Starting phenix.real_space_refine on Sat Dec 9 05:19:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/12_2023/6ks8_0760.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/12_2023/6ks8_0760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/12_2023/6ks8_0760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/12_2023/6ks8_0760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/12_2023/6ks8_0760.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks8_0760/12_2023/6ks8_0760.pdb" } resolution = 4.69 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= 0.021 sd= 0.143 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 316 5.16 5 C 38884 2.51 5 N 10714 2.21 5 O 12029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z ARG 14": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 61943 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3908 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 10, 'TRANS': 508} Chain breaks: 1 Chain: "A" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3859 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 10, 'TRANS': 501} Chain breaks: 2 Chain: "b" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3811 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 10, 'TRANS': 491} Chain: "B" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3708 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 10, 'TRANS': 478} Chain breaks: 1 Chain: "d" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3816 Classifications: {'peptide': 499} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 485} Chain breaks: 1 Chain: "D" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3655 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 467} Chain breaks: 2 Chain: "e" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 15, 'TRANS': 502} Chain: "E" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3848 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 15, 'TRANS': 486} Chain breaks: 1 Chain: "g" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3775 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 18, 'TRANS': 474} Chain breaks: 2 Chain: "G" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3709 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 2 Chain: "h" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3882 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 12, 'TRANS': 494} Chain: "H" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3882 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 12, 'TRANS': 494} Chain: "q" Number of atoms: 3974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3974 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 18, 'TRANS': 504} 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: "z" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4086 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 15, 'TRANS': 515} 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} Time building chain proxies: 23.42, per 1000 atoms: 0.38 Number of scatterers: 61943 At special positions: 0 Unit cell: (192.428, 192.428, 204.29, 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 316 16.00 O 12029 8.00 N 10714 7.00 C 38884 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: 17.98 Conformation dependent library (CDL) restraints added in 8.4 seconds 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15120 Finding SS restraints... Secondary structure from input PDB file: 333 helices and 92 sheets defined 55.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'a' and resid 22 through 41 removed outlier: 4.157A pdb=" N ARG a 26 " --> pdb=" O GLY a 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN a 27 " --> pdb=" O ASP a 23 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL a 30 " --> pdb=" O ARG a 26 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL a 36 " --> pdb=" O ALA a 32 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 73 removed outlier: 3.539A pdb=" N ILE a 69 " --> pdb=" O ASP a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 94 removed outlier: 3.668A pdb=" N VAL a 84 " --> pdb=" O GLY a 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU a 93 " --> pdb=" O GLN a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 115 removed outlier: 3.519A pdb=" N VAL a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE a 103 " --> pdb=" O THR a 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU a 107 " --> pdb=" O ILE a 103 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU a 115 " --> pdb=" O ARG a 111 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 142 removed outlier: 3.651A pdb=" N ARG a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN a 141 " --> pdb=" O ILE a 137 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 removed outlier: 3.872A pdb=" N ALA a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER a 163 " --> pdb=" O ILE a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 167 No H-bonds generated for 'chain 'a' and resid 165 through 167' Processing helix chain 'a' and resid 168 through 188 removed outlier: 4.191A pdb=" N ASP a 172 " --> pdb=" O ILE a 168 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP a 174 " --> pdb=" O GLY a 170 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE a 175 " --> pdb=" O ALA a 171 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS a 188 " --> pdb=" O LEU a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 Processing helix chain 'a' and resid 277 through 290 removed outlier: 3.917A pdb=" N VAL a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG a 284 " --> pdb=" O ILE a 280 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL a 285 " --> pdb=" O VAL a 281 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS a 287 " --> pdb=" O GLU a 283 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 313 removed outlier: 3.778A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA a 313 " --> pdb=" O GLU a 309 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 334 removed outlier: 3.588A pdb=" N ARG a 327 " --> pdb=" O LYS a 323 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.750A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 437 removed outlier: 3.658A 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 443 through 455 removed outlier: 3.898A pdb=" N ALA a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU a 455 " --> pdb=" O PHE a 451 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 465 removed outlier: 3.545A pdb=" N LEU a 462 " --> pdb=" O ILE a 458 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA a 463 " --> pdb=" O PRO a 459 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL a 464 " --> pdb=" O LYS a 460 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 removed outlier: 3.543A pdb=" N LEU a 473 " --> pdb=" O ASP a 469 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL a 474 " --> pdb=" O SER a 470 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA a 475 " --> pdb=" O SER a 471 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR a 480 " --> pdb=" O LYS a 476 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) Processing helix chain 'a' and resid 512 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.514A pdb=" N GLU a 533 " --> pdb=" O LYS a 529 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA a 537 " --> pdb=" O GLU a 533 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE a 538 " --> pdb=" O ALA a 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.994A pdb=" N ARG A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.690A pdb=" N ILE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 removed outlier: 4.214A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.554A pdb=" N VAL A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.504A pdb=" N ILE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.808A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 4.294A pdb=" N ASP A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 277 through 291 removed outlier: 4.352A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.630A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 removed outlier: 4.032A pdb=" N ARG A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.700A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.630A pdb=" N ASN A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.743A 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 443 through 454 removed outlier: 3.914A pdb=" N ALA A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.624A pdb=" N ARG A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.745A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 34 removed outlier: 3.522A pdb=" N LEU b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 37 No H-bonds generated for 'chain 'b' and resid 35 through 37' Processing helix chain 'b' and resid 59 through 67 Processing helix chain 'b' and resid 73 through 88 removed outlier: 4.180A pdb=" N LEU b 77 " --> pdb=" O ALA b 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL b 83 " --> pdb=" O ASN b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 111 removed outlier: 3.505A pdb=" N GLU b 107 " --> pdb=" O LEU b 103 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS b 108 " --> pdb=" O ARG b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 removed outlier: 3.553A pdb=" N ALA b 129 " --> pdb=" O ARG b 125 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA b 130 " --> pdb=" O LEU b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 161 removed outlier: 3.581A pdb=" N PHE b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 168 Processing helix chain 'b' and resid 169 through 183 removed outlier: 4.685A pdb=" N GLU b 175 " --> pdb=" O ASP b 171 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.607A 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 254 through 278 removed outlier: 3.501A pdb=" N ALA b 259 " --> pdb=" O THR b 255 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN b 260 " --> pdb=" O ALA b 256 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU b 261 " --> pdb=" O LYS b 257 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA b 264 " --> pdb=" O GLN b 260 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU b 265 " --> pdb=" O LEU b 261 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG b 266 " --> pdb=" O GLU b 262 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN b 271 " --> pdb=" O GLU b 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 301 removed outlier: 3.856A pdb=" N THR b 299 " --> pdb=" O GLU b 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP b 300 " --> pdb=" O GLN b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 310 through 319 removed outlier: 3.605A pdb=" N LEU b 319 " --> pdb=" O GLU b 315 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 394 removed outlier: 3.558A pdb=" N GLU b 379 " --> pdb=" O GLN b 375 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG b 382 " --> pdb=" O ASP b 378 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL b 390 " --> pdb=" O ASP b 386 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN b 393 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 removed outlier: 3.535A pdb=" N MET b 409 " --> pdb=" O GLY b 405 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS b 413 " --> pdb=" O MET b 409 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA b 414 " --> pdb=" O VAL b 410 " (cutoff:3.500A) Processing helix chain 'b' and resid 423 through 438 removed outlier: 4.481A pdb=" N LEU b 428 " --> pdb=" O GLY b 424 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA b 429 " --> pdb=" O LYS b 425 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE b 433 " --> pdb=" O ALA b 429 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG b 438 " --> pdb=" O ALA b 434 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 449 Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.560A