Starting phenix.real_space_refine on Fri Dec 8 22:26:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kre_0757/12_2023/6kre_0757.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kre_0757/12_2023/6kre_0757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kre_0757/12_2023/6kre_0757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kre_0757/12_2023/6kre_0757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kre_0757/12_2023/6kre_0757.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kre_0757/12_2023/6kre_0757.pdb" } resolution = 4.45 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= 0.026 sd= 0.195 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 308 5.16 5 C 37865 2.51 5 N 10434 2.21 5 O 11714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "z ARG 14": "NH1" <-> "NH2" Residue "z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 60321 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3807 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 10, 'TRANS': 495} Chain breaks: 1 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3832 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 10, 'TRANS': 498} Chain breaks: 1 Chain: "B" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3833 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 10, 'TRANS': 494} Chain: "d" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3646 Classifications: {'peptide': 479} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 466} Chain breaks: 2 Chain: "D" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3531 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain breaks: 2 Chain: "e" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3804 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 15, 'TRANS': 481} Chain breaks: 1 Chain: "E" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3847 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 15, 'TRANS': 486} Chain breaks: 1 Chain: "g" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3765 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 19, 'TRANS': 473} Chain breaks: 1 Chain: "G" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3506 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 440} Chain breaks: 2 Chain: "h" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3650 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Chain: "H" Number of atoms: 3729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3729 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 12, 'TRANS': 475} Chain breaks: 2 Chain: "q" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3978 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 18, 'TRANS': 505} Chain: "Q" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3909 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 18, 'TRANS': 496} Chain breaks: 1 Chain: "z" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4070 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "Z" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4056 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "b" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3358 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 9, 'TRANS': 434} Chain breaks: 2 Time building chain proxies: 23.60, per 1000 atoms: 0.39 Number of scatterers: 60321 At special positions: 0 Unit cell: (197.7, 201.654, 196.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 308 16.00 O 11714 8.00 N 10434 7.00 C 37865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.12 Conformation dependent library (CDL) restraints added in 8.3 seconds 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14728 Finding SS restraints... Secondary structure from input PDB file: 320 helices and 91 sheets defined 54.9% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'a' and resid 22 through 41 removed outlier: 3.684A pdb=" N ARG a 26 " --> pdb=" O GLY a 22 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 65 through 73 removed outlier: 3.571A pdb=" N ILE a 69 " --> pdb=" O ASP a 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU a 70 " --> pdb=" O GLY a 66 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER a 71 " --> pdb=" O ALA a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 94 removed outlier: 3.506A pdb=" N ILE a 82 " --> pdb=" O PRO a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 118 removed outlier: 3.635A pdb=" N VAL a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU a 109 " --> pdb=" O ALA a 105 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN a 113 " --> pdb=" O LEU a 109 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU a 114 " --> pdb=" O LYS a 110 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU a 115 " --> pdb=" O ARG a 111 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS a 117 " --> pdb=" O ASN a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 144 removed outlier: 4.022A pdb=" N ARG a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE a 139 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 removed outlier: 4.096A pdb=" N ALA a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS a 161 " --> pdb=" O ILE a 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR a 162 " --> pdb=" O ASN a 158 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER a 163 " --> pdb=" O ILE a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 171 Processing helix chain 'a' and resid 172 through 186 removed outlier: 4.390A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.575A pdb=" N SER a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 292 removed outlier: 3.554A pdb=" N ARG a 284 " --> pdb=" O ILE a 280 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE a 288 " --> pdb=" O ARG a 284 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE a 289 " --> pdb=" O VAL a 285 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 313 removed outlier: 3.776A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU a 312 " --> pdb=" O LYS a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 334 removed outlier: 3.611A pdb=" N ARG a 327 " --> pdb=" O LYS a 323 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.518A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG a 400 " --> pdb=" O ASP a 396 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS a 403 " --> pdb=" O GLU a 399 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL a 409 " --> pdb=" O SER a 405 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 439 removed outlier: 3.745A pdb=" N ILE a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP a 434 " --> pdb=" O ASN a 430 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN a 435 " --> pdb=" O ILE a 431 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR a 438 " --> pdb=" O ASP a 434 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR a 439 " --> pdb=" O ASN a 435 " (cutoff:3.500A) Processing helix chain 'a' and resid 444 through 454 Processing helix chain 'a' and resid 456 through 466 removed outlier: 3.547A pdb=" N ASN a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 removed outlier: 3.573A pdb=" N ALA a 475 " --> pdb=" O SER a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 511 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.642A pdb=" N ALA a 537 " --> pdb=" O GLU a 533 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE a 538 " --> pdb=" O ALA a 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 42 removed outlier: 3.877A pdb=" N ARG A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.546A pdb=" N ILE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.565A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.525A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.551A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.897A pdb=" N ILE A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 4.439A pdb=" N ASP A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.563A pdb=" N GLU A 215 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 216' Processing helix chain 'A' and resid 278 through 290 removed outlier: 3.547A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 4.205A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 removed outlier: 3.506A pdb=" N ARG A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.826A pdb=" N GLU A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.573A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.722A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.615A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 35 removed outlier: 3.579A pdb=" N GLY B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.780A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 3.597A pdb=" N GLN B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 138 removed outlier: 4.408A pdb=" N ILE B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.668A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.670A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.895A pdb=" N PHE B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.948A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 4.240A pdb=" N LYS B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.523A pdb=" N PHE B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.599A pdb=" N VAL B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 394 removed outlier: 3.587A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 Processing helix chain 'B' and resid 425 through 438 removed outlier: 4.256A pdb=" N ALA B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.696A pdb=" N THR B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 465 removed outlier: 3.550A pdb=" N SER B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 510 removed outlier: 3.515A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 37 removed outlier: 3.548A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR d 37 " --> pdb=" O ASP d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 68 Processing helix chain 'd' and resid 76 through 89 removed outlier: 3.899A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 113 removed outlier: 3.816A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG d 109 " --> pdb=" O GLY d 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU d 110 " --> pdb=" O ALA d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.525A pdb=" N ILE d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN d 125 " --> pdb=" O ALA d 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 3.691A pdb=" N ALA d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 161 No H-bonds generated for 'chain 'd' and resid 159 through 161' Processing helix chain 'd' and resid 166 through 183 removed outlier: 3.571A pdb=" N LEU d 170 " --> pdb=" O TYR d 166 " (cutoff:3.500A) Proline residue: d 172 - end of helix removed outlier: 3.713A pdb=" N LYS d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP d 183 " --> pdb=" O LEU d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 194 removed outlier: 3.740A pdb=" N ASP d 193 " --> pdb=" O ASP d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 267 through 281 removed outlier: 3.568A pdb=" N ASN d 273 " --> pdb=" O ALA d 269 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE d 274 " --> pdb=" O TYR d 270 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE d 278 " --> pdb=" O ILE d 274 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA d 281 " --> pdb=" O LYS d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 309 removed outlier: 3.809A pdb=" N HIS d 303 " --> pdb=" O ASP d 299 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE d 304 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS d 307 " --> pdb=" O HIS d 303 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU d 308 " --> pdb=" O PHE d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 328 removed outlier: 4.348A pdb=" N GLU d 322 " --> pdb=" O ARG d 318 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU d 328 " --> pdb=" O LEU d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.764A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU