc_start: 0.7820 (mmp) cc_final: 0.6953 (mmt) REVERT: D 46 ASP cc_start: 0.6974 (m-30) cc_final: 0.6759 (m-30) REVERT: D 161 GLU cc_start: 0.6004 (mm-30) cc_final: 0.4414 (tm-30) REVERT: D 192 MET cc_start: 0.6701 (ptm) cc_final: 0.5959 (tmm) REVERT: D 323 MET cc_start: 0.2928 (mpp) cc_final: 0.2281 (mtt) REVERT: E 35 HIS cc_start: 0.7011 (m90) cc_final: 0.6513 (m-70) REVERT: E 58 MET cc_start: 0.5623 (ttt) cc_final: 0.5331 (ttt) REVERT: E 197 MET cc_start: 0.0969 (ttt) cc_final: -0.0171 (ptm) REVERT: E 315 ASN cc_start: 0.4377 (OUTLIER) cc_final: 0.4068 (t0) REVERT: E 321 ARG cc_start: 0.3018 (ptt180) cc_final: 0.1824 (mtm180) REVERT: E 369 MET cc_start: 0.1803 (mmm) cc_final: 0.1538 (mmm) REVERT: E 372 ILE cc_start: 0.1816 (pt) cc_final: 0.1607 (pt) REVERT: E 436 ASP cc_start: 0.6397 (m-30) cc_final: 0.4783 (t0) REVERT: G 28 ASN cc_start: 0.7999 (m-40) cc_final: 0.7656 (m110) REVERT: G 219 MET cc_start: 0.3852 (ptp) cc_final: 0.2662 (mtp) REVERT: G 222 LYS cc_start: 0.2009 (tttm) cc_final: 0.1225 (tptp) REVERT: G 286 LYS cc_start: 0.3817 (mttt) cc_final: 0.2914 (ptpp) REVERT: H 25 ASN cc_start: 0.8741 (m-40) cc_final: 0.8498 (m-40) REVERT: H 46 ASP cc_start: 0.7358 (m-30) cc_final: 0.7046 (m-30) REVERT: H 49 ILE cc_start: 0.7645 (mm) cc_final: 0.7365 (mm) REVERT: H 139 ILE cc_start: 0.8510 (tp) cc_final: 0.8252 (tp) REVERT: H 194 MET cc_start: 0.3599 (mmm) cc_final: 0.2583 (mmt) REVERT: H 218 LYS cc_start: 0.5266 (tttt) cc_final: 0.4632 (tppt) REVERT: H 252 ASN cc_start: 0.4384 (OUTLIER) cc_final: 0.3963 (m110) REVERT: H 306 ARG cc_start: 0.4510 (mpt180) cc_final: 0.4212 (mpt180) REVERT: H 357 ARG cc_start: 0.4743 (mmt90) cc_final: 0.3538 (ptp90) REVERT: Q 50 ASN cc_start: 0.7508 (m110) cc_final: 0.7155 (m-40) REVERT: Q 378 ARG cc_start: 0.6376 (ttm-80) cc_final: 0.5060 (ttt-90) REVERT: Z 131 LEU cc_start: 0.8068 (mt) cc_final: 0.7846 (tt) REVERT: Z 221 MET cc_start: 0.2987 (mmp) cc_final: 0.1078 (ptm) REVERT: Z 305 LEU cc_start: 0.4793 (tt) cc_final: 0.3107 (mt) REVERT: b 213 TYR cc_start: 0.6235 (t80) cc_final: 0.5997 (t80) REVERT: b 268 GLU cc_start: 0.1056 (mm-30) cc_final: 0.0410 (tp30) REVERT: d 29 LYS cc_start: 0.7396 (tttm) cc_final: 0.7183 (pptt) REVERT: d 355 MET cc_start: 0.3711 (tmm) cc_final: 0.3254 (tmm) REVERT: e 71 ASP cc_start: 0.7721 (t70) cc_final: 0.7360 (t0) REVERT: e 197 MET cc_start: 0.4586 (ttm) cc_final: 0.4063 (tpt) REVERT: e 283 PHE cc_start: -0.0846 (m-80) cc_final: -0.2391 (m-10) REVERT: e 391 MET cc_start: 0.4720 (ptp) cc_final: 0.4200 (ptp) REVERT: e 446 MET cc_start: 0.7715 (mmp) cc_final: 0.7375 (mmm) REVERT: e 458 MET cc_start: 0.7208 (mmm) cc_final: 0.6985 (mmm) REVERT: g 54 MET cc_start: 0.5724 (mpp) cc_final: 0.5502 (mpp) REVERT: g 104 GLU cc_start: 0.7394 (tp30) cc_final: 0.7149 (tp30) REVERT: g 133 MET cc_start: 0.7425 (mtm) cc_final: 0.7089 (mtm) REVERT: g 145 