pdb=" N LEU b 459 " --> pdb=" O LEU b 455 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER b 462 " --> pdb=" O LYS b 458 " (cutoff:3.500A) removed outlier: 4.505A 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: 3.529A pdb=" N ALA b 496 " --> pdb=" O LYS b 492 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU b 508 " --> pdb=" O ALA b 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 3.578A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.848A 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 71 through 88 removed outlier: 3.519A pdb=" N VAL B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.658A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 138 removed outlier: 3.675A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.695A pdb=" N GLU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.628A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 removed outlier: 4.644A pdb=" N GLU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 176 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 3.623A 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 257 through 278 removed outlier: 3.906A pdb=" N LEU B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.545A pdb=" N PHE B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.578A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 397 removed outlier: 3.714A pdb=" N GLU B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.593A pdb=" N MET B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 425 through 438 removed outlier: 4.182A pdb=" N ALA B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 451 through 465 removed outlier: 3.522A pdb=" N VAL B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.239A 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: 3.529A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 36 removed outlier: 3.588A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA d 34 " --> pdb=" O SER d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 68 Processing helix chain 'd' and resid 72 through 89 removed outlier: 3.611A pdb=" N MET d 77 " --> pdb=" O PRO d 73 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU d 78 " --> pdb=" O VAL d 74 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 107 removed outlier: 3.862A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 113 removed outlier: 3.818A pdb=" N ASN d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS d 113 " --> pdb=" O ARG d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.843A pdb=" N GLN d 125 " --> pdb=" O ALA d 121 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER d 126 " --> pdb=" O ASP d 122 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 157 removed outlier: 4.035A pdb=" N LEU d 150 " --> pdb=" O ASP d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 166 through 182 removed outlier: 3.878A pdb=" N LEU d 170 " --> pdb=" O TYR d 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA d 171 " --> pdb=" O SER d 167 " (cutoff:3.500A) Proline residue: d 172 - end of helix removed outlier: 3.587A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 194 removed outlier: 3.742A pdb=" N ASP d 193 " --> pdb=" O ASP d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 256 through 280 removed outlier: 3.583A pdb=" N ILE d 274 " --> pdb=" O TYR d 270 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS d 275 " --> pdb=" O LEU d 271 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS d 277 " --> pdb=" O ASN d 273 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE d 278 " --> pdb=" O ILE d 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 308 removed outlier: 3.827A pdb=" N LYS d 307 " --> pdb=" O HIS d 303 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU d 308 " --> pdb=" O PHE d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 320 through 328 removed outlier: 3.942A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU d 328 " --> pdb=" O LEU d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 344 removed outlier: 3.596A pdb=" N ARG d 343 " --> pdb=" O THR d 340 " (cutoff:3.500A) Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.800A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.695A pdb=" N ILE d 419 " --> pdb=" O GLY d 415 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 433 removed outlier: 5.984A pdb=" N GLU d 433 " --> pdb=" O ARG d 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 430 through 433' Processing helix chain 'd' and resid 434 through 440 removed outlier: 4.081A pdb=" N PHE d 438 " --> pdb=" O GLY d 434 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP d 440 " --> pdb=" O GLN d 436 " (cutoff:3.500A) Processing helix chain 'd' and resid 441 through 446 removed outlier: 3.955A pdb=" N SER d 445 " --> pdb=" O GLN d 441 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA d 446 " --> pdb=" O GLU d 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 441 through 446' Processing helix chain 'd' and resid 448 through 458 Processing helix chain 'd' and resid 461 through 476 removed outlier: 3.511A pdb=" N VAL d 466 " --> pdb=" O SER d 462 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS d 472 " --> pdb=" O GLU d 468 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU d 474 " --> pdb=" O ARG d 470 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN d 475 " --> pdb=" O SER d 471 " (cutoff:3.500A) Processing helix chain 'd' and resid 501 through 520 removed outlier: 3.763A pdb=" N ILE d 508 " --> pdb=" O SER d 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 36 removed outlier: 3.584A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 72 through 89 removed outlier: 3.548A pdb=" N MET D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.874A pdb=" N VAL D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.559A pdb=" N GLN D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.919A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.678A pdb=" N SER D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 removed outlier: 4.156A pdb=" N LEU D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.524A pdb=" N ILE D 274 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 removed outlier: 3.778A pdb=" N LYS D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.969A pdb=" N GLU D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.659A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 389 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 430 removed outlier: 3.569A pdb=" N SER D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 427 " --> pdb=" O ARG D 423 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG D 430 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.704A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.609A pdb=" N ILE D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 513 " --> pdb=" O THR D 509 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 63 removed outlier: 3.643A pdb=" N HIS e 50 " --> pdb=" O ALA e 46 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR e 63 " --> pdb=" O SER e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 94 removed outlier: 3.537A pdb=" N ILE e 90 " --> pdb=" O ASP e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 115 removed outlier: 3.615A pdb=" N LEU e 103 " --> pdb=" O GLU e 99 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER e 108 " --> pdb=" O LEU e 104 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER e 110 " --> pdb=" O GLN e 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 removed outlier: 4.199A pdb=" N VAL e 123 " --> pdb=" O THR e 119 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU e 129 " --> pdb=" O LEU e 125 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU e 136 " --> pdb=" O GLN e 132 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN e 138 " --> pdb=" O LEU e 134 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS e 139 " --> pdb=" O GLU e 135 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 163 removed outlier: 3.661A pdb=" N GLU e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 173 through 188 removed outlier: 3.785A pdb=" N ARG e 177 " --> pdb=" O ASP e 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG e 182 " --> pdb=" O ASP e 178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS e 185 " --> pdb=" O LEU e 181 " (cutoff:3.500A) removed outlier: 4.049A 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) removed outlier: 3.567A pdb=" N LEU e 188 " --> pdb=" O ALA e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 195 Processing helix chain 'e' and resid 196 through 211 removed outlier: 4.782A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET e 203 " --> pdb=" O ARG e 199 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA e 204 " --> pdb=" O PHE e 200 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL e 205 " --> pdb=" O ALA e 201 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL e 208 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE e 209 " --> pdb=" O VAL e 205 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN e 210 " --> pdb=" O GLU e 206 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 237 removed outlier: 3.625A pdb=" N ASP e 236 " --> pdb=" O SER e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 291 through 317 removed outlier: 3.529A pdb=" N TYR e 295 " --> pdb=" O SER e 291 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE e 306 " --> pdb=" O GLU e 302 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS e 307 " --> pdb=" O GLN e 303 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU e 308 " --> pdb=" O ASP e 304 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE e 310 " --> pdb=" O PHE e 306 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS e 314 " --> pdb=" O ILE e 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 removed outlier: 3.646A pdb=" N GLN e 337 " --> pdb=" O HIS e 333 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN e 338 " --> pdb=" O LEU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 358 removed outlier: 3.516A pdb=" N LEU e 351 " --> pdb=" O GLY e 347 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS e 353 " --> pdb=" O GLN e 349 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE e 354 " --> pdb=" O GLU e 350 " (cutoff:3.500A) Processing helix chain 'e' and resid 412 through 436 removed outlier: 3.573A pdb=" N ASN e 432 " --> pdb=" O CYS e 428 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 462 removed outlier: 3.881A pdb=" N VAL e 448 " --> pdb=" O GLY e 444 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA e 453 " --> pdb=" O THR e 449 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL e 454 " --> pdb=" O MET e 450 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER e 455 " --> pdb=" O SER e 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU e 456 " --> pdb=" O LEU e 452 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU e 457 " --> pdb=" O ALA e 453 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP e 459 " --> pdb=" O SER e 455 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN e 461 " --> pdb=" O GLU e 457 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG e 462 " --> pdb=" O ALA e 458 " (cutoff:3.500A) Processing helix chain 'e' and resid 465 through 477 Processing helix chain 'e' and resid 477 through 487 removed outlier: 3.655A pdb=" N ASN e 486 " --> pdb=" O THR e 482 " (cutoff:3.500A) Processing helix chain 'e' and resid 490 through 502 removed outlier: 3.668A pdb=" N GLN e 502 " --> pdb=" O LEU e 498 " (cutoff:3.500A) Processing helix chain 'e' and resid 512 through 516 removed outlier: 3.538A pdb=" N LEU e 515 " --> pdb=" O VAL e 512 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 526 removed outlier: 3.635A pdb=" N PHE e 526 " --> pdb=" O LYS e 523 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'E' and resid 44 through 59 removed outlier: 