d 389 " --> pdb=" O MET d 385 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP d 396 " --> pdb=" O ARG d 392 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU d 404 " --> pdb=" O VAL d 400 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL d 405 " --> pdb=" O ILE d 401 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.653A pdb=" N SER d 422 " --> pdb=" O GLU d 418 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS d 427 " --> pdb=" O ARG d 423 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 432 No H-bonds generated for 'chain 'd' and resid 430 through 432' Processing helix chain 'd' and resid 434 through 448 removed outlier: 4.337A pdb=" N PHE d 438 " --> pdb=" O GLY d 434 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE d 439 " --> pdb=" O VAL d 435 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN d 441 " --> pdb=" O ALA d 437 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU d 448 " --> pdb=" O ALA d 444 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 removed outlier: 3.546A pdb=" N ALA d 458 " --> pdb=" O LEU d 454 " (cutoff:3.500A) Processing helix chain 'd' and resid 461 through 472 Processing helix chain 'd' and resid 473 through 475 No H-bonds generated for 'chain 'd' and resid 473 through 475' Processing helix chain 'd' and resid 501 through 519 removed outlier: 3.579A pdb=" N ILE d 508 " --> pdb=" O SER d 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.583A pdb=" N ARG D 21 " --> pdb=" O PRO D 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.939A pdb=" N VAL D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.557A pdb=" N PHE D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.102A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.812A pdb=" N SER D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 183 removed outlier: 3.924A pdb=" N LEU D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.828A pdb=" N ASP D 193 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 removed outlier: 3.551A pdb=" N LYS D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 328 removed outlier: 4.203A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.897A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.690A pdb=" N ILE D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 434 through 447 removed outlier: 3.992A pdb=" N PHE D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP D 440 " --> pdb=" O GLN D 436 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.528A pdb=" N ILE D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing helix chain 'e' and resid 43 through 62 removed outlier: 3.625A pdb=" N LYS e 47 " --> pdb=" O GLY e 43 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU e 52 " --> pdb=" O LYS e 48 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 94 Processing helix chain 'e' and resid 98 through 115 removed outlier: 3.705A pdb=" N LYS e 102 " --> pdb=" O ASN e 98 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU e 103 " --> pdb=" O GLU e 99 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER e 110 " --> pdb=" O GLN e 106 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 removed outlier: 3.567A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 3.612A pdb=" N ILE e 146 " --> pdb=" O HIS e 142 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER e 159 " --> pdb=" O LYS e 155 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS e 160 " --> pdb=" O LEU e 156 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 188 removed outlier: 3.708A pdb=" N LEU e 180 " --> pdb=" O PHE e 176 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS e 185 " --> pdb=" O LEU e 181 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR e 186 " --> pdb=" O ARG e 182 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 195 Processing helix chain 'e' and resid 196 through 211 removed outlier: 3.677A pdb=" N PHE e 200 " --> pdb=" O ASP e 196 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET e 203 " --> pdb=" O ARG e 199 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL e 205 " --> pdb=" O ALA e 201 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL e 208 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) Processing helix chain 'e' and resid 220 through 222 No H-bonds generated for 'chain 'e' and resid 220 through 222' Processing helix chain 'e' and resid 233 through 237 removed outlier: 3.750A pdb=" N ASP e 236 " --> pdb=" O SER e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 306 through 317 removed outlier: 3.583A pdb=" N ASP e 311 " --> pdb=" O LYS e 307 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 removed outlier: 3.931A pdb=" N ASN e 332 " --> pdb=" O ASP e 328 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS e 333 " --> pdb=" O ASP e 329 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN e 337 " --> pdb=" O HIS e 333 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN e 338 " --> pdb=" O LEU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 358 removed outlier: 4.026A pdb=" N GLU e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS e 353 " --> pdb=" O GLN e 349 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE e 354 " --> pdb=" O GLU e 350 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA e 355 " --> pdb=" O LEU e 351 " (cutoff:3.500A) Processing helix chain 'e' and resid 412 through 436 Processing helix chain 'e' and resid 444 through 459 removed outlier: 4.197A pdb=" N ASP e 459 " --> pdb=" O SER e 455 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 477 removed outlier: 4.010A pdb=" N ALA e 468 " --> pdb=" O ILE e 464 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP e 477 " --> pdb=" O ALA e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 477 through 487 Processing helix chain 'e' and resid 490 through 502 Processing helix chain 'e' and resid 521 through 526 removed outlier: 3.603A pdb=" N GLU e 524 " --> pdb=" O ASP e 521 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'E' and resid 45 through 62 removed outlier: 3.814A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.577A pdb=" N ILE E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.903A pdb=" N VAL E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 139 removed outlier: 4.561A pdb=" N GLY E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 122 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 165 removed outlier: 3.633A pdb=" N SER E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.694A pdb=" N ARG E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.636A pdb=" N THR E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.866A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET E 203 " --> pdb=" O ARG E 199 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE E 209 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 317 removed outlier: 3.822A pdb=" N GLU E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL E 313 " --> pdb=" O MET E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 338 removed outlier: 3.907A pdb=" N ASN E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS E 333 " --> pdb=" O ASP E 329 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.533A pdb=" N LEU E 351 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU E 352 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS E 353 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 removed outlier: 3.579A pdb=" N VAL E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 459 removed outlier: 3.605A pdb=" N VAL E 448 " --> pdb=" O GLY E 444 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 477 removed outlier: 3.523A pdb=" N ALA E 468 " --> pdb=" O ILE E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 487 Processing helix chain 'E' and resid 490 through 502 removed outlier: 3.542A pdb=" N THR E 497 " --> pdb=" O GLY E 493 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN E 502 " --> pdb=" O LEU E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 526 removed outlier: 4.004A pdb=" N LEU E 525 " --> pdb=" O ASP E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 550 Processing helix chain 'g' and resid 18 through 35 removed outlier: 3.969A pdb=" N VAL g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE g 35 " --> pdb=" O VAL g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 39 removed outlier: 4.189A pdb=" N LEU g 39 " --> pdb=" O ARG g 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 36 through 39' Processing helix chain 'g' and resid 60 through 66 removed outlier: 3.508A pdb=" N ILE g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG g 66 " --> pdb=" O HIS g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 removed outlier: 3.811A pdb=" N LYS g 76 " --> pdb=" O HIS g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.715A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA g 105 " --> pdb=" O GLY g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 112 Processing helix chain 'g' and resid 117 through 140 Processing helix chain 'g' and resid 149 through 156 removed outlier: 4.138A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU g 154 " --> pdb=" O ALA g 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 159 No H-bonds generated for 'chain 'g' and resid 157 through 159' Processing helix chain 'g' and resid 162 through 166 removed outlier: 4.149A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 4.029A pdb=" N GLU g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA g 178 " --> pdb=" O LEU g 174 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL g 182 " --> pdb=" O ALA g 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 279 through 288 removed outlier: 3.717A pdb=" N ILE g 287 " --> pdb=" O MET g 283 " (cutoff:3.500A) Processing helix chain 'g' and resid 289 through 291 No H-bonds generated for 'chain 'g' and resid 289 through 291' Processing helix chain 'g' and resid 302 through 311 removed outlier: 3.583A pdb=" N GLN g 306 " --> pdb=" O SER g 302 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR g 308 " --> pdb=" O LEU g 304 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS g 311 " --> pdb=" O HIS g 307 " (cutoff:3.500A) Processing helix chain 'g' and resid 321 through 333 removed outlier: 3.560A pdb=" N ASN g 325 " --> pdb=" O LYS g 321 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN g 326 " --> pdb=" O LYS g 322 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG g 327 " --> pdb=" O SER g 323 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 385 through 409 removed outlier: 3.681A pdb=" N ARG g 394 " --> pdb=" O ASN g 390 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER g 409 " --> pdb=" O ASN g 405 " (cutoff:3.500A) Processing helix chain 'g' and resid 417 through 431 removed outlier: 3.544A pdb=" N SER g 424 " --> pdb=" O GLU g 420 " (cutoff:3.500A) Processing helix chain 'g' and resid 438 through 450 removed outlier: 3.513A pdb=" N ALA g 444 " --> pdb=" O TRP g 440 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL g 445 " --> pdb=" O PRO g 441 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA g 446 " --> pdb=" O TYR g 442 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP g 447 " --> pdb=" O GLN g 443 " (cutoff:3.500A) Processing helix chain 'g' and resid 450 through 461 Processing helix chain 'g' and resid 463 through 478 removed outlier: 3.848A pdb=" N ALA g 473 " --> pdb=" O SER g 469 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS g 475 " --> pdb=" O LEU g 471 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA g 476 " --> pdb=" O ARG g 472 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN g 477 " --> pdb=" O ALA g 473 " (cutoff:3.500A) Processing helix chain 'g' and resid 494 through 498 Processing helix chain 'g' and resid 503 through 523 removed outlier: 3.773A pdb=" N VAL g 523 " --> pdb=" O LEU g 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 4.028A pdb=" N ALA G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 39 removed outlier: 3.840A