ASP cc_start: 0.7837 (p0) cc_final: 0.7563 (p0) REVERT: g 156 ILE cc_start: 0.6954 (mt) cc_final: 0.6703 (mt) REVERT: g 196 LYS cc_start: 0.5702 (mmtt) cc_final: 0.5444 (mmtt) REVERT: g 228 ARG cc_start: 0.3367 (mtt-85) cc_final: 0.1678 (mmp80) REVERT: g 270 MET cc_start: 0.4263 (ppp) cc_final: 0.3721 (ppp) REVERT: g 512 THR cc_start: 0.8387 (t) cc_final: 0.8138 (m) REVERT: q 129 ILE cc_start: 0.8687 (tt) cc_final: 0.8289 (tp) REVERT: q 164 LEU cc_start: 0.8654 (mt) cc_final: 0.8407 (mt) REVERT: q 179 LEU cc_start: 0.7847 (mt) cc_final: 0.7635 (mt) REVERT: q 266 MET cc_start: -0.0073 (ptt) cc_final: -0.0373 (mmt) REVERT: q 317 SER cc_start: 0.3318 (p) cc_final: 0.2848 (m) REVERT: q 385 MET cc_start: 0.6001 (ttm) cc_final: 0.4891 (tpp) REVERT: z 44 MET cc_start: 0.6998 (mtt) cc_final: 0.6687 (mtt) REVERT: z 59 ASP cc_start: 0.5083 (t0) cc_final: 0.4636 (t0) REVERT: z 138 LYS cc_start: 0.7556 (pttt) cc_final: 0.7000 (ttpt) REVERT: z 206 LEU cc_start: 0.7442 (mt) cc_final: 0.7014 (tt) REVERT: a 306 MET cc_start: 0.0672 (ttt) cc_final: -0.1743 (mmm) REVERT: a 344 MET cc_start: 0.3194 (ppp) cc_final: 0.2852 (ppp) outliers start: 4 outliers final: 1 residues processed: 1032 average time/residue: 0.5880 time to fit residues: 1048.5297 Evaluate side-chains 805 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 802 time to evaluate : 5.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 711 optimal weight: 0.0050 chunk 749 optimal weight: 5.9990 chunk 684 optimal weight: 9.9990 chunk 729 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 572 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 659 optimal weight: 8.9990 chunk 689 optimal weight: 1.9990 chunk 726 optimal weight: 0.0030 overall best weight: 2.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN G 111 HIS G 390 ASN H 252 ASN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 346 HIS ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 175 HIS d 129 HIS e 288 GLN e 315 ASN e 497 ASN ** e 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 HIS ** q 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 320 ASN ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 63926 Z= 0.220 Angle : 0.645 14.864 86360 Z= 0.328 Chirality : 0.046 0.347 10322 Planarity : 0.006 0.416 10999 Dihedral : 7.822 98.795 9257 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.03 % Allowed : 0.69 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8173 helix: -0.08 (0.08), residues: 3971 sheet: -1.06 (0.19), residues: 713 loop : -1.38 (0.10), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 302 HIS 0.029 0.001 HIS z 161 PHE 0.029 0.002 PHE E 449 TYR 0.038 0.002 TYR h 423 ARG 0.045 0.001 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1033 time to evaluate : 5.482 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: A 390 ARG cc_start: 0.4827 (ptm-80) cc_final: 0.3330 (mmm160) REVERT: B 50 LYS cc_start: 0.6253 (mtmt) cc_final: 0.5993 (mtmt) REVERT: B 62 MET cc_start: 0.6995 (tmm) cc_final: 0.5951 (tpt) REVERT: B 159 LEU cc_start: 0.6021 (mt) cc_final: 0.5779 (mt) REVERT: B 488 MET cc_start: 0.7778 (mmp) cc_final: 0.6929 (mmt) REVERT: D 42 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7657 (ttmt) REVERT: D 161 GLU cc_start: 0.5924 (mm-30) cc_final: 0.4328 (tm-30) REVERT: D 192 MET cc_start: 0.6561 (ptm) cc_final: 0.5947 (tmm) REVERT: D 323 MET cc_start: 0.3141 (mpp) cc_final: 0.2273 (mtt) REVERT: E 35 HIS cc_start: 0.6946 (m90) cc_final: 0.6376 (m-70) REVERT: E 197 MET cc_start: 0.0811 (ttt) cc_final: -0.0364 (ptm) REVERT: E 321 ARG cc_start: 0.2797 (ptt180) cc_final: 0.2275 (mtp180) REVERT: E 369 MET cc_start: 0.1772 (mmm) cc_final: 0.1533 (mmm) REVERT: E 436 ASP cc_start: 0.6054 (m-30) cc_final: 0.4623 (t0) REVERT: G 28 ASN cc_start: 0.7974 (m-40) cc_final: 0.7565 (m110) REVERT: G 59 MET cc_start: 0.7447 (tpp) cc_final: 0.7173 (mmm) REVERT: G 219 MET cc_start: 0.4522 (ptp) cc_final: 0.3485 (mtm) REVERT: G 222 LYS cc_start: 0.1934 (tttm) cc_final: 0.1197 (tptp) REVERT: H 25 ASN cc_start: 0.8663 (m-40) cc_final: 0.8438 (m-40) REVERT: H 46 ASP cc_start: 0.7312 (m-30) cc_final: 0.6957 (m-30) REVERT: H 139 ILE cc_start: 0.8385 (tp) cc_final: 0.8154 (tp) REVERT: H 194 MET cc_start: 0.3974 (mmm) cc_final: 0.3049 (mmt) REVERT: H 218 LYS cc_start: 0.5454 (tttt) cc_final: 0.4880 (tppt) REVERT: H 306 ARG cc_start: 0.4157 (mpt180) cc_final: 0.3813 (mpt180) REVERT: H 357 ARG cc_start: 0.4718 (mmt90) cc_final: 0.3608 (ptp90) REVERT: Q 50 ASN cc_start: 0.7654 (m110) cc_final: 0.7348 (m-40) REVERT: Q 73 LEU cc_start: 0.8345 (mm) cc_final: 0.8117 (mm) REVERT: Q 130 GLU cc_start: 0.7295 (pp20) cc_final: 0.6854 (pp20) REVERT: Q 249 MET cc_start: 0.1098 (mpp) cc_final: 0.0845 (pmm) REVERT: Q 378 ARG cc_start: 0.6303 (ttm-80) cc_final: 0.5100 (ttt-90) REVERT: Z 131 LEU cc_start: 0.8015 (mt) cc_final: 0.7658 (tt) REVERT: Z 221 MET cc_start: 0.2784 (mmp) cc_final: 0.1134 (ptp) REVERT: Z 305 LEU cc_start: 0.4893 (tt) cc_final: 0.3308 (mt) REVERT: b 114 GLU cc_start: 0.6332 (pp20) cc_final: 0.5831 (pp20) REVERT: b 268 GLU cc_start: 0.1346 (mm-30) cc_final: 0.0550 (tp30) REVERT: b 290 PHE cc_start: 0.4178 (t80) cc_final: 0.3527 (t80) REVERT: d 29 LYS cc_start: 0.7531 (tttm) cc_final: 0.7189 (pptt) REVERT: d 355 MET cc_start: 0.3781 (tmm) cc_final: 0.3328 (tmm) REVERT: e 58 MET cc_start: 0.6383 (mmp) cc_final: 0.6145 (mmp) REVERT: e 71 ASP cc_start: 0.7617 (t70) cc_final: 0.7305 (t0) REVERT: e 197 MET cc_start: 0.4570 (ttm) cc_final: 0.4060 (tpt) REVERT: e 283 PHE cc_start: -0.0848 (m-80) cc_final: -0.2312 (m-10) REVERT: e 391 MET cc_start: 0.4778 (ptp) cc_final: 0.4188 (ptp) REVERT: e 446 MET cc_start: 0.7598 (mmp) cc_final: 0.7392 (mmm) REVERT: e 454 