3.712A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 98 through 115 removed outlier: 3.946A pdb=" N LEU E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 139 removed outlier: 4.103A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 130 " --> pdb=" O ALA E 126 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 164 removed outlier: 3.574A pdb=" N ASP E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 152 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.537A pdb=" N ARG E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 188 removed outlier: 4.502A pdb=" N SER E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 188' Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 211 removed outlier: 4.623A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET E 203 " --> pdb=" O ARG E 199 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) removed outlier: 3.819A 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 302 through 317 removed outlier: 3.554A pdb=" N LYS E 307 " --> pdb=" O GLN E 303 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 4.237A pdb=" N LEU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 335' Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.960A pdb=" N GLU E 352 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS E 353 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.506A pdb=" N LEU E 369 " --> pdb=" O PHE E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 Processing helix chain 'E' and resid 445 through 459 removed outlier: 4.485A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 477 removed outlier: 3.740A 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 501 removed outlier: 4.029A pdb=" N SER E 496 " --> pdb=" O ILE E 492 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 501 " --> pdb=" O THR E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 550 Processing helix chain 'g' and resid 19 through 33 removed outlier: 3.564A pdb=" N VAL g 31 " --> pdb=" O ALA g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 39 removed outlier: 4.099A pdb=" N THR g 37 " --> pdb=" O VAL g 34 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU g 39 " --> pdb=" O ARG g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 67 removed outlier: 3.531A pdb=" N LEU g 65 " --> pdb=" O GLY g 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG g 66 " --> pdb=" O HIS g 62 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU g 67 " --> pdb=" O ALA g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 removed outlier: 3.975A pdb=" N LYS g 76 " --> pdb=" O HIS g 72 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET g 78 " --> pdb=" O ALA g 74 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU g 87 " --> pdb=" O ARG g 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU g 88 " --> pdb=" O THR g 84 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.702A pdb=" N VAL g 96 " --> pdb=" O GLY g 92 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) removed outlier: 3.908A 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: 3.568A pdb=" N LYS g 127 " --> pdb=" O GLN g 123 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR g 130 " --> pdb=" O LYS g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 147 through 156 removed outlier: 3.574A pdb=" N LYS g 152 " --> pdb=" O ASP g 148 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 3.674A 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: 4.166A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 3.742A pdb=" N GLU g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL g 179 " --> pdb=" O ALA g 175 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR g 181 " --> pdb=" O ASP g 177 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL g 182 " --> pdb=" O ALA g 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 272 through 288 removed outlier: 3.533A pdb=" N GLN g 286 " --> pdb=" O LEU g 282 " (cutoff:3.500A) removed outlier: 4.061A 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 309 removed outlier: 3.769A pdb=" N HIS g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR g 308 " --> pdb=" O LEU g 304 " (cutoff:3.500A) Processing helix chain 'g' and resid 321 through 333 removed outlier: 3.536A pdb=" N ASN g 325 " --> pdb=" O LYS g 321 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN g 326 " --> pdb=" O LYS g 322 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG g 327 " --> pdb=" O SER g 323 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 removed outlier: 3.788A pdb=" N LEU g 343 " --> pdb=" O VAL g 340 " (cutoff:3.500A) Processing helix chain 'g' and resid 445 through 468 removed outlier: 3.699A pdb=" N ARG g 454 " --> pdb=" O ASN g 450 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL g 462 " --> pdb=" O ASP g 458 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET g 467 " --> pdb=" O ALA g 463 " (cutoff:3.500A) Processing helix chain 'g' and resid 477 through 490 removed outlier: 3.637A pdb=" N SER g 484 " --> pdb=" O GLU g 480 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA g 488 " --> pdb=" O SER g 484 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU g 489 " --> pdb=" O VAL g 485 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS g 490 " --> pdb=" O LYS g 486 " (cutoff:3.500A) Processing helix chain 'g' and resid 491 through 494 Processing helix chain 'g' and resid 498 through 510 removed outlier: 3.585A pdb=" N TYR g 502 " --> pdb=" O GLN g 498 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA g 504 " --> pdb=" O TRP g 500 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL g 505 " --> pdb=" O PRO g 501 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA g 506 " --> pdb=" O TYR g 502 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU g 510 " --> pdb=" O ALA g 506 " (cutoff:3.500A) Processing helix chain 'g' and resid 510 through 521 removed outlier: 3.585A pdb=" N LEU g 516 " --> pdb=" O ILE g 512 " (cutoff:3.500A) Processing helix chain 'g' and resid 523 through 538 removed outlier: 3.710A pdb=" N ALA g 536 " --> pdb=" O ARG g 532 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN g 537 " --> pdb=" O ALA g 533 " (cutoff:3.500A) Processing helix chain 'g' and resid 563 through 583 removed outlier: 3.837A pdb=" N VAL g 583 " --> pdb=" O LEU g 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 3.770A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'G' and resid 60 through 67 removed outlier: 3.569A pdb=" N ARG G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 4.062A pdb=" N LYS G 76 " --> pdb=" O HIS G 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.703A pdb=" N VAL G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 117 through 140 Processing helix chain 'G' and resid 149 through 160 removed outlier: 3.988A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER G 158 " --> pdb=" O LEU G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.041A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.780A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 183 " --> pdb=" O VAL G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 Processing helix chain 'G' and resid 278 through 288 removed outlier: 3.814A 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: 3.683A pdb=" N HIS G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.536A pdb=" N ASN G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN G 326 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG G 327 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 removed outlier: 3.611A pdb=" N LEU G 343 " --> pdb=" O VAL G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 468 removed outlier: 3.749A pdb=" N ARG G 454 " --> pdb=" O ASN G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 493 removed outlier: 3.626A pdb=" N LYS G 486 " --> pdb=" O ALA G 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS G 492 " --> pdb=" O ALA G 488 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN G 493 " --> pdb=" O GLU G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 510 removed outlier: 3.717A pdb=" N ALA G 504 " --> pdb=" O TRP G 500 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL G 505 " --> pdb=" O PRO G 501 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA G 506 " --> pdb=" O TYR G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 521 Processing helix chain 'G' and resid 523 through 537 removed outlier: 3.546A pdb=" N SER G 529 " --> pdb=" O ILE G 525 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 582 removed outlier: 3.532A pdb=" N GLU G 575 " --> pdb=" O LYS G 571 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 580 " --> pdb=" O SER G 576 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 41 removed outlier: 3.803A pdb=" N VAL h 36 " --> pdb=" O ALA h 32 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU h 40 " --> pdb=" O VAL h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 72 Processing helix chain 'h' and resid 77 through 94 removed outlier: 3.627A pdb=" N LYS h 81 " --> pdb=" O HIS h 77 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR h 82 " --> pdb=" O PRO h 78 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 112 removed outlier: 3.775A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU h 108 " --> pdb=" O LEU h 104 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET h 109 " --> pdb=" O ALA h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 118 removed outlier: 3.727A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU h 118 " --> pdb=" O PRO h 114 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.676A pdb=" N ILE h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG h 130 " --> pdb=" O MET h 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA h 132 " --> pdb=" O GLY h 128 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU h 135 " --> pdb=" O LYS h 131 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU h 138 " --> pdb=" O SER h 134 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU h 142 " --> pdb=" O GLU h 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 153 through 166 removed outlier: 3.767A pdb=" N LEU h 158 " --> pdb=" O GLY h 154 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG h 163 " --> pdb=" O GLU h 159 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA h 165 " --> pdb=" O CYS h 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 188 removed outlier: 3.623A pdb=" N PHE h 178 " --> pdb=" O ASN h 174 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP h 184 " --> pdb=" O LYS h 180 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL h 186 " --> pdb=" O CYS h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 195 through 197 No H-bonds generated for 'chain 'h' and resid 195 through 197' Processing helix chain 'h' and resid 208 through 212 removed outlier: 3.673A pdb=" N GLU h 211 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 4.050A 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 265 through 289 removed outlier: 3.995A pdb=" N ALA h 269 " --> pdb=" O GLU h 265 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS h 281 " --> pdb=" O LEU h 277 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 removed outlier: 3.644A pdb=" N THR h 304 " --> pdb=" O GLY h 300 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA h 308 " --> pdb=" O THR h 304 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP h 309 " --> pdb=" O GLN h 305 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG h 310 " --> pdb=" O PHE h 306 " (cutoff:3.500A) Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.618A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) removed outlier: 3.734A 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: 3.612A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA h 396 " --> pdb=" O SER h 392 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU h 404 " --> pdb=" O VAL h 400 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN h 405 " --> pdb=" O LYS h 401 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 430 removed outlier: 3.564A pdb=" N SER h 421 " --> pdb=" O GLU h 417 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU h 424 " --> pdb=" O VAL h 420 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP h 426 " --> pdb=" O LYS h 422 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 Processing helix chain 'h' and resid 447 through 458 removed outlier: 3.544A pdb=" N ALA h 457 " --> pdb=" O LEU h 453 " (cutoff:3.500A) Processing helix chain 'h' and resid 460 through 472 removed outlier: 3.611A pdb=" N LEU h 465 " --> pdb=" O ALA h 461 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN h 466 " --> pdb=" O ILE h 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG h 469 " --> pdb=" O LEU h 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU h 470 " --> pdb=" O ASN h 466 " (cutoff:3.500A) removed outlier: 4.236A 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: 3.539A pdb=" N ASN H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.947A pdb=" N ASP H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 94 removed outlier: 3.624A pdb=" N LEU H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 112 removed outlier: 3.912A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.871A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.504A pdb=" N TYR H 129 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS H 131 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 166 removed outlier: 4.416A pdb=" N LEU H 158 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 4.115A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 186 " --> pdb=" O CYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 208 through 212 removed outlier: 3.582A pdb=" N GLU H 211 " --> pdb=" O ALA H 208 " (cutoff:3.500A) removed outlier: 3.622A 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 263 through 289 removed outlier: 3.613A pdb=" N TYR H 267 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN H 268 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL H 271 " --> pdb=" O TYR H 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 278 " --> pdb=" O GLU H 274 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS H 281 " --> pdb=" O LEU H 277 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 289 " --> pdb=" O VAL H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 310 removed outlier: 3.824A pdb=" N THR H 304 " --> pdb=" O GLY H 300 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP H 309 " --> pdb=" O GLN H 305 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG H 310 " --> pdb=" O PHE H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 331 removed outlier: 3.784A 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 382 through 406 removed outlier: 3.562A pdb=" N GLU H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU H 404 " --> pdb=" O VAL H 400 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN H 405 " --> pdb=" O LYS H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 429 removed outlier: 3.786A pdb=" N SER H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 424 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 446 Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 460 through 473 removed outlier: 3.545A pdb=" N ILE H 464 " --> pdb=" O ASP H 460 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN H 466 " --> pdb=" O ILE H 462 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA H 471 " --> pdb=" O LYS H 467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER H 473 " --> pdb=" O ARG H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 491 through 495 Processing helix chain 'H' and resid 500 through 519 removed outlier: 3.614A pdb=" N LEU H 507 " --> pdb=" O LYS H 503 " (cutoff:3.500A) Processing helix chain 'q' and resid 28 through 44 removed outlier: 3.602A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR q 44 " --> pdb=" O GLN q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.902A pdb=" N MET q 71 " --> pdb=" O ASP q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 94 removed outlier: 4.020A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 114 removed outlier: 3.782A pdb=" N MET q 104 " --> pdb=" O THR q 100 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) Processing helix chain 'q' and resid 114 through 121 Processing helix chain 'q' and resid 123 through 145 removed outlier: 3.511A pdb=" N ILE q 127 " --> pdb=" O SER q 123 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP q 143 " --> pdb=" O LEU q 139 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU q 144 " --> pdb=" O LYS q 140 " (cutoff:3.500A) Processing helix chain 'q' and resid 155 through 168 removed outlier: 3.537A pdb=" N LEU q 160 " --> pdb=" O LYS q 156 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS q 161 " --> pdb=" O ASN q 157 " (cutoff:3.500A) removed outlier: 4.058A 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 176 through 190 removed outlier: 4.387A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU q 181 " --> pdb=" O ILE q 177 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL q 189 " --> pdb=" O ALA q 185 " (cutoff:3.500A) Processing helix chain 'q' and resid 216 through 220 removed outlier: 3.800A pdb=" N ASN q 219 " --> pdb=" O SER q 216 " (cutoff:3.500A) Processing helix chain 'q' and resid 269 through 293 removed outlier: 3.624A pdb=" N MET q 273 " --> pdb=" O ASN q 269 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU q 274 " --> pdb=" O ALA q 270 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU q 290 " --> pdb=" O ALA q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 306 through 316 removed outlier: 3.562A pdb=" N HIS q 311 " --> pdb=" O GLU q 307 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR q 312 " --> pdb=" O LEU q 308 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU q 313 " --> pdb=" O ALA q 309 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR q 316 " --> pdb=" O TYR q 312 " (cutoff:3.500A) Processing helix chain 'q' and resid 325 through 334 removed outlier: 3.945A pdb=" N LEU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS q 333 " --> pdb=" O LEU q 329 " (cutoff:3.500A) removed outlier: 4.135A 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 409 removed outlier: 3.502A pdb=" N ASP q 396 " --> pdb=" O ASN q 392 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU q 398 " --> pdb=" O LEU q 394 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG q 399 " --> pdb=" O ASP q 395 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL q 408 " --> pdb=" O GLY q 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS q 409 " --> pdb=" O VAL q 405 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 441 removed outlier: 3.539A pdb=" N ILE q 428 " --> pdb=" O GLY q 424 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER q 432 " --> pdb=" O ILE q 428 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG q 433 " --> pdb=" O GLU q 429 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS q 436 " --> pdb=" O SER q 432 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR q 437 " --> pdb=" O ARG q 433 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU q 439 " --> pdb=" O THR q 435 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG q 440 " --> pdb=" O LYS q 436 " (cutoff:3.500A) Processing helix chain 'q' and resid 444 through 455 removed outlier: 4.260A pdb=" N ALA q 448 " --> pdb=" O LEU q 444 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 467 Processing helix chain 'q' and resid 470 through 483 Proline residue: q 476 - end of helix Processing helix chain 'q' and resid 511 through 516 removed outlier: 3.878A pdb=" N GLU q 515 " --> pdb=" O ASP q 511 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 539 removed outlier: 3.541A pdb=" N GLU q 533 " --> pdb=" O ASN q 529 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL q 538 " --> pdb=" O ALA q 534 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU q 539 " --> pdb=" O ALA q 535 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 44 removed outlier: 3.708A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 75 Processing helix chain 'Q' and resid 79 through 96 removed outlier: 3.732A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP Q 95 " --> pdb=" O GLN Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 114 removed outlier: 3.701A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN Q 112 " --> pdb=" O GLY Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 121 Processing helix chain 'Q' and resid 123 through 143 removed outlier: 3.941A pdb=" N ASP Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 168 removed outlier: 3.962A pdb=" N LYS Q 161 " --> pdb=" O ASN Q 157 " (cutoff:3.500A) removed outlier: 4.081A 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 176 through 190 removed outlier: 4.365A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Q 184 " --> pdb=" O GLU Q 180 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA Q 185 " --> pdb=" O LEU Q 181 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER Q 187 " --> pdb=" O SER Q 183 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS Q 188 " --> pdb=" O GLU Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 216 through 220 Processing helix chain 'Q' and resid 270 through 294 removed outlier: 4.024A pdb=" N LEU Q 274 " --> pdb=" O ALA Q 270 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP Q 275 " --> pdb=" O GLN Q 271 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS Q 282 " --> pdb=" O LYS Q 278 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU Q 290 " --> pdb=" O ALA Q 286 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Q 291 " --> pdb=" O MET Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 316 removed outlier: 3.829A pdb=" N TYR Q 312 " --> pdb=" O LEU Q 308 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN Q 314 " --> pdb=" O LEU Q 310 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 333 removed outlier: 3.947A pdb=" N LEU Q 329 " --> pdb=" O SER Q 325 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG Q 330 " --> pdb=" O LYS Q 326 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS Q 333 " --> pdb=" O LEU Q 329 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 352 Processing helix chain 'Q' and resid 390 through 409 removed outlier: 3.642A pdb=" N ASP Q 396 " --> pdb=" O ASN Q 392 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA Q 406 " --> pdb=" O ASP Q 402 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA Q 407 " --> pdb=" O ASP Q 403 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL Q 408 " --> pdb=" O GLY Q 404 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS Q 409 " --> pdb=" O VAL Q 405 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 412 No H-bonds generated for 'chain 'Q' and resid 410 through 412' Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.779A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU Q 429 " --> pdb=" O ALA Q 425 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR Q 437 " --> pdb=" O ARG Q 433 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU Q 439 " --> pdb=" O THR Q 435 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 445 through 455 removed outlier: 3.528A pdb=" N ALA Q 453 " --> pdb=" O ILE Q 449 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Q 454 " --> pdb=" O LYS Q 450 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 467 Processing helix chain 'Q' and resid 473 through 483 removed outlier: 3.822A pdb=" N TYR Q 479 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA Q 480 " --> pdb=" O PRO Q 476 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA Q 481 " --> pdb=" O ASN Q 477 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS Q 482 " --> pdb=" O LEU Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 511 through 516 