pdb=" N LEU G 39 " --> pdb=" O ARG G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 36 through 39' Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.750A pdb=" N ARG G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.754A pdb=" N LYS G 76 " --> pdb=" O HIS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.545A pdb=" N VAL G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 117 through 140 removed outlier: 3.721A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 157 removed outlier: 3.719A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.200A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.808A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.509A pdb=" N GLU G 197 " --> pdb=" O PRO G 194 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 194 through 198' Processing helix chain 'G' and resid 303 through 309 removed outlier: 4.080A pdb=" N HIS G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.630A pdb=" N ASN G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN G 326 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG G 327 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 408 removed outlier: 3.801A pdb=" N ARG G 394 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL G 402 " --> pdb=" O ASP G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 432 removed outlier: 3.651A pdb=" N SER G 424 " --> pdb=" O GLU G 420 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS G 432 " --> pdb=" O ALA G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 450 removed outlier: 3.564A pdb=" N TYR G 442 " --> pdb=" O GLN G 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN G 443 " --> pdb=" O GLN G 439 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA G 444 " --> pdb=" O TRP G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 461 removed outlier: 3.535A pdb=" N LEU G 456 " --> pdb=" O ILE G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 478 removed outlier: 3.583A pdb=" N LEU G 468 " --> pdb=" O PRO G 464 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS G 475 " --> pdb=" O LEU G 471 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA G 476 " --> pdb=" O ARG G 472 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN G 477 " --> pdb=" O ALA G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 522 removed outlier: 3.514A pdb=" N LEU G 521 " --> pdb=" O ALA G 517 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 41 removed outlier: 3.541A pdb=" N CYS h 33 " --> pdb=" O ASN h 29 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 74 removed outlier: 4.280A pdb=" N ASP h 74 " --> pdb=" O LEU h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 94 removed outlier: 3.772A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 112 removed outlier: 4.018A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA h 112 " --> pdb=" O LEU h 108 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 118 removed outlier: 3.657A pdb=" N LEU h 116 " --> pdb=" O ALA h 112 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU h 118 " --> pdb=" O PRO h 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 112 through 118' Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.662A pdb=" N ILE h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU h 138 " --> pdb=" O SER h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 162 removed outlier: 4.268A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 162 through 167 Processing helix chain 'h' and resid 174 through 188 removed outlier: 4.072A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS h 182 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL h 183 " --> pdb=" O VAL h 179 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP h 184 " --> pdb=" O LYS h 180 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL h 186 " --> pdb=" O CYS h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 208 through 212 removed outlier: 3.575A pdb=" N GLU h 211 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER h 212 " --> pdb=" O MET h 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 208 through 212' Processing helix chain 'h' and resid 279 through 289 removed outlier: 3.530A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 removed outlier: 3.607A pdb=" N THR h 304 " --> pdb=" O GLY h 300 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE h 306 " --> pdb=" O LEU h 302 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP h 309 " --> pdb=" O GLN h 305 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG h 310 " --> pdb=" O PHE h 306 " (cutoff:3.500A) Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.998A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE h 327 " --> pdb=" O MET h 323 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN h 328 " --> pdb=" O ASN h 324 " (cutoff:3.500A) Processing helix chain 'h' and resid 342 through 346 Processing helix chain 'h' and resid 382 through 406 removed outlier: 3.635A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA h 396 " --> pdb=" O SER h 392 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG h 402 " --> pdb=" O MET h 398 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA h 403 " --> pdb=" O ILE h 399 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN h 405 " --> pdb=" O LYS h 401 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN h 406 " --> pdb=" O ARG h 402 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 430 removed outlier: 3.605A pdb=" N ARG h 425 " --> pdb=" O SER h 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP h 426 " --> pdb=" O LYS h 422 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 removed outlier: 3.506A pdb=" N ILE h 438 " --> pdb=" O LYS h 434 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 458 Processing helix chain 'h' and resid 460 through 473 removed outlier: 3.790A pdb=" N ASN h 466 " --> pdb=" O ILE h 462 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA h 471 " --> pdb=" O LYS h 467 " (cutoff:3.500A) Processing helix chain 'h' and resid 491 through 495 Processing helix chain 'h' and resid 500 through 519 Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.789A pdb=" N ILE H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.705A pdb=" N ILE H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 94 removed outlier: 3.505A pdb=" N LEU H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL H 84 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 112 removed outlier: 3.940A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.697A pdb=" N LEU H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 112 through 118' Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.652A pdb=" N ILE H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 167 removed outlier: 3.961A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 173 removed outlier: 4.409A pdb=" N ASN H 173 " --> pdb=" O LEU H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 4.510A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS H 182 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL H 183 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 185 " --> pdb=" O MET H 181 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL H 186 " --> pdb=" O CYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 289 removed outlier: 3.571A pdb=" N GLN H 284 " --> pdb=" O GLU H 280 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 310 removed outlier: 3.933A pdb=" N THR H 304 " --> pdb=" O GLY H 300 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN H 305 " --> pdb=" O ASP H 301 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP H 309 " --> pdb=" O GLN H 305 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG H 310 " --> pdb=" O PHE H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 331 removed outlier: 3.504A pdb=" N ASN H 324 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 356 through 360 removed outlier: 3.763A pdb=" N GLU H 360 " --> pdb=" O ILE H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 406 removed outlier: 3.507A pdb=" N SER H 392 " --> pdb=" O GLU H 388 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG H 402 " --> pdb=" O MET H 398 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA H 403 " --> pdb=" O ILE H 399 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN H 406 " --> pdb=" O ARG H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 427 removed outlier: 3.577A pdb=" N SER H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 428 through 430 No H-bonds generated for 'chain 'H' and resid 428 through 430' Processing helix chain 'H' and resid 433 through 446 removed outlier: 3.885A pdb=" N MET H 437 " --> pdb=" O GLY H 433 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE H 438 " --> pdb=" O LYS H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 460 through 474 removed outlier: 3.704A pdb=" N LEU H 465 " --> pdb=" O ALA H 461 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN H 466 " --> pdb=" O ILE H 462 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 491 through 495 Processing helix chain 'H' and resid 500 through 519 Processing helix chain 'q' and resid 27 through 44 removed outlier: 3.551A pdb=" N ILE q 32 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.924A pdb=" N ARG q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU q 74 " --> pdb=" O THR q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 95 removed outlier: 3.955A pdb=" N LYS q 83 " --> pdb=" O HIS q 79 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL q 84 " --> pdb=" O PRO q 80 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN q 92 " --> pdb=" O ALA q 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP q 95 " --> pdb=" O GLN q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 121 removed outlier: 3.615A pdb=" N LEU q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN q 112 " --> pdb=" O GLY q 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS q 116 " --> pdb=" O ASN q 112 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU q 117 " --> pdb=" O VAL q 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY q 121 " --> pdb=" O LEU q 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 123 through 143 removed outlier: 3.516A pdb=" N LYS q 140 " --> pdb=" O LYS q 136 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP q 143 " --> pdb=" O LEU q 139 " (cutoff:3.500A) Processing helix chain 'q' and resid 158 through 168 removed outlier: 4.248A pdb=" N MET q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 174 through 190 removed outlier: 4.119A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU q 181 " --> pdb=" O ILE q 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA q 185 " --> pdb=" O LEU q 181 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER q 187 " --> pdb=" O SER q 183 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS q 188 " --> pdb=" O GLU q 184 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL q 189 " --> pdb=" O ALA q 185 " (cutoff:3.500A) Processing helix chain 'q' and resid 270 through 294 removed outlier: 4.113A pdb=" N LEU q 274 " --> pdb=" O ALA q 270 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU q 290 " --> pdb=" O ALA q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 306 through 316 removed outlier: 3.850A pdb=" N LEU q 310 " --> pdb=" O GLY q 306 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS q 311 " --> pdb=" O GLU q 307 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR q 312 " --> pdb=" O LEU q 308 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN q 314 " --> pdb=" O LEU q 310 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) Processing helix chain 'q' and resid 325 through 334 removed outlier: 3.769A pdb=" N LEU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG q 334 " --> pdb=" O ARG q 330 " (cutoff:3.500A) Processing helix chain 'q' and resid 390 through 410 removed outlier: 3.719A pdb=" N ASP q 402 " --> pdb=" O GLU q 398 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP q 403 " --> pdb=" O ARG q 