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6960 (mt-10) REVERT: e 524 MET cc_start: 0.7944 (tpp) cc_final: 0.7688 (ttm) REVERT: g 71 GLN cc_start: 0.8009 (pp30) cc_final: 0.7243 (pt0) REVERT: g 133 MET cc_start: 0.7384 (mtm) cc_final: 0.6621 (mtm) REVERT: g 156 ILE cc_start: 0.6882 (mt) cc_final: 0.6630 (mt) REVERT: g 228 ARG cc_start: 0.3478 (mtt-85) cc_final: 0.1883 (mmp80) REVERT: g 270 MET cc_start: 0.4275 (ppp) cc_final: 0.3710 (ppp) REVERT: g 330 ARG cc_start: 0.4354 (ttt180) cc_final: 0.1876 (mmt180) REVERT: g 444 LEU cc_start: 0.8437 (mt) cc_final: 0.8121 (mt) REVERT: q 223 PHE cc_start: 0.4794 (m-80) cc_final: 0.4578 (m-80) REVERT: z 44 MET cc_start: 0.6973 (mtt) cc_final: 0.6603 (mtt) REVERT: z 59 ASP cc_start: 0.5041 (t0) cc_final: 0.4693 (t0) REVERT: z 138 LYS cc_start: 0.7595 (pttt) cc_final: 0.6966 (ttpt) REVERT: z 167 VAL cc_start: 0.6966 (p) cc_final: 0.6744 (p) REVERT: z 206 LEU cc_start: 0.7324 (mt) cc_final: 0.6979 (tt) REVERT: a 78 LEU cc_start: 0.5412 (pp) cc_final: 0.5190 (pp) REVERT: a 306 MET cc_start: 0.0675 (ttt) cc_final: 0.0000 (ttm) outliers start: 2 outliers final: 0 residues processed: 1034 average time/residue: 0.5685 time to fit residues: 1017.3008 Evaluate side-chains 812 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 812 time to evaluate : 5.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 478 optimal weight: 5.9990 chunk 771 optimal weight: 1.9990 chunk 470 optimal weight: 5.9990 chunk 365 optimal weight: 1.9990 chunk 536 optimal weight: 8.9990 chunk 808 optimal weight: 8.9990 chunk 744 optimal weight: 0.0050 chunk 644 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 497 optimal weight: 0.6980 chunk 394 optimal weight: 0.5980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS G 481 ASN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 124 GLN b 453 ASN d 129 HIS g 73 GLN ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 68 GLN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 477 ASN a 498 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 63926 Z= 0.164 Angle : 0.589 12.224 86360 Z= 0.301 Chirality : 0.044 0.332 10322 Planarity : 0.004 0.132 10999 Dihedral : 7.553 89.823 9257 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % 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: -0.87 (0.09), residues: 8173 helix: 0.11 (0.08), residues: 4013 sheet: -0.87 (0.19), residues: 720 loop : -1.26 (0.10), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 322 HIS 0.026 0.001 HIS z 161 PHE 0.024 0.001 PHE E 449 TYR 0.030 0.001 TYR h 423 ARG 0.014 0.000 ARG z 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1034 time to evaluate : 5.406 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: A 390 ARG cc_start: 0.4914 (ptm-80) cc_final: 0.3465 (mmm160) REVERT: B 50 LYS cc_start: 0.6011 (mtmt) cc_final: 0.5767 (mtmt) REVERT: B 62 MET