removed outlier: 3.964A pdb=" N GLU Q 515 " --> pdb=" O ASP Q 511 " (cutoff:3.500A) Processing helix chain 'Q' and resid 521 through 541 removed outlier: 3.577A pdb=" N PHE Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN Q 529 " --> pdb=" O LYS Q 525 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL Q 538 " --> pdb=" O ALA Q 534 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 34 removed outlier: 3.529A pdb=" N VAL z 32 " --> pdb=" O GLY z 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 35 through 37 No H-bonds generated for 'chain 'z' and resid 35 through 37' Processing helix chain 'z' and resid 58 through 64 removed outlier: 3.600A pdb=" N LEU z 62 " --> pdb=" O ASP z 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 70 through 87 removed outlier: 3.660A pdb=" N VAL z 74 " --> pdb=" O SER z 70 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE z 76 " --> pdb=" O THR z 72 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA z 82 " --> pdb=" O ARG z 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU z 85 " --> pdb=" O ALA z 81 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 110 removed outlier: 3.625A pdb=" N LEU z 102 " --> pdb=" O VAL z 98 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG z 107 " --> pdb=" O ARG z 103 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 removed outlier: 3.523A pdb=" N ILE z 118 " --> pdb=" O HIS z 114 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE z 122 " --> pdb=" O ILE z 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS z 131 " --> pdb=" O LYS z 127 " (cutoff:3.500A) removed outlier: 3.667A 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: 4.241A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER z 156 " --> pdb=" O GLN z 152 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER z 157 " --> pdb=" O VAL z 153 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.552A pdb=" N VAL z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU z 179 " --> pdb=" O THR z 175 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 190 through 194 removed outlier: 3.531A pdb=" N MET z 193 " --> pdb=" O ASP z 190 " (cutoff:3.500A) Processing helix chain 'z' and resid 203 through 207 removed outlier: 3.617A pdb=" N THR z 207 " --> pdb=" O PRO z 204 " (cutoff:3.500A) Processing helix chain 'z' and resid 255 through 284 removed outlier: 3.773A pdb=" N ASP z 260 " --> pdb=" O ALA z 256 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS z 261 " --> pdb=" O ASP z 257 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU z 266 " --> pdb=" O LEU z 262 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS z 273 " --> pdb=" O PHE z 269 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE z 277 " --> pdb=" O LYS z 273 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS z 281 " --> pdb=" O ILE z 277 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN z 282 " --> pdb=" O ILE z 278 " (cutoff:3.500A) Processing helix chain 'z' and resid 302 through 312 removed outlier: 3.710A pdb=" N LEU z 306 " --> pdb=" O ASP z 302 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP z 307 " --> pdb=" O PRO z 303 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL z 308 " --> pdb=" O MET z 304 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS z 311 " --> pdb=" O ASP z 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS z 312 " --> pdb=" O VAL z 308 " (cutoff:3.500A) Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.763A pdb=" N GLU z 326 " --> pdb=" O ARG z 322 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG z 327 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN z 329 " --> pdb=" O MET z 325 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 339 through 343 Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.871A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA z 394 " --> pdb=" O GLN z 390 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG z 400 " --> pdb=" O ARG z 396 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU z 406 " --> pdb=" O VAL z 402 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 4.185A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN z 432 " --> pdb=" O SER z 428 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.264A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU z 451 " --> pdb=" O PHE z 447 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 462 removed outlier: 3.619A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER z 462 " --> pdb=" O LEU z 458 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.670A pdb=" N MET z 472 " --> pdb=" O ASP z 468 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL z 473 " --> pdb=" O VAL z 469 " (cutoff:3.500A) removed outlier: 3.561A 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: 3.658A pdb=" N ASN z 515 " --> pdb=" O ARG z 511 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE z 517 " --> pdb=" O LEU z 513 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU z 528 " --> pdb=" O ALA z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 34 removed outlier: 3.807A pdb=" N VAL Z 21 " --> pdb=" O ALA Z 17 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL Z 32 " --> pdb=" O GLY Z 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Z 33 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 41 removed outlier: 3.536A pdb=" N LYS Z 40 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 removed outlier: 3.758A pdb=" N THR Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 87 removed outlier: 3.819A pdb=" N ALA Z 82 " --> pdb=" O ARG Z 78 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.572A pdb=" N VAL Z 95 " --> pdb=" O THR Z 91 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG Z 107 " --> pdb=" O ARG Z 103 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN Z 110 " --> pdb=" O HIS Z 106 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 removed outlier: 3.515A pdb=" N PHE Z 122 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS Z 131 " --> pdb=" O LYS Z 127 " (cutoff:3.500A) removed outlier: 3.547A 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: 4.076A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG Z 155 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER Z 156 " --> pdb=" O GLN Z 152 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER Z 157 " --> pdb=" O VAL Z 153 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS Z 161 " --> pdb=" O SER Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 182 Proline residue: Z 172 - end of helix removed outlier: 3.708A pdb=" N VAL Z 178 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU Z 179 " --> pdb=" O THR Z 175 " (cutoff:3.500A) removed outlier: 4.103A 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: 3.524A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS Z 261 " --> pdb=" O ASP Z 257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Z 263 " --> pdb=" O ARG Z 259 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS Z 276 " --> pdb=" O ALA Z 272 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE Z 277 " --> pdb=" O LYS Z 273 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN Z 282 " --> pdb=" O ILE Z 278 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL Z 284 " --> pdb=" O LEU Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 312 removed outlier: 3.521A pdb=" N LEU Z 306 " --> pdb=" O ASP Z 302 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL Z 308 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS Z 311 " --> pdb=" O ASP Z 307 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 333 removed outlier: 3.509A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN Z 329 " --> pdb=" O MET Z 325 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 339 through 343 Processing helix chain 'Z' and resid 384 through 408 removed outlier: 3.557A pdb=" N LEU Z 388 " --> pdb=" O THR Z 384 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP Z 393 " --> pdb=" O ALA Z 389 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA Z 394 " --> pdb=" O GLN Z 390 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU Z 406 " --> pdb=" O VAL Z 402 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.819A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) Processing helix chain 'Z' and resid 439 through 451 removed outlier: 4.281A pdb=" N GLY Z 443 " --> pdb=" O LYS Z 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU Z 451 " --> pdb=" O PHE Z 447 " (cutoff:3.500A) Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.717A pdb=" N VAL Z 459 " --> pdb=" O PRO Z 455 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 484 removed outlier: 3.663A pdb=" N VAL Z 469 " --> pdb=" O ASP Z 465 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU Z 470 " --> pdb=" O PRO Z 466 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP Z 479 " --> pdb=" O ASP Z 475 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN Z 481 " --> pdb=" O LEU Z 477 " (cutoff:3.500A) removed outlier: 3.811A 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: 3.516A pdb=" N THR Z 518 " --> pdb=" O ARG Z 514 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 19 through 21 removed outlier: 3.993A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS d 46 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 60 through 63 removed outlier: 3.672A pdb=" N THR a 61 " --> pdb=" O LEU a 53 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL g 587 " --> pdb=" O MET a 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 204 through 208 removed outlier: 5.691A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER a 384 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 4.120A 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 223 through 224 removed outlier: 3.599A pdb=" N LEU a 373 " --> pdb=" O VAL a 362 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL a 362 " --> pdb=" O LEU a 373 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL a 361 " --> pdb=" O ILE a 237 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE a 237 " --> pdb=" O VAL a 361 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 244 through 246 removed outlier: 3.508A pdb=" N VAL a 296 " --> pdb=" O MET a 316 " (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 500 through 503 removed outlier: 3.783A pdb=" N VAL a 510 " --> pdb=" O GLY a 501 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS a 508 " --> pdb=" O ASP a 503 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.161A pdb=" N ILE A 541 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N MET D 47 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 48 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 63 removed outlier: 4.421A pdb=" N THR A 63 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS A 51 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL G 587 " --> pdb=" O MET A 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 204 through 207 removed outlier: 6.065A pdb=" N ASN A 204 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 387 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 219 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 222 through 224 removed outlier: 4.055A pdb=" N LYS A 375 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU A 360 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.569A pdb=" N THR A 298 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'b' and resid 56 through 57 removed outlier: 4.061A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP b 43 " --> pdb=" O ILE d 521 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP d 523 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU b 45 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA d 525 " --> pdb=" O LEU b 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 193 through 199 removed outlier: 6.299A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY b 371 " --> pdb=" O