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA q 406 " --> pdb=" O ASP q 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA q 407 " --> pdb=" O ASP q 403 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL q 408 " --> pdb=" O GLY q 404 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS q 409 " --> pdb=" O VAL q 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY q 410 " --> pdb=" O ALA q 406 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 439 removed outlier: 3.566A pdb=" N ILE q 428 " --> pdb=" O GLY q 424 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE q 431 " --> pdb=" O GLU q 427 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER q 432 " --> pdb=" O ILE q 428 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG q 433 " --> pdb=" O GLU q 429 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU q 439 " --> pdb=" O THR q 435 " (cutoff:3.500A) Processing helix chain 'q' and resid 445 through 455 Processing helix chain 'q' and resid 457 through 467 Processing helix chain 'q' and resid 470 through 483 removed outlier: 3.518A pdb=" N LEU q 475 " --> pdb=" O VAL q 471 " (cutoff:3.500A) Proline residue: q 476 - end of helix removed outlier: 3.535A pdb=" N HIS q 482 " --> pdb=" O LEU q 478 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 541 removed outlier: 3.611A pdb=" N ASN q 529 " --> pdb=" O LYS q 525 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 44 removed outlier: 3.546A pdb=" N ILE Q 32 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE Q 35 " --> pdb=" O SER Q 31 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS Q 42 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 75 removed outlier: 3.525A pdb=" N MET Q 71 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU Q 74 " --> pdb=" O THR Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 95 removed outlier: 3.596A pdb=" N VAL Q 84 " --> pdb=" O PRO Q 80 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN Q 91 " --> pdb=" O MET Q 87 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 114 removed outlier: 3.938A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE Q 105 " --> pdb=" O ASN Q 101 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN Q 112 " --> pdb=" O GLY Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 120 Processing helix chain 'Q' and resid 123 through 143 removed outlier: 3.604A pdb=" N ILE Q 127 " --> pdb=" O SER Q 123 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 168 removed outlier: 4.302A pdb=" N MET Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 174 through 190 removed outlier: 4.094A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 276 through 294 removed outlier: 3.575A pdb=" N GLU Q 281 " --> pdb=" O SER Q 277 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE Q 291 " --> pdb=" O MET Q 287 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET Q 294 " --> pdb=" O GLU Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 317 removed outlier: 3.891A pdb=" N LEU Q 310 " --> pdb=" O GLY Q 306 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS Q 311 " --> pdb=" O GLU Q 307 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR Q 312 " --> pdb=" O LEU Q 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN Q 314 " --> pdb=" O LEU Q 310 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 326 through 334 removed outlier: 3.998A pdb=" N ARG Q 330 " --> pdb=" O LYS Q 326 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG Q 334 " --> pdb=" O ARG Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 352 Processing helix chain 'Q' and resid 390 through 410 removed outlier: 3.633A pdb=" N LEU Q 394 " --> pdb=" O THR Q 390 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP Q 396 " --> pdb=" O ASN Q 392 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA Q 407 " --> pdb=" O ASP Q 403 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL Q 408 " --> pdb=" O GLY Q 404 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS Q 409 " --> pdb=" O VAL Q 405 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY Q 410 " --> pdb=" O ALA Q 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.770A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG Q 433 " --> pdb=" O GLU Q 429 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU Q 439 " --> pdb=" O THR Q 435 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 455 removed outlier: 4.433A pdb=" N ALA Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 466 Processing helix chain 'Q' and resid 470 through 483 removed outlier: 3.617A pdb=" N VAL Q 474 " --> pdb=" O ASP Q 470 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Q 475 " --> pdb=" O VAL Q 471 " (cutoff:3.500A) Proline residue: Q 476 - end of helix Processing helix chain 'Q' and resid 511 through 515 Processing helix chain 'Q' and resid 521 through 541 removed outlier: 3.743A pdb=" N ASN Q 529 " --> pdb=" O LYS Q 525 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL Q 538 " --> pdb=" O ALA Q 534 " (cutoff:3.500A) Processing helix chain 'z' and resid 18 through 35 removed outlier: 3.572A pdb=" N VAL z 32 " --> pdb=" O GLY z 28 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR z 35 " --> pdb=" O SER z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 65 Processing helix chain 'z' and resid 71 through 87 removed outlier: 3.998A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE z 76 " --> pdb=" O THR z 72 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 112 removed outlier: 3.729A pdb=" N VAL z 95 " --> pdb=" O THR z 91 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG z 107 " --> pdb=" O ARG z 103 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN z 110 " --> pdb=" O HIS z 106 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU z 111 " --> pdb=" O ARG z 107 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 removed outlier: 3.724A pdb=" N LYS z 131 " --> pdb=" O LYS z 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE z 132 " --> pdb=" O GLU z 128 " (cutoff:3.500A) Processing helix chain 'z' and resid 143 through 145 No H-bonds generated for 'chain 'z' and resid 143 through 145' Processing helix chain 'z' and resid 146 through 162 removed outlier: 3.958A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER z 156 " --> pdb=" O GLN z 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER z 157 " --> pdb=" O VAL z 153 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL z 162 " --> pdb=" O LEU z 158 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.733A pdb=" N VAL z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU z 179 " --> pdb=" O THR z 175 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 203 through 207 Processing helix chain 'z' and resid 255 through 284 removed outlier: 4.114A pdb=" N ASP z 260 " --> pdb=" O ALA z 256 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS z 261 " --> pdb=" O ASP z 257 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU z 266 " --> pdb=" O LEU z 262 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS z 273 " --> pdb=" O PHE z 269 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP z 279 " --> pdb=" O LYS z 275 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU z 280 " --> pdb=" O LYS z 276 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS z 281 " --> pdb=" O ILE z 277 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN z 282 " --> pdb=" O ILE z 278 " (cutoff:3.500A) Processing helix chain 'z' and resid 303 through 312 removed outlier: 4.303A pdb=" N ASP z 307 " --> pdb=" O PRO z 303 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL z 308 " --> pdb=" O MET z 304 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS z 312 " --> pdb=" O VAL z 308 " (cutoff:3.500A) Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.504A pdb=" N GLU z 326 " --> pdb=" O ARG z 322 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG z 327 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN z 329 " --> pdb=" O MET z 325 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 344 through 348 removed outlier: 3.645A pdb=" N LEU z 348 " --> pdb=" O PRO z 345 " (cutoff:3.500A) Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.737A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN z 404 " --> pdb=" O ARG z 400 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 3.537A pdb=" N ARG z 427 " --> pdb=" O SER z 423 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN z 430 " --> pdb=" O LEU z 426 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN z 432 " --> pdb=" O SER z 428 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.289A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA z 446 " --> pdb=" O THR z 442 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE z 447 " --> pdb=" O GLY z 443 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU z 451 " --> pdb=" O PHE z 447 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 462 removed outlier: 3.652A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER z 462 " --> pdb=" O LEU z 458 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.626A pdb=" N ASP z 479 " --> pdb=" O ASP z 475 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP z 482 " --> pdb=" O ASP z 478 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER z 483 " --> pdb=" O ASP z 479 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 removed outlier: 3.526A pdb=" N ILE z 517 " --> pdb=" O LEU z 513 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU z 527 " --> pdb=" O ILE z 523 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU z 528 " --> pdb=" O ALA z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 21 through 35 removed outlier: 3.631A pdb=" N LEU Z 29 " --> pdb=" O SER Z 25 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 65 removed outlier: 3.608A pdb=" N LEU Z 62 " --> pdb=" O ASP Z 58 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU Z 65 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 80 removed outlier: 3.658A pdb=" N VAL Z 74 " --> pdb=" O SER Z 70 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU Z 75 " --> pdb=" O PRO Z 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE Z 76 " --> pdb=" O THR Z 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA Z 80 " --> pdb=" O ILE Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 85 removed outlier: 3.616A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.518A pdb=" N LEU Z 102 " --> pdb=" O VAL Z 98 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG Z 107 " --> pdb=" O ARG Z 103 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 removed outlier: 3.537A pdb=" N LYS Z 131 " --> pdb=" O LYS Z 127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU Z 135 " --> pdb=" O LYS Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 143 through 145 No H-bonds generated for 'chain 'Z' and resid 143 through 145' Processing helix chain 'Z' and resid 146 through 162 removed outlier: 4.280A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER Z 156 " --> pdb=" O GLN Z 152 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER Z 157 " --> pdb=" O VAL Z 153 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS Z 161 " --> pdb=" O SER Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 181 Proline residue: Z 172 - end of helix removed outlier: 3.790A pdb=" N VAL Z 178 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU Z 179 " --> pdb=" O THR Z 175 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL Z 181 " --> pdb=" O ALA Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 192 No H-bonds generated for 'chain 'Z' and resid 190 through 192' Processing helix chain 'Z' and resid 203 through 207 Processing helix chain 'Z' and resid 255 through 284 removed outlier: 3.566A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS Z 261 " --> pdb=" O ASP Z 257 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS Z 276 " --> pdb=" O ALA Z 272 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU Z 280 " --> pdb=" O LYS Z 276 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN Z 282 " --> pdb=" O ILE Z 278 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL Z 284 " --> pdb=" O LEU Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 304 through 312 removed outlier: 3.855A pdb=" N VAL Z 308 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS Z 311 " --> pdb=" O ASP Z 307 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 332 removed outlier: 3.869A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG Z 327 " --> pdb=" O ARG Z 323 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 348 Processing helix chain 'Z' and resid 384 through 408 removed outlier: 3.921A pdb=" N LEU Z 388 " --> pdb=" O THR Z 384 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR Z 391 " --> pdb=" O ALA Z 387 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN Z 404 " --> pdb=" O ARG Z 400 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.513A pdb=" N ARG Z 427 " --> pdb=" O SER Z 423 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN Z 432 " --> pdb=" O SER Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 440 through 451 Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.762A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 483 removed outlier: 3.520A pdb=" N VAL Z 469 " --> pdb=" O ASP Z 465 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP Z 482 " --> pdb=" O ASP Z 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 505 Processing helix chain 'Z' and resid 510 through 529 removed outlier: 3.536A pdb=" N ASN Z 515 " --> pdb=" O ARG Z 511 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 34 removed outlier: 3.503A pdb=" N VAL b 29 " --> pdb=" O GLY b 25 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 67 Processing helix chain 'b' and resid 73 through 88 removed outlier: 4.207A pdb=" N LEU b 77 " --> pdb=" O ALA b 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 111 removed outlier: 4.168A pdb=" N LYS b 108 " --> pdb=" O ARG b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 removed outlier: 3.539A pdb=" N ALA b 129 " --> pdb=" O ARG b 125 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA b 130 " --> pdb=" O LEU b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 161 Processing helix chain 'b' and resid 164 through 168 Processing helix chain 'b' and resid 169 through 183 removed outlier: 4.601A pdb=" N GLU b 175 " --> pdb=" O ASP b 171 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG b 183 " --> pdb=" O ASN b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 191 No H-bonds generated for 'chain 'b' and resid 189 through 191' Processing helix chain 'b' and resid 202 through 206 Processing helix chain 'b' and resid 291 through 301 removed outlier: 3.726A pdb=" N THR b 299 " --> pdb=" O GLU b 295 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP b 300 " --> pdb=" O GLN b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 310 through 319 removed outlier: 3.570A pdb=" N LEU b 319 " --> pdb=" O GLU b 315 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 394 removed outlier: 4.244A pdb=" N ARG b 382 " --> pdb=" O ASP b 378 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL b 390 " --> pdb=" O ASP b 386 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN b 393 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 removed outlier: 3.509A pdb=" N ASP b 416 " --> pdb=" O SER b 412 " (cutoff:3.500A) Processing helix chain 'b' and resid 423 through 438 removed outlier: 4.554A pdb=" N LEU b 428 " --> pdb=" O GLY b 424 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA b 429 " --> pdb=" O LYS b 425 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE b 433 " --> pdb=" O ALA b 429 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG b 438 " --> pdb=" O ALA b 434 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 448 removed outlier: 3.522A pdb=" N ALA b 448 " --> pdb=" O LEU b 444 " (cutoff:3.500A) Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.616A pdb=" N SER b 457 " --> pdb=" O SER b 453 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER b 462 " --> pdb=" O LYS b 458 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN b 465 " --> pdb=" O SER b 461 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 486 Processing helix chain 'b' and resid 491 through 511 removed outlier: 3.582A pdb=" N VAL b 507 " --> pdb=" O GLU b 503 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU b 508 " --> pdb=" O ALA b 504 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL b 511 " --> pdb=" O VAL b 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 19 through 21 removed outlier: 3.978A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS d 46 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE d 48 " --> pdb=" O ILE d 56 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE d 56 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 62 through 63 removed outlier: 4.169A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 204 through 207 removed outlier: 6.278A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER a 384 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL a 219 " --> pdb=" O SER a 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 222 through 225 removed outlier: 7.514A pdb=" N ILE a 374 " --> pdb=" O VAL a 361 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL a 361 " --> pdb=" O ILE a 374 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLY a 376 " --> pdb=" O ASP a 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 244 through 247 removed outlier: 3.566A pdb=" N THR a 298 " --> pdb=" O VAL a 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.239A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 48 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 62 through 63 removed outlier: 3.801A pdb=" N THR A 63 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 205 through 208 removed outlier: 4.315A pdb=" N ILE A 386 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A 217 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 225 removed outlier: 3.837A pdb=" N LYS A 375 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 360 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL A 361 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 237 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.522A pdb=" N THR A 298 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AB4, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.618A pdb=" N MET B 55 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 43 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP D 523 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 45 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 525 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 193 through 199 removed outlier: 6.411A pdb=" N GLN B 194 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 369 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 196 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLY B 371 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 198 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 207 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 213 through 215 removed outlier: 6.074A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU B 339 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS B 230 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP B 341 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 233 through 234 removed outlier: 3.725A pdb=" N ALA B 234 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AB9, first strand: chain 'B' and resid 470 through 473 Processing sheet with id=AC1, first strand: chain 'B' and resid 511 through 514 removed outlier: 7.964A pdb=" N ILE E 73 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE B 514 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ILE E 75 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS E 72 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR E 84 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 195 through 200 removed outlier: 6.430A pdb=" N ARG d 195 " --> pdb=" O VAL d 377 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE d 379 " --> pdb=" O ARG d 195 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.538A pdb=" N VAL d 363 " --> pdb=" O VAL d 213 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE d 360 " --> pdb=" O ILE d 353 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU d 351 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR d 364 " --> pdb=" O LEU d 349 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 234 through 237 removed outlier: 4.187A pdb=" N GLY d 235 " --> pdb=" O VAL d 285 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU d 287 " --> pdb=" O GLY d 235 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN d 289 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU d 286 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP d 315 " --> pdb=" O LEU d 286 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE d 288 " --> pdb=" O ASP d 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 410 through 411 Processing sheet with id=AC6, first strand: chain 'd' and resid 524 through 526 removed outlier: 6.627A pdb=" N ALA d 525 " --> pdb=" O GLN b 47 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU b 46 " --> pdb=" O MET b 55 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET b 55 " --> pdb=" O LEU b 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 195 through 200 removed outlier: 3.858A pdb=" N GLY D 381 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 213 through 214 removed outlier: 3.700A pdb=" N VAL D 363 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 360 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR D 364 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP D 348 " --> pdb=" O LYS D 231 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 236 through 237 removed outlier: 7.228A pdb=" N LEU D 236 " --> pdb=" O ILE D 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 285 through 289 removed outlier: 9.909A pdb=" N LEU D 286 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE D 316 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE D 288 " --> pdb=" O ILE D 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 410 through 411 Processing sheet with id=AD3, first strand: chain 'e' and resid 72 through 75 removed outlier: 3.671A pdb=" N THR e 84 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU e 74 " --> pdb=" O THR e 82 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR e 82 " --> pdb=" O LEU e 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'e' and resid 166 through 167 removed outlier: 3.548A pdb=" N ASP e 166 " --> pdb=" O VAL e 439 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 224 through 230 removed outlier: 6.282A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL e 408 " --> pdb=" O LYS e 225 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN e 227 " --> pdb=" O VAL e 408 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N GLY e 410 " --> pdb=" O GLN e 227 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 342 through 343 removed outlier: 6.550A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL e 320 " --> pdb=" O LYS e 268 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY e 375 " --> pdb=" O LEU e 269 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'e' and resid 379 through 381 removed outlier: 4.302A pdb=" N ARG e 379 " --> pdb=" O GLU e 396 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU e 396 " --> pdb=" O ARG e 379 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR e 381 " --> pdb=" O ILE e 394 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 554 through 556 removed outlier: 7.118A pdb=" N ILE e 555 " --> pdb=" O VAL h 54 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE h 51 " --> pdb=" O SER h 63 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER h 63 " --> pdb=" O ILE h 51 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE h 53 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR h 61 " --> pdb=" O ILE h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AE1, first strand: chain 'E' and resid 224 through 230 removed outlier: 6.419A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY E 410 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG E 229 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE E 240 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 342 through 343 removed outlier: 3.563A pdb=" N VAL E 320 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 379 through 382 removed outlier: 4.345A pdb=" N ARG E 379 " --> pdb=" O GLU E 396 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 396 " --> pdb=" O ARG E 379 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 553 through 556 removed outlier: 6.474A pdb=" N ASN E 553 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL H 54 " --> pdb=" O ASN E 553 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE E 555 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE H 53 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR H 61 " --> pdb=" O ILE H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'g' and resid 55 through 56 Processing sheet with id=AE6, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'g' and resid 207 through 208 removed outlier: 3.947A pdb=" N GLU g 207 " --> pdb=" O ILE g 379 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU g 381 " --> pdb=" O GLU g 207 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 224 through 225 Processing sheet with id=AE9, first strand: chain 'g' and resid 294 through 296 Processing sheet with id=AF1, first strand: chain 'g' and resid 482 through 484 removed outlier: 3.621A pdb=" N VAL g 492 " --> pdb=" O GLY g 483 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 55 through 56 removed outlier: 3.782A pdb=" N VAL G 56 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 48 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AF4, first strand: chain 'G' and resid 206 through 208 removed outlier: 3.680A pdb=" N LEU G 381 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 294 through 296 Processing sheet with id=AF6, first strand: chain 'G' and resid 482 through 484 Processing sheet with id=AF7, first strand: chain 'h' and resid 201 through 205 removed outlier: 3.846A pdb=" N GLY h 380 " --> pdb=" O ILE h 204 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE h 215 " --> pdb=" O THR h 375 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU h 377 " --> pdb=" O LEU h 213 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU h 213 " --> pdb=" O LEU h 377 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 219 through 220 removed outlier: 3.672A pdb=" N PHE h 220 " --> pdb=" O ASN h 363 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN h 363 " --> pdb=" O PHE h 220 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU h 364 " --> pdb=" O GLU h 353 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU h 353 " --> pdb=" O LEU h 364 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN h 366 " --> pdb=" O LEU h 351 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU h 351 " --> pdb=" O GLN h 366 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 241 through 243 removed outlier: 6.224A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 409 through 411 Processing sheet with id=AG2, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.688A pdb=" N GLY h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 200 through 205 removed outlier: 6.393A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLY H 380 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE H 204 " --> pdb=" O GLY H 380 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR H 375 " --> pdb=" O ILE H 215 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 215 " --> pdb=" O THR H 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'H' and resid 241 through 243 removed outlier: 4.174A pdb=" N LEU H 294 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL H 293 " --> pdb=" O ALA H 315 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 351 through 352 removed outlier: 3.868A pdb=" N LEU H 351 " --> pdb=" O GLN H 366 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN H 366 " --> pdb=" O LEU H 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'H' and resid 409 through 411 removed outlier: 3.641A pdb=" N GLU H 498 " --> pdb=" O VAL H 410 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 479 through 481 Processing sheet with id=AG8, first strand: chain 'H' and resid 523 through 525 removed outlier: 6.866A pdb=" N ILE H 524 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS Q 53 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR Q 65 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'q' and resid 53 through 56 removed outlier: 3.684A pdb=" N LYS q 53 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE q 55 " --> pdb=" O ILE q 63 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'q' and resid 207 through 213 removed outlier: 3.514A pdb=" N ILE q 212 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY q 388 " --> pdb=" O ILE q 212 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR q 383 " --> pdb=" O ILE q 223 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'q' and resid 319 through 321 removed outlier: 7.377A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N LEU q 341 " --> pdb=" O VAL q 247 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL q 249 " --> pdb=" O LEU q 341 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 319 through 321 removed outlier: 7.377A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'q' and resid 360 through 362 Processing sheet with id=AH5, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AH6, first strand: chain 'q' and resid 544 through 545 removed outlier: 3.917A pdb=" N ILE q 545 " --> pdb=" O MET z 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'Q' and resid 207 through 213 removed outlier: 3.644A pdb=" N ILE Q 384 " --> pdb=" O ARG Q 208 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE Q 212 " --> pdb=" O LEU Q 386 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 319 through 322 removed outlier: 7.213A pdb=" N GLU Q 297 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU Q 321 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE Q 299 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS Q 246 " --> pdb=" O VAL Q 296 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N LEU Q 341 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL Q 249 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 319 through 322 removed outlier: 7.213A pdb=" N GLU Q 297 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU Q 321 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE Q 299 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS Q 246 " --> pdb=" O VAL Q 296 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 357 through 363 removed outlier: 3.874A pdb=" N THR Q 357 " --> pdb=" O LYS Q 372 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS Q 372 " --> pdb=" O THR Q 357 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP Q 366 " --> pdb=" O ILE Q 363 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 419 through 420 Processing sheet with id=AI3, first strand: chain 'Q' and resid 544 through 545 removed outlier: 6.259A pdb=" N ILE Q 545 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS Z 44 " --> pdb=" O THR Z 56 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS Z 54 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AI5, first strand: chain 'z' and resid 194 through 199 removed outlier: 6.479A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'z' and resid 227 through 228 Processing sheet with id=AI7, first strand: chain 'z' and resid 292 through 295 removed outlier: 5.967A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLN z 337 " --> pdb=" O VAL z 233 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE z 235 " --> pdb=" O GLN z 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AI9, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AJ1, first strand: chain 'Z' and resid 194 through 197 removed outlier: 6.251A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Z' and resid 214 through 215 removed outlier: 3.837A pdb=" N THR Z 365 " --> pdb=" O LEU Z 215 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Z' and resid 227 through 228 Processing sheet with id=AJ4, first strand: chain 'Z' and resid 315 through 316 removed outlier: 3.840A pdb=" N LEU Z 315 " --> pdb=" O PHE Z 293 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Z' and resid 490 through 491 Processing sheet with id=AJ6, first strand: chain 'b' and resid 193 through 199 removed outlier: 6.282A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLY b 371 " --> pdb=" O ILE b 196 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE b 198 " --> pdb=" O GLY b 371 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL b 368 " --> pdb=" O PHE b 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE b 207 " --> pdb=" O VAL b 368 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'b' and resid 213 through 214 removed outlier: 6.570A pdb=" N VAL b 342 " --> pdb=" O GLU b 227 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU b 227 " --> pdb=" O VAL b 342 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'b' and resid 231 through 234 removed outlier: 3.794A pdb=" N LEU b 232 " --> pdb=" O THR b 283 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'b' and resid 400 through 401 Processing sheet with id=AK1, first strand: chain 'b' and resid 470 through 472 removed outlier: 3.786A pdb=" N ALA b 480 " --> pdb=" O GLY b 471 " (cutoff:3.500A) 2627 hydrogen bonds defined for protein. 7638 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: 19.75 Time building geometry restraints manager: 18.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 20411 1.34 - 1.46: 10204 1.46 - 1.58: 29864 1.58 - 1.69: 0 1.69 - 1.81: 497 Bond restraints: 60976 Sorted by residual: bond pdb=" C ALA q 346 " pdb=" N PRO q 347 " ideal model delta sigma weight residual 1.334 1.434 -0.101 2.34e-02 1.83e+03 1.85e+01 bond pdb=" C ALA Q 346 " pdb=" N PRO Q 347 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.18e+01 bond pdb=" C SER G 409 " pdb=" N PRO G 410 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.27e+00 bond pdb=" C ALA A 232 " pdb=" N MET A 233 " ideal model delta sigma weight residual 1.331 1.346 -0.015 2.07e-02 2.33e+03 5.21e-01 bond pdb=" C LYS q 413 " pdb=" N PRO q 414 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.20e-01 ... (remaining 60971 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.03: 1228 107.03 - 113.77: 35767 113.77 - 120.52: 24250 120.52 - 127.26: 20627 127.26 - 134.00: 380 Bond angle restraints: 82252 Sorted by residual: angle pdb=" C ARG Z 14 " pdb=" N ARG Z 15 " pdb=" CA ARG Z 15 " ideal model delta sigma weight residual 121.76 128.11 -6.35 2.19e+00 2.09e-01 8.42e+00 angle pdb=" C THR e 478 " pdb=" N ILE e 479 " pdb=" CA ILE e 479 " ideal model delta sigma weight residual 120.33 122.49 -2.16 8.00e-01 1.56e+00 7.26e+00 angle pdb=" C GLY B 466 " pdb=" N ILE B 467 " pdb=" CA ILE B 467 " ideal model delta sigma weight residual 121.97 126.81 -4.84 1.80e+00 3.09e-01 7.24e+00 angle pdb=" CA LEU Z 13 " pdb=" CB LEU Z 13 " pdb=" CG LEU Z 13 " ideal model delta sigma weight residual 116.30 125.71 -9.41 3.50e+00 8.16e-02 7.23e+00 angle pdb=" C SER a 442 " pdb=" N ARG a 443 " pdb=" CA ARG a 443 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.06e+00 ... (remaining 82247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 37255 16.19 - 32.39: 324 32.39 - 48.58: 196 48.58 - 64.77: 52 64.77 - 80.96: 3 Dihedral angle restraints: 37830 sinusoidal: 15108 harmonic: 22722 Sorted by residual: dihedral pdb=" CA VAL H 246 " pdb=" C VAL H 246 " pdb=" N GLU H 247 " pdb=" CA GLU H 247 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLU H 247 " pdb=" C GLU H 247 " pdb=" N LEU H 248 " pdb=" CA