cc_start: 0.7400 (tmm) cc_final: 0.5767 (tpt) REVERT: B 159 LEU cc_start: 0.5761 (mt) cc_final: 0.5494 (mt) REVERT: B 182 LEU cc_start: 0.5703 (tp) cc_final: 0.5302 (pp) REVERT: B 445 MET cc_start: 0.7926 (tpp) cc_final: 0.7696 (ttm) REVERT: B 488 MET cc_start: 0.7640 (mmp) cc_final: 0.6584 (mmt) REVERT: D 42 LYS cc_start: 0.7514 (ttmt) cc_final: 0.7136 (ttmt) REVERT: D 139 LYS cc_start: 0.7600 (ttmt) cc_final: 0.7052 (ttmt) REVERT: D 161 GLU cc_start: 0.6055 (mm-30) cc_final: 0.4397 (tm-30) REVERT: D 192 MET cc_start: 0.6494 (ptm) cc_final: 0.6142 (tmm) REVERT: D 323 MET cc_start: 0.2888 (mpp) cc_final: 0.1996 (mtt) REVERT: D 349 ASP cc_start: 0.4573 (p0) cc_final: 0.4362 (t0) REVERT: E 35 HIS cc_start: 0.6871 (m90) cc_final: 0.6304 (m-70) REVERT: E 89 MET cc_start: 0.8256 (mpp) cc_final: 0.7821 (mtt) REVERT: E 197 MET cc_start: 0.0205 (ttt) cc_final: -0.0885 (ptm) REVERT: E 321 ARG cc_start: 0.2500 (ptt180) cc_final: 0.2034 (mtp180) REVERT: E 436 ASP cc_start: 0.5832 (m-30) cc_final: 0.4667 (t0) REVERT: G 105 MET cc_start: 0.6439 (mtm) cc_final: 0.6224 (mtp) REVERT: G 219 MET cc_start: 0.4403 (ptp) cc_final: 0.3356 (mtm) REVERT: H 25 ASN cc_start: 0.8633 (m-40) cc_final: 0.8414 (m-40) REVERT: H 46 ASP cc_start: 0.7277 (m-30) cc_final: 0.6959 (m-30) REVERT: H 139 ILE cc_start: 0.8293 (tp) cc_final: 0.8048 (tp) REVERT: H 194 MET cc_start: 0.4018 (mmm) cc_final: 0.3104 (mmt) REVERT: H 216 PHE cc_start: 0.2602 (p90) cc_final: 0.2298 (p90) REVERT: H 218 LYS cc_start: 0.5502 (tttt) cc_final: 0.4911 (tppt) REVERT: H 306 ARG cc_start: 0.4124 (mpt180) cc_final: 0.3799 (mpt180) REVERT: H 357 ARG cc_start: 0.4494 (mmt90) cc_final: 0.3322 (ptp90) REVERT: H 425 ARG cc_start: 0.6146 (mtt180) cc_final: 0.5491 (ptp-170) REVERT: Q 50 ASN cc_start: 0.7657 (m110) cc_final: 0.7278 (m-40) REVERT: Q 513 ASN cc_start: 0.7626 (m-40) cc_final: 0.7347 (t0) REVERT: Z 104 LYS cc_start: 0.8466 (tptp) cc_final: 0.8217 (tptt) REVERT: Z 221 MET cc_start: 0.2683 (mmp) cc_final: 0.1183 (ptp) REVERT: Z 305 LEU cc_start: 0.4725 (tt) cc_final: 0.3243 (mt) REVERT: b 111 ARG cc_start: 0.6295 (ttm110) cc_final: 0.5565 (tmt-80) REVERT: b 114 GLU cc_start: 0.6399 (pp20) cc_final: 0.6184 (pp20) REVERT: b 268 GLU cc_start: 0.1113 (mm-30) cc_final: 0.0637 (tp30) REVERT: b 290 PHE cc_start: 0.4310 (t80) cc_final: 0.3656 (t80) REVERT: d 131 THR cc_start: 0.7435 (t) cc_final: 0.7217 (t) REVERT: d 355 MET cc_start: 0.3733 (tmm) cc_final: 0.3416 (tmm) REVERT: e 71 ASP cc_start: 0.7625 (t70) cc_final: 0.7301 (t0) REVERT: e 283 PHE cc_start: -0.0941 (m-80) cc_final: -0.2076 (m-10) REVERT: e 391 MET cc_start: 0.4624 (ptp) cc_final: 0.4150 (ptp) REVERT: e 446 MET cc_start: 0.7534 (mmp) cc_final: 0.7333 (mmm) REVERT: e 449 PHE cc_start: 0.7299 (t80) cc_final: 0.6960 (t80) REVERT: g 133 MET cc_start: 0.7330 (mtm) cc_final: 0.6591 (mtm) REVERT: g 156 ILE