ILE b 196 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE b 198 " --> pdb=" O GLY b 371 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL b 368 " --> pdb=" O PHE b 207 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE b 207 " --> pdb=" O VAL b 368 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 226 through 229 removed outlier: 6.832A pdb=" N GLU b 227 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL b 342 " --> pdb=" O GLU b 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 231 through 233 removed outlier: 6.913A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 400 through 401 Processing sheet with id=AC1, first strand: chain 'b' and resid 470 through 472 removed outlier: 3.629A pdb=" N ALA b 480 " --> pdb=" O GLY b 471 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 511 through 516 removed outlier: 6.991A pdb=" N ASP e 71 " --> pdb=" O VAL b 511 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN b 513 " --> pdb=" O ASP e 71 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE e 73 " --> pdb=" O ASN b 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.844A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 525 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 193 through 199 removed outlier: 6.007A pdb=" N GLN B 194 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU B 369 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 196 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY B 371 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 198 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 368 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 207 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 225 through 229 removed outlier: 6.925A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AC7, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AC8, first strand: chain 'B' and resid 470 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 514 through 516 Processing sheet with id=AD1, first strand: chain 'd' and resid 196 through 200 removed outlier: 5.952A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU d 208 " --> pdb=" O VAL d 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.597A pdb=" N GLU d 351 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 236 through 237 removed outlier: 3.868A pdb=" N GLN d 289 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP d 315 " --> pdb=" O ILE d 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 410 through 411 Processing sheet with id=AD5, first strand: chain 'D' and resid 194 through 200 removed outlier: 6.263A pdb=" N ARG D 195 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE D 379 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 197 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY D 381 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS D 199 " --> pdb=" O GLY D 381 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU D 208 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 229 through 232 removed outlier: 6.725A pdb=" N ASP D 348 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 285 through 289 removed outlier: 3.916A pdb=" N ASP D 315 " --> pdb=" O ILE D 288 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 410 through 411 removed outlier: 3.720A pdb=" N ILE D 411 " --> pdb=" O GLN D 499 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 166 through 167 removed outlier: 3.582A pdb=" N VAL e 440 " --> pdb=" O ASP e 529 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP e 529 " --> pdb=" O VAL e 440 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 224 through 225 removed outlier: 6.509A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR e 405 " --> pdb=" O ILE e 240 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE e 240 " --> pdb=" O THR e 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'e' and resid 229 through 230 removed outlier: 6.357A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'e' and resid 342 through 343 removed outlier: 6.907A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA e 270 " --> pdb=" O ILE e 322 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL e 363 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE e 271 " --> pdb=" O VAL e 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'e' and resid 380 through 382 Processing sheet with id=AE5, first strand: chain 'e' and resid 551 through 556 removed outlier: 6.548A pdb=" N ASP h 50 " --> pdb=" O ILE e 551 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN e 553 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE h 53 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR h 61 " --> pdb=" O ILE h 53 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 166 through 167 removed outlier: 3.855A pdb=" N VAL E 440 " --> pdb=" O ASP E 529 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 224 through 228 removed outlier: 6.813A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 342 through 343 removed outlier: 5.918A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 320 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 379 through 382 removed outlier: 4.322A pdb=" N ARG E 379 " --> pdb=" O GLU E 396 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 551 through 556 removed outlier: 4.012A pdb=" N ILE E 551 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU H 52 " --> pdb=" O ILE E 551 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN E 553 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL H 54 " --> pdb=" O ASN E 553 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE E 555 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'g' and resid 55 through 56 removed outlier: 3.748A pdb=" N LEU g 48 " --> pdb=" O VAL g 56 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU g 45 " --> pdb=" O CYS z 530 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU z 532 " --> pdb=" O LEU g 45 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET g 47 " --> pdb=" O GLU z 532 " (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: 6.823A pdb=" N GLU g 207 " --> pdb=" O LEU g 441 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 245 through 246 removed outlier: 3.710A pdb=" N LEU g 246 " --> pdb=" O ILE g 296 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 542 through 544 removed outlier: 3.612A pdb=" N GLY g 543 " --> pdb=" O VAL g 552 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL g 552 " --> pdb=" O GLY g 543 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'G' and resid 55 through 56 removed outlier: 4.127A pdb=" N VAL G 56 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU G 48 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU G 45 " --> pdb=" O CYS Z 530 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU Z 532 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET G 47 " --> pdb=" O GLU Z 532 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU Z 534 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 207 through 209 removed outlier: 3.677A pdb=" N GLU G 207 " --> pdb=" O ILE G 439 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 441 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG G 218 " --> pdb=" O MET G 440 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AG1, first strand: chain 'G' and resid 243 through 245 Processing sheet with id=AG2, first strand: chain 'G' and resid 472 through 473 Processing sheet with id=AG3, first strand: chain 'G' and resid 542 through 544 removed outlier: 3.604A pdb=" N VAL G 552 " --> pdb=" O GLY G 543 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AG5, first strand: chain 'h' and resid 199 through 205 removed outlier: 5.959A pdb=" N GLY h 200 " --> pdb=" O LEU h 376 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU h 378 " --> pdb=" O GLY h 200 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS h 202 " --> pdb=" O LEU h 378 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLY h 380 " --> pdb=" O LYS h 202 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE h 204 " --> pdb=" O GLY h 380 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 235 through 236 removed outlier: 4.011A pdb=" N PHE h 352 " --> pdb=" O PHE h 236 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU h 353 " --> pdb=" O LEU h 364 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU h 364 " --> pdb=" O GLU h 353 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET h 355 " --> pdb=" O TYR h 362 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 241 through 243 removed outlier: 6.703A pdb=" N LEU h 242 " --> pdb=" O LEU h 294 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.864A pdb=" N GLY h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'h' and resid 523 through 525 removed outlier: 7.002A pdb=" N ILE h 524 " --> pdb=" O VAL q 56 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS q 53 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 145 through 146 removed outlier: 3.680A pdb=" N VAL H 145 " --> pdb=" O ILE H 409 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE H 409 " --> pdb=" O VAL H 145 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 199 through 204 removed outlier: 6.549A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 313 through 315 removed outlier: 6.476A pdb=" N VAL H 293 " --> pdb=" O ALA H 315 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY H 347 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 351 through 355 removed outlier: 3.963A pdb=" N GLU H 353 " --> pdb=" O LEU H 364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU H 364 " --> pdb=" O GLU H 353 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 479 through 481 removed outlier: 3.699A pdb=" N GLY H 489 " --> pdb=" O GLY H 480 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 523 through 525 removed outlier: 3.926A pdb=" N LYS Q 53 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR Q 65 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 207 through 213 removed outlier: 6.784A pdb=" N ARG q 208 " --> pdb=" O ILE q 384 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU q 386 " --> pdb=" O ARG q 208 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL q 210 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY q 388 " --> pdb=" O VAL q 210 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE q 212 " --> pdb=" O GLY q 388 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR q 383 " --> pdb=" O ILE q 223 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE q 223 " --> pdb=" O THR q 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'q' and resid 246 through 250 removed outlier: 6.462A pdb=" N LYS q 246 " --> pdb=" O CYS q 298 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL q 300 " --> pdb=" O LYS q 246 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA q 248 " --> pdb=" O VAL q 300 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'q' and resid 360 through 363 Processing sheet with id=AI1, first strand: chain 'q' and resid 419 through 421 removed outlier: 3.526A pdb=" N LEU q 420 " --> pdb=" O ASP q 519 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP q 519 " --> pdb=" O LEU q 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'q' and resid 544 through 546 removed outlier: 6.152A pdb=" N ILE q 545 " --> pdb=" O VAL z 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU z 46 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS z 54 " --> pdb=" O LEU z 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'Q' and resid 207 through 213 removed outlier: 3.695A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR Q 221 " --> pdb=" O ILE Q 385 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 319 through 322 removed outlier: 7.111A pdb=" N GLU Q 297 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU Q 321 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE Q 299 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 360 through 363 Processing sheet with id=AI6, first strand: chain 'Q' and resid 419 through 421 Processing sheet with id=AI7, first strand: chain 'Q' and resid 545 through 546 removed outlier: 3.516A pdb=" N VAL Z 47 " --> pdb=" O ILE Q 545 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AI9, first strand: chain 'z' and resid 195 through 199 removed outlier: 6.192A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'z' and resid 214 through 215 removed outlier: 3.868A pdb=" N THR z 365 " --> pdb=" O LEU z 215 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'z' and resid 227 through 228 Processing sheet with id=AJ3, first strand: chain 'z' and resid 232 through 233 removed outlier: 3.912A pdb=" N VAL z 233 " --> pdb=" O GLY z 349 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'z' and resid 294 through 295 Processing sheet with id=AJ5, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AJ6, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AJ7, first strand: chain 'Z' and resid 195 through 199 removed outlier: 5.681A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE Z 380 " --> pdb=" O GLU Z 195 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N MET Z 197 " --> pdb=" O ILE Z 380 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 227 through 228 Processing sheet with id=AJ9, first strand: chain 'Z' and resid 231 through 232 removed outlier: 3.596A pdb=" N VAL Z 294 " --> pdb=" O TYR Z 232 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Z 315 " --> pdb=" O PHE Z 293 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 235 through 236 removed outlier: 6.405A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'Z' and resid 490 through 491 2645 hydrogen bonds defined for protein. 