LEU H 248 " ideal model delta harmonic sigma weight residual 180.00 155.39 24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASN B 465 " pdb=" C ASN B 465 " pdb=" N GLY B 466 " pdb=" CA GLY B 466 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 37827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 7184 0.036 - 0.072: 1958 0.072 - 0.108: 557 0.108 - 0.144: 210 0.144 - 0.180: 4 Chirality restraints: 9913 Sorted by residual: chirality pdb=" CB ILE e 244 " pdb=" CA ILE e 244 " pdb=" CG1 ILE e 244 " pdb=" CG2 ILE e 244 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CB ILE A 196 " pdb=" CA ILE A 196 " pdb=" CG1 ILE A 196 " pdb=" CG2 ILE A 196 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 9910 not shown) Planarity restraints: 10565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 372 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO D 373 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 297 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO H 298 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO H 298 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 298 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR Q 339 " 0.015 5.00e-02 4.00e+02 2.20e-02 7.73e-01 pdb=" N PRO Q 340 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO Q 340 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO Q 340 " 0.012 5.00e-02 4.00e+02 ... (remaining 10562 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 11314 2.78 - 3.31: 56336 3.31 - 3.84: 90477 3.84 - 4.37: 107530 4.37 - 4.90: 184323 Nonbonded interactions: 449980 Sorted by model distance: nonbonded pdb=" O ASP d 193 " pdb=" OG1 THR d 374 " model vdw 2.244 2.440 nonbonded pdb=" O ASN g 351 " pdb=" ND2 ASN g 370 " model vdw 2.252 2.520 nonbonded pdb=" O PRO q 421 " pdb=" OG1 THR q 426 " model vdw 2.258 2.440 nonbonded pdb=" O LEU E 223 " pdb=" OG1 THR E 403 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR Z 182 " pdb=" O GLN Z 185 " model vdw 2.264 2.440 ... (remaining 449975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 254 or resid 279 through 547)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 17 through 234 or resid 279 through 322 or resid 339 throu \ gh 520)) selection = chain 'b' } ncs_group { reference = (chain 'D' and (resid 17 through 479 or resid 492 through 528)) selection = (chain 'd' and (resid 17 through 243 or resid 282 through 528)) } ncs_group { reference = (chain 'E' and (resid 43 through 281 or resid 305 through 560)) selection = (chain 'e' and (resid 43 through 281 or resid 305 through 560)) } ncs_group { reference = chain 'G' selection = (chain 'g' and (resid 18 through 251 or resid 290 through 333 or resid 349 throu \ gh 530)) } ncs_group { reference = (chain 'H' and (resid 22 through 249 or resid 278 through 528)) selection = chain 'h' } ncs_group { reference = chain 'Q' selection = (chain 'q' and (resid 27 through 266 or resid 275 through 549)) } ncs_group { reference = chain 'Z' selection = (chain 'z' and resid 12 through 538) } 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 4.340 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 116.490 Find NCS groups from input model: 5.550 Set up NCS constraints: 0.310 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: 0.000 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 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 : 0.001 0.101 60976 Z= 0.085 Angle : 0.393 9.411 82252 Z= 0.221 Chirality : 0.039 0.180 9913 Planarity : 0.001 0.037 10565 Dihedral : 7.111 80.964 23102 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.07), residues: 7857 helix: -3.43 (0.05), residues: 3639 sheet: -0.68 (0.19), residues: 598 loop : -1.17 (0.09), residues: 3620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP z 507 HIS 0.003 0.000 HIS H 172 PHE 0.014 0.001 PHE d 239 TYR 0.008 0.001 TYR G 442 ARG 0.003 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2628 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2626 time to evaluate : 5.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 2628 average time/residue: 0.6081 time to fit residues: 2628.4579 Evaluate side-chains 1358 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1358 time to evaluate : 5.041 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 661 optimal weight: 5.9990 chunk 593 optimal weight: 0.9980 chunk 329 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 400 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 613 optimal weight: 0.5980 chunk 237 optimal weight: 6.9990 chunk 373 optimal weight: 8.9990 chunk 456 optimal weight: 0.0070 chunk 711 optimal weight: 7.9990 overall best weight: 2.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 77 HIS ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN A 363 GLN B 47 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 289 GLN d 499 GLN D 284 ASN D 289 GLN e 383 GLN e 424 HIS e 432 ASN e 466 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN E 353 HIS E 424 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN ** g 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 443 GLN g 470 GLN g 475 HIS G 24 ASN G 62 HIS G 188 GLN G 405 ASN ** G 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN h 216 ASN h 356 GLN ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 508 ASN ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 515 ASN Q 203 ASN Q 258 ASN Q 314 ASN Q 477 ASN ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 145 ASN ** z 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 356 GLN z 390 GLN ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 GLN Z 356 GLN Z 526 ASN ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 60976 Z= 0.235 Angle : 0.641 10.005 82252 Z= 0.338 Chirality : 0.045 0.345 9913 Planarity : 0.004 0.049 10565 Dihedral : 3.583 24.826 8348 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Rotamer: Outliers : 0.18 % Allowed : 2.63 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.08), residues: 7857 helix: -0.70 (0.07), residues: 3796 sheet: -0.37 (0.19), residues: 613 loop : -0.92 (0.09), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP g 167 HIS 0.010 0.001 HIS z 114 PHE 0.039 0.002 PHE D 438 TYR 0.042 0.002 TYR B 124 ARG 0.010 0.001 ARG e 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1719 time to evaluate : 5.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 1724 average time/residue: 0.5556 time to fit residues: 1629.1043 Evaluate side-chains 1234 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1232 time to evaluate : 5.040 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4307 time to fit residues: 8.8914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 395 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 591 optimal weight: 0.6980 chunk 484 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 712 optimal weight: 20.0000 chunk 769 optimal weight: 10.0000 chunk 634 optimal weight: 3.9990 chunk 706 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 571 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 77 HIS a 88 GLN ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 ASN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN A 380 HIS A 403 HIS A 445 GLN A 514 HIS B 47 GLN d 24 ASN D 24 ASN D 140 HIS D 395 HIS e 93 GLN ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 GLN e 432 ASN ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 543 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 286 GLN g 325 ASN g 405 ASN ** g 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN h 452 GLN h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 508 ASN ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 394 HIS H 435 GLN ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 39 HIS q 92 GLN q 112 ASN q 446 GLN Q 91 GLN ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 314 ASN ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 114 HIS ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 337 GLN Z 430 ASN ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 60976 Z= 0.246 Angle : 0.648 12.183 82252 Z= 0.335 Chirality : 0.045 0.269 9913 Planarity : 0.004 0.085 10565 Dihedral : 4.039 31.026 8348 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 0.20 % Allowed : 3.15 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.54 (0.09), residues: 7857 helix: 0.14 (0.08), residues: 3849 sheet: -0.39 (0.20), residues: 601 loop : -0.83 (0.10), residues: 3407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 500 HIS 0.011 0.001 HIS g 117 PHE 0.042 0.002 PHE Q 137 TYR 0.067 0.002 TYR Z 425 ARG 0.010 0.001 ARG D 423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1603 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1590 time to evaluate : 5.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 1599 average time/residue: 0.5739 time to fit residues: 1553.3733 Evaluate side-chains 1211 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1210 time to evaluate : 5.082 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4483 time to fit residues: 8.1300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 703 optimal weight: 2.9990 chunk 535 optimal weight: 3.9990 chunk 369 optimal weight: 30.0000 chunk 78 optimal weight: 4.9990 chunk 339 optimal weight: 7.9990 chunk 478 optimal weight: 2.9990 chunk 714 optimal weight: 4.9990 chunk 756 optimal weight: 0.7980 chunk 373 optimal weight: 0.0020 chunk 677 optimal weight: 0.3980 chunk 203 optimal weight: 5.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 485 GLN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN B 118 GLN B 351 GLN d 24 ASN d 240 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS D 441 GLN D 457 ASN e 132 GLN ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN E 466 GLN g 325 ASN g 405 ASN g 443 GLN g 458 GLN g 507 GLN G 24 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 395 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 GLN h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 104 GLN ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 217 HIS ** Z 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 GLN ** b 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 60976 Z= 0.172 Angle : 0.556 13.829 82252 Z= 0.286 Chirality : 0.043 0.298 9913 Planarity : 0.003 0.128 10565 Dihedral : 3.866 31.872 8348 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.19 (0.09), residues: 7857 helix: 0.50 (0.08), residues: 3860 sheet: -0.28 (0.20), residues: 617 loop : -0.73 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 440 HIS 0.006 0.001 HIS g 475 PHE 0.040 0.002 PHE a 129 TYR 0.027 0.001 TYR Z 425 ARG 0.011 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1511 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1507 time to evaluate : 5.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 1511 average time/residue: 0.5624 time to fit residues: 1457.7160 Evaluate side-chains 1217 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1217 time to evaluate : 5.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 630 optimal weight: 6.9990 chunk 429 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 563 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 645 optimal weight: 1.9990 chunk 523 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 679 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 252 GLN a 465 ASN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN B 351 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 502 GLN ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 543 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN E 466 GLN g 443 GLN G 21 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 477 ASN ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 217 HIS Z 83 GLN ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 60976 Z= 0.163 Angle : 0.549 13.203 82252 Z= 0.280 Chirality : 0.043 0.283 9913 Planarity : 0.003 0.098 10565 Dihedral : 3.823 31.636 8348 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 0.06 % Allowed : 1.73 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.01 (0.09), residues: 7857 helix: 0.69 (0.08), residues: 3861 sheet: -0.25 (0.20), residues: 633 loop : -0.64 (0.10), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 440 HIS 0.013 0.001 HIS q 39 PHE 0.033 0.001 PHE E 179 TYR 0.066 0.001 TYR Z 425 ARG 0.013 0.000 ARG a 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1483 time to evaluate : 5.