cc_start: 0.6872 (mt) cc_final: 0.6650 (mt) REVERT: g 228 ARG cc_start: 0.3277 (mtt-85) cc_final: 0.1766 (mmp80) REVERT: g 270 MET cc_start: 0.4053 (ppp) cc_final: 0.3662 (ppp) REVERT: g 330 ARG cc_start: 0.4331 (ttt180) cc_final: 0.1782 (tpt170) REVERT: g 444 LEU cc_start: 0.8485 (mt) cc_final: 0.8140 (mt) REVERT: q 223 PHE cc_start: 0.4789 (m-80) cc_final: 0.4480 (m-80) REVERT: q 300 MET cc_start: 0.4394 (ttm) cc_final: 0.3539 (mpp) REVERT: z 44 MET cc_start: 0.6902 (mtt) cc_final: 0.6690 (mtt) REVERT: z 47 LEU cc_start: 0.6965 (tt) cc_final: 0.6752 (tp) REVERT: z 59 ASP cc_start: 0.4906 (t0) cc_final: 0.4458 (t0) REVERT: z 137 VAL cc_start: 0.7964 (t) cc_final: 0.7733 (p) REVERT: z 138 LYS cc_start: 0.7392 (pttt) cc_final: 0.6827 (ttpt) REVERT: z 206 LEU cc_start: 0.7406 (mt) cc_final: 0.7185 (tt) REVERT: a 83 ASP cc_start: 0.7007 (p0) cc_final: 0.6763 (p0) REVERT: a 306 MET cc_start: 0.0510 (ttt) cc_final: -0.1705 (mmm) outliers start: 6 outliers final: 1 residues processed: 1038 average time/residue: 0.5723 time to fit residues: 1028.2353 Evaluate side-chains 832 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 831 time to evaluate : 5.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 511 optimal weight: 0.9980 chunk 686 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 593 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 645 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 662 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 0.0020 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN ** E 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 GLN G 111 HIS G 154 ASN ** H 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS ** g 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 HIS ** q 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 68 GLN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.194396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.184199 restraints weight = 134340.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.182576 restraints weight = 180437.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.183202 restraints weight = 163943.982| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 63926 Z= 0.182 Angle : 0.603 12.877 86360 Z= 0.306 Chirality : 0.045 0.359 10322 Planarity : 0.004 0.164 10999 Dihedral : 7.747 158.279 9257 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.03 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.09), residues: 8173 helix: 0.16 (0.08), residues: 4002 sheet: -0.94 (0.19), residues: 731 loop : -1.25 (0.10), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 496 HIS 0.024 0.001 HIS z 161 PHE 0.025 0.001 PHE A 167 TYR 0.033 0.001 TYR h 423 ARG 0.027 0.000 ARG Z 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16599.96 seconds wall clock time: 286 minutes 55.03 seconds (17215.03 seconds total)