7647 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: 21.80 Time building geometry restraints manager: 19.90 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: 20966 1.34 - 1.46: 11480 1.46 - 1.58: 29660 1.58 - 1.70: 0 1.70 - 1.81: 512 Bond restraints: 62618 Sorted by residual: bond pdb=" C GLU q 231 " pdb=" N PRO q 232 " ideal model delta sigma weight residual 1.334 1.439 -0.105 2.34e-02 1.83e+03 2.03e+01 bond pdb=" C ALA q 346 " pdb=" N PRO q 347 " ideal model delta sigma weight residual 1.334 1.433 -0.099 2.34e-02 1.83e+03 1.80e+01 bond pdb=" C SER g 469 " pdb=" N PRO g 470 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.01e+00 bond pdb=" CA ARG Z 14 " pdb=" C ARG Z 14 " ideal model delta sigma weight residual 1.524 1.543 -0.019 9.50e-03 1.11e+04 4.17e+00 bond pdb=" C ARG Z 14 " pdb=" O ARG Z 14 " ideal model delta sigma weight residual 1.243 1.231 0.012 9.50e-03 1.11e+04 1.73e+00 ... (remaining 62613 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.01: 1249 107.01 - 113.77: 36756 113.77 - 120.52: 24724 120.52 - 127.27: 21344 127.27 - 134.02: 386 Bond angle restraints: 84459 Sorted by residual: angle pdb=" C LEU Z 13 " pdb=" CA LEU Z 13 " pdb=" CB LEU Z 13 " ideal model delta sigma weight residual 117.23 109.15 8.08 1.36e+00 5.41e-01 3.53e+01 angle pdb=" N ARG z 14 " pdb=" CA ARG z 14 " pdb=" C ARG z 14 " ideal model delta sigma weight residual 113.18 106.04 7.14 1.21e+00 6.83e-01 3.48e+01 angle pdb=" CA LEU Z 13 " pdb=" C LEU Z 13 " pdb=" N ARG Z 14 " ideal model delta sigma weight residual 119.98 115.83 4.15 8.50e-01 1.38e+00 2.39e+01 angle pdb=" N ARG Z 15 " pdb=" CA ARG Z 15 " pdb=" C ARG Z 15 " ideal model delta sigma weight residual 109.59 117.02 -7.43 1.61e+00 3.86e-01 2.13e+01 angle pdb=" N ILE Z 296 " pdb=" CA ILE Z 296 " pdb=" C ILE Z 296 " ideal model delta sigma weight residual 112.29 108.52 3.77 9.40e-01 1.13e+00 1.61e+01 ... (remaining 84454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 38294 15.98 - 31.96: 329 31.96 - 47.94: 208 47.94 - 63.92: 54 63.92 - 79.89: 3 Dihedral angle restraints: 38888 sinusoidal: 15564 harmonic: 23324 Sorted by residual: dihedral pdb=" CA ARG Z 14 " pdb=" C ARG Z 14 " pdb=" N ARG Z 15 " pdb=" CA ARG Z 15 " ideal model delta harmonic sigma weight residual -180.00 -151.86 -28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASP Z 16 " pdb=" C ASP Z 16 " pdb=" N ALA Z 17 " pdb=" CA ALA Z 17 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA HIS Q 494 " pdb=" C HIS Q 494 " pdb=" N LEU Q 495 " pdb=" CA LEU Q 495 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 38885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 6869 0.031 - 0.063: 2296 0.063 - 0.094: 465 0.094 - 0.126: 518 0.126 - 0.157: 18 Chirality restraints: 10166 Sorted by residual: chirality pdb=" CB ILE z 296 " pdb=" CA ILE z 296 " pdb=" CG1 ILE z 296 " pdb=" CG2 ILE z 296 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.16e-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 5.14e-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 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 10163 not shown) Planarity restraints: 10848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 372 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO D 373 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG d 372 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO d 373 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO d 373 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO d 373 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 225 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C ASN A 225 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN A 225 " -0.008 2.00e-02 2.50e+03 pdb=" N CYS A 226 " -0.007 2.00e-02 2.50e+03 ... (remaining 10845 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 9825 2.76 - 3.30: 57926 3.30 - 3.83: 92127 3.83 - 4.37: 109679 4.37 - 4.90: 189641 Nonbonded interactions: 459198 Sorted by model distance: nonbonded pdb=" O SER e 194 " pdb=" ND1 HIS e 197 " model vdw 2.228 2.520 nonbonded pdb=" OH TYR Z 182 " pdb=" O GLN Z 185 " model vdw 2.229 2.440 nonbonded pdb=" O LEU B 317 " pdb=" OG1 THR B 321 " model vdw 2.241 2.440 nonbonded pdb=" O MET d 432 " pdb=" OG SER E 500 " model vdw 2.242 2.440 nonbonded pdb=" O LEU h 198 " pdb=" OG1 THR h 373 " model vdw 2.246 2.440 ... (remaining 459193 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' selection = (chain 'a' and (resid 18 through 256 or resid 264 through 547)) } ncs_group { reference = chain 'B' selection = (chain 'b' and (resid 19 through 242 or resid 256 through 520)) } ncs_group { reference = (chain 'D' and (resid 17 through 479 or resid 493 through 528)) selection = (chain 'd' and (resid 17 through 245 or resid 266 through 528)) } ncs_group { reference = chain 'E' selection = (chain 'e' and (resid 43 through 284 or resid 301 through 560)) } ncs_group { reference = chain 'G' selection = (chain 'g' and (resid 18 through 253 or resid 277 through 590)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = (chain 'Q' and resid 27 through 549) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and resid 10 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: 0.630 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: 0.040 Extract box with map and model: 5.870 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 121.160 Find NCS groups from input model: 5.700 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 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 0.105 62618 Z= 0.091 Angle : 0.393 8.081 84459 Z= 0.227 Chirality : 0.039 0.157 10166 Planarity : 0.001 0.032 10848 Dihedral : 7.123 79.894 23768 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 0.01 % Allowed : 0.10 % 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: -3.61 (0.07), residues: 8065 helix: -3.55 (0.05), residues: 3734 sheet: -1.03 (0.18), residues: 622 loop : -1.14 (0.09), residues: 3709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 440 HIS 0.003 0.000 HIS z 106 PHE 0.016 0.001 PHE H 224 TYR 0.008 0.001 TYR Z 182 ARG 0.003 0.000 ARG Z 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2489 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2488 time to evaluate : 5.225 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 2489 average time/residue: 0.6339 time to fit residues: 2551.5272 Evaluate side-chains 1234 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1234 time to evaluate : 5.206 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 678 optimal weight: 0.0060 chunk 609 optimal weight: 0.0570 chunk 338 optimal weight: 8.9990 chunk 208 optimal weight: 0.6980 chunk 411 optimal weight: 8.9990 chunk 325 optimal weight: 20.0000 chunk 630 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 383 optimal weight: 6.9990 chunk 469 optimal weight: 10.0000 chunk 730 optimal weight: 0.1980 overall best weight: 0.9916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN a 465 ASN A 190 GLN A 465 ASN A 499 ASN b 84 GLN ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** b 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 112 GLN B 192 HIS d 85 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 GLN d 284 ASN d 289 GLN d 461 ASN ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN e 397 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 461 GLN ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 432 ASN E 466 GLN E 509 ASN E 536 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 188 GLN g 286 GLN g 519 ASN g 530 GLN ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN G 188 GLN G 465 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 HIS h 172 HIS h 505 ASN ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 ASN H 436 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 482 HIS Q 27 GLN Q 66 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS Q 314 ASN ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN z 30 GLN z 69 GLN z 201 HIS z 230 ASN ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 356 GLN ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN Z 106 HIS ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 430 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62618 Z= 0.192 Angle : 0.616 9.607 84459 Z= 0.322 Chirality : 0.045 0.284 10166 Planarity : 0.004 0.089 10848 Dihedral : 3.413 28.490 8568 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.00 % Rotamer: Outliers : 0.16 % Allowed : 2.63 % Favored : 97.21 % 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: -1.60 (0.08), residues: 8065 helix: -1.10 (0.07), residues: 3847 sheet: -0.65 (0.18), residues: 637 loop : -0.89 (0.09), residues: 3581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 275 HIS 0.014 0.001 HIS e 50 PHE 0.039 0.002 PHE h 492 TYR 0.040 0.001 TYR e 381 ARG 0.013 0.001 ARG d 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1572 time to evaluate : 5.527 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 revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 1580 average time/residue: 0.5875 time to fit residues: 1563.7020 Evaluate side-chains 1111 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1110 time to evaluate : 5.318 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5106 time to fit residues: 8.2761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 405 optimal weight: 0.7980 chunk 226 optimal weight: 0.5980 chunk 607 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 731 optimal weight: 10.0000 chunk 790 optimal weight: 0.8980 chunk 651 optimal weight: 5.9990 chunk 725 optimal weight: 0.9990 chunk 249 optimal weight: 0.1980 chunk 586 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 403 HIS ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 284 ASN e 106 GLN e 251 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 ASN ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 519 ASN g 530 GLN ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 568 GLN G 106 GLN G 503 GLN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 394 HIS h 406 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN H 268 GLN H 436 GLN q 132 ASN q 482 HIS ** q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 237 ASN z 298 GLN ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62618 Z= 0.170 Angle : 0.565 10.616 84459 Z= 0.291 Chirality : 0.044 0.282 10166 Planarity : 0.003 0.061 10848 Dihedral : 3.462 25.570 8568 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.09), residues: 8065 helix: -0.27 (0.08), residues: 3857 sheet: -0.48 (0.19), residues: 638 loop : -0.75 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 440 HIS 0.011 0.001 HIS e 197 PHE 0.024 0.001 PHE b 433 TYR 0.018 0.001 TYR e 381 ARG 0.017 0.001 ARG g 582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1413 time to evaluate : 5.309 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: 5 outliers final: 1 residues processed: 1416 average time/residue: 0.6002 time to fit residues: 1461.1732 Evaluate side-chains 1060 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1059 time to evaluate : 5.230 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4514 time to fit residues: 8.2898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 722 optimal weight: 10.0000 chunk 549 optimal weight: 10.0000 chunk 379 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 349 optimal weight: 5.9990 chunk 491 optimal weight: 9.9990 chunk 734 optimal weight: 0.0030 chunk 777 optimal weight: 0.7980 chunk 383 optimal weight: 7.9990 chunk 695 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 overall best weight: 4.