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 1483 average time/residue: 0.5470 time to fit residues: 1400.9765 Evaluate side-chains 1209 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1208 time to evaluate : 5.112 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5169 time to fit residues: 8.1581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 254 optimal weight: 5.9990 chunk 681 optimal weight: 9.9990 chunk 149 optimal weight: 0.0570 chunk 444 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 757 optimal weight: 30.0000 chunk 628 optimal weight: 9.9990 chunk 350 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 397 optimal weight: 1.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 77 HIS ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 ASN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS D 473 HIS ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN E 332 ASN E 424 HIS E 466 GLN ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 325 ASN ** g 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 458 GLN G 21 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 104 GLN ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 60976 Z= 0.180 Angle : 0.565 12.056 82252 Z= 0.290 Chirality : 0.043 0.204 9913 Planarity : 0.003 0.137 10565 Dihedral : 3.912 32.729 8348 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.13 (0.09), residues: 7857 helix: 0.83 (0.08), residues: 3843 sheet: -0.28 (0.20), residues: 635 loop : -0.62 (0.10), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 440 HIS 0.014 0.001 HIS q 39 PHE 0.041 0.002 PHE a 129 TYR 0.019 0.001 TYR Z 425 ARG 0.009 0.001 ARG q 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1476 time to evaluate : 5.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1477 average time/residue: 0.5593 time to fit residues: 1433.0138 Evaluate side-chains 1190 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1190 time to evaluate : 5.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 730 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 431 optimal weight: 10.0000 chunk 553 optimal weight: 4.9990 chunk 428 optimal weight: 7.9990 chunk 637 optimal weight: 0.1980 chunk 423 optimal weight: 5.9990 chunk 754 optimal weight: 20.0000 chunk 472 optimal weight: 6.9990 chunk 460 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 ASN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN B 112 GLN ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 HIS e 210 ASN e 353 HIS ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN E 424 HIS E 466 GLN E 486 ASN ** g 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 ASN ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 515 ASN q 39 HIS q 154 ASN q 283 GLN Q 39 HIS ** z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 201 HIS z 217 HIS z 312 HIS z 410 ASN ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 ASN Z 185 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.7356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 60976 Z= 0.245 Angle : 0.658 13.655 82252 Z= 0.341 Chirality : 0.046 0.287 9913 Planarity : 0.004 0.140 10565 Dihedral : 4.348 34.111 8348 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.12 (0.09), residues: 7857 helix: 0.63 (0.08), residues: 3875 sheet: -0.47 (0.20), residues: 662 loop : -0.74 (0.10), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 345 HIS 0.011 0.002 HIS E 50 PHE 0.038 0.002 PHE e 469 TYR 0.021 0.002 TYR A 432 ARG 0.012 0.001 ARG q 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1511 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1509 time to evaluate : 5.110 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 outliers start: 2 outliers final: 1 residues processed: 1510 average time/residue: 0.5454 time to fit residues: 1417.6630 Evaluate side-chains 1207 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1206 time to evaluate : 5.158 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4121 time to fit residues: 8.1215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 466 optimal weight: 0.2980 chunk 301 optimal weight: 5.9990 chunk 450 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 479 optimal weight: 6.9990 chunk 514 optimal weight: 0.5980 chunk 373 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 593 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 HIS ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN E 486 ASN g 443 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 395 ASN h 90 GLN ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 515 ASN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 106 HIS ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 201 HIS ** z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 390 GLN Z 110 GLN b 118 GLN ** b 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.7531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 60976 Z= 0.175 Angle : 0.591 14.536 82252 Z= 0.301 Chirality : 0.044 0.308 9913 Planarity : 0.003 0.090 10565 Dihedral : 4.144 31.529 8348 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 0.09 % Allowed : 0.80 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.07 (0.09), residues: 7857 helix: 0.81 (0.08), residues: 3873 sheet: -0.34 (0.20), residues: 651 loop : -0.70 (0.10), residues: 3333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 440 HIS 0.010 0.001 HIS D 116 PHE 0.046 0.001 PHE a 129 TYR 0.025 0.001 TYR g 163 ARG 0.008 0.000 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1481 time to evaluate : 5.141 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 outliers start: 6 outliers final: 0 residues processed: 1483 average time/residue: 0.5579 time to fit residues: 1434.1509 Evaluate side-chains 1185 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1185 time to evaluate : 5.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 686 optimal weight: 10.0000 chunk 723 optimal weight: 0.9980 chunk 659 optimal weight: 8.9990 chunk 703 optimal weight: 20.0000 chunk 722 optimal weight: 8.9990 chunk 423 optimal weight: 6.9990 chunk 306 optimal weight: 0.0270 chunk 552 optimal weight: 0.0030 chunk 215 optimal weight: 5.9990 chunk 635 optimal weight: 0.0020 chunk 665 optimal weight: 0.0060 overall best weight: 0.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN D 24 ASN D 62 HIS ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** g 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 115 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN ** h 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 435 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 201 HIS z 356 GLN z 390 GLN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 GLN ** b 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 60976 Z= 0.157 Angle : 0.581 13.645 82252 Z= 0.294 Chirality : 0.043 0.253 9913 Planarity : 0.003 0.050 10565 Dihedral : 3.955 30.144 8348 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.17 (0.09), residues: 7857 helix: 0.89 (0.08), residues: 3843 sheet: -0.22 (0.20), residues: 673 loop : -0.66 (0.10), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 478 HIS 0.009 0.001 HIS D 116 PHE 0.023 0.001 PHE z 418 TYR 0.043 0.001 TYR b 464 ARG 0.019 0.000 ARG h 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1474 time to evaluate : 5.191 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 outliers start: 4 outliers final: 0 residues processed: 1475 average time/residue: 0.5482 time to fit residues: 1404.0582 Evaluate side-chains 1195 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1195 time to evaluate : 5.156 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 700 optimal weight: 0.3980 chunk 461 optimal weight: 1.9990 chunk 743 optimal weight: 0.5980 chunk 453 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 516 optimal weight: 10.0000 chunk 780 optimal weight: 0.9990 chunk 717 optimal weight: 2.9990 chunk 621 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 479 optimal weight: 0.0670 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 77 HIS ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 303 GLN ** g 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 475 HIS G 21 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 HIS h 90 GLN ** h 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 39 HIS ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 390 GLN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 60976 Z= 0.160 Angle : 0.590 13.683 82252 Z= 0.298 Chirality : 0.044 0.443 9913 Planarity : 0.003 0.042 10565 Dihedral : 3.896 30.107 8348 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 0.02 % Allowed : 0.23 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.20 (0.09), residues: 7857 helix: 0.91 (0.08), residues: 3852 sheet: -0.12 (0.20), residues: 658 loop : -0.64 (0.11), residues: 3347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 440 HIS 0.009 0.001 HIS D 116 PHE 0.050 0.001 PHE a 129 TYR 0.042 0.001 TYR b 464 ARG 0.008 0.000 ARG q 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15714 Ramachandran restraints generated. 7857 Oldfield, 0 Emsley, 7857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1428 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1427 time to evaluate : 5.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1427 average time/residue: 0.5486 time to fit residues: 1361.5914 Evaluate side-chains 1188 residues out of total 6664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1188 time to evaluate : 5.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 380 optimal weight: 9.9990 chunk 493 optimal weight: 6.9990 chunk 661 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 572 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 622 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 638 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 77 HIS ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 403 HIS a 430 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN d 441 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 HIS ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN E 424 HIS ** g 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 443 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN ** h 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 491 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 39 HIS ** q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 132 ASN ** z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 390 GLN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 GLN ** b 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.205659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.175240 restraints weight = 142063.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.178612 restraints weight = 93669.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.179985 restraints weight = 64491.929| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.7808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 60976 Z= 0.167 Angle : 0.584 14.785 82252 Z= 0.297 Chirality : 0.044 0.267 9913 Planarity : 0.003 0.043 10565 Dihedral : 3.905 30.393 8348 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.21 (0.09), residues: 7857 helix: 0.92 (0.08), residues: 3865 sheet: -0.10 (0.21), residues: 655 loop : -0.67 (0.11), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 478 HIS 0.013 0.001 HIS D 116 PHE 0.038 0.002 PHE E 179 TYR 0.032 0.001 TYR b 124 ARG 0.009 0.000 ARG H 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20227.58 seconds wall clock time: 352 minutes 23.73 seconds (21143.73 seconds total)