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN a 90 GLN ** a 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS A 113 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 172 HIS b 228 ASN b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN B 420 GLN d 85 GLN d 116 HIS d 303 HIS D 112 ASN ** D 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 50 HIS e 132 GLN e 251 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS g 85 GLN ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 455 ASN ** g 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 505 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN H 436 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 188 HIS Q 27 GLN Q 39 HIS Q 66 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 329 GLN ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN ** Z 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 62618 Z= 0.297 Angle : 0.721 12.338 84459 Z= 0.375 Chirality : 0.047 0.290 10166 Planarity : 0.005 0.063 10848 Dihedral : 4.137 25.505 8568 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Rotamer: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.09), residues: 8065 helix: 0.02 (0.08), residues: 3951 sheet: -0.49 (0.19), residues: 667 loop : -0.81 (0.10), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 478 HIS 0.012 0.002 HIS E 353 PHE 0.029 0.002 PHE Q 327 TYR 0.025 0.002 TYR Q 437 ARG 0.022 0.001 ARG a 443 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1389 time to evaluate : 5.410 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 outliers start: 6 outliers final: 0 residues processed: 1393 average time/residue: 0.5810 time to fit residues: 1386.0617 Evaluate side-chains 1051 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1051 time to evaluate : 5.264 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 647 optimal weight: 0.9980 chunk 441 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 578 optimal weight: 20.0000 chunk 320 optimal weight: 1.9990 chunk 663 optimal weight: 30.0000 chunk 537 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 697 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN a 90 GLN ** a 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS a 403 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 HIS ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 436 GLN ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 251 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 553 ASN E 132 GLN E 353 HIS ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN ** g 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 276 GLN H 436 GLN ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 HIS Q 66 ASN ** Q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 391 GLN ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 142 ASN z 201 HIS ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 526 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 62618 Z= 0.189 Angle : 0.596 11.674 84459 Z= 0.307 Chirality : 0.044 0.253 10166 Planarity : 0.003 0.070 10848 Dihedral : 3.945 25.265 8568 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.09), residues: 8065 helix: 0.27 (0.08), residues: 3933 sheet: -0.41 (0.19), residues: 683 loop : -0.70 (0.10), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 478 HIS 0.011 0.001 HIS a 403 PHE 0.061 0.002 PHE e 150 TYR 0.027 0.002 TYR Q 496 ARG 0.012 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1381 time to evaluate : 5.387 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 outliers start: 2 outliers final: 0 residues processed: 1382 average time/residue: 0.5720 time to fit residues: 1356.6732 Evaluate side-chains 1048 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1048 time to evaluate : 5.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 261 optimal weight: 0.1980 chunk 699 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 456 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 777 optimal weight: 10.0000 chunk 645 optimal weight: 4.9990 chunk 360 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 408 optimal weight: 3.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 113 ASN a 380 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN e 251 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 499 GLN g 519 ASN ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 174 ASN ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 69 GLN z 201 HIS ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 110 GLN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 526 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 62618 Z= 0.165 Angle : 0.578 9.482 84459 Z= 0.296 Chirality : 0.044 0.240 10166 Planarity : 0.003 0.054 10848 Dihedral : 3.869 23.493 8568 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.09), residues: 8065 helix: 0.39 (0.08), residues: 3934 sheet: -0.39 (0.19), residues: 682 loop : -0.67 (0.10), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 478 HIS 0.012 0.001 HIS d 473 PHE 0.032 0.001 PHE Q 137 TYR 0.015 0.001 TYR a 480 ARG 0.010 0.000 ARG H 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1362 time to evaluate : 5.378 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 outliers start: 3 outliers final: 1 residues processed: 1365 average time/residue: 0.5794 time to fit residues: 1357.2820 Evaluate side-chains 1037 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1036 time to evaluate : 5.333 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5162 time to fit residues: 8.3220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 749 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 443 optimal weight: 6.9990 chunk 568 optimal weight: 10.0000 chunk 440 optimal weight: 5.9990 chunk 654 optimal weight: 0.0870 chunk 434 optimal weight: 0.9990 chunk 774 optimal weight: 10.0000 chunk 484 optimal weight: 7.9990 chunk 472 optimal weight: 20.0000 chunk 357 optimal weight: 3.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN a 380 HIS a 403 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 118 GLN b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** d 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN e 50 HIS ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 HIS g 499 GLN g 519 ASN ** g 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 235 HIS ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Q 39 HIS Q 92 GLN ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 GLN Z 526 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.7709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 62618 Z= 0.197 Angle : 0.608 11.454 84459 Z= 0.314 Chirality : 0.044 0.216 10166 Planarity : 0.003 0.070 10848 Dihedral : 3.982 23.188 8568 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.09), residues: 8065 helix: 0.44 (0.08), residues: 3947 sheet: -0.47 (0.19), residues: 737 loop : -0.67 (0.10), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 440 HIS 0.010 0.001 HIS a 403 PHE 0.052 0.002 PHE e 150 TYR 0.016 0.001 TYR Q 496 ARG 0.011 0.001 ARG H 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1334 time to evaluate : 5.321 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 outliers start: 3 outliers final: 0 residues processed: 1337 average time/residue: 0.5664 time to fit residues: 1306.8268 Evaluate side-chains 1043 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1043 time to evaluate : 5.293 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 479 optimal weight: 8.9990 chunk 309 optimal weight: 0.9980 chunk 462 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 492 optimal weight: 9.9990 chunk 527 optimal weight: 0.5980 chunk 383 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 609 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 ASN b 172 HIS b 375 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 474 GLN ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 499 GLN g 519 ASN g 530 GLN ** g 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 526 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.7840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 62618 Z= 0.167 Angle : 0.598 11.335 84459 Z= 0.303 Chirality : 0.044 0.239 10166 Planarity : 0.003 0.047 10848 Dihedral : 3.907 20.991 8568 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 0.03 % Allowed : 0.82 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.09), residues: 8065 helix: 0.50 (0.08), residues: 3920 sheet: -0.47 (0.19), residues: 691 loop : -0.63 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 560 HIS 0.012 0.001 HIS d 303 PHE 0.040 0.001 PHE Q 137 TYR 0.019 0.001 TYR Q 496 ARG 0.010 0.000 ARG H 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1333 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1331 time to evaluate : 5.317 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 outliers start: 2 outliers final: 1 residues processed: 1333 average time/residue: 0.5760 time to fit residues: 1331.7940 Evaluate side-chains 1049 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1048 time to evaluate : 5.287 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4397 time to fit residues: 8.1777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 704 optimal weight: 6.9990 chunk 742 optimal weight: 1.9990 chunk 677 optimal weight: 5.9990 chunk 722 optimal weight: 0.6980 chunk 434 optimal weight: 2.9990 chunk 314 optimal weight: 20.0000 chunk 567 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 652 optimal weight: 0.8980 chunk 682 optimal weight: 30.0000 chunk 719 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN ** b 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 GLN e 142 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 519 ASN g 530 GLN ** g 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 201 HIS Z 22 ASN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.8284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62618 Z= 0.197 Angle : 0.634 16.141 84459 Z= 0.325 Chirality : 0.045 0.285 10166 Planarity : 0.003 0.078 10848 Dihedral : 4.019 20.754 8568 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 0.01 % Allowed : 0.48 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.09), residues: 8065 helix: 0.46 (0.08), residues: 3930 sheet: -0.53 (0.19), residues: 688 loop : -0.66 (0.10), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 478 HIS 0.011 0.001 HIS h 472 PHE 0.043 0.002 PHE Q 137 TYR 0.025 0.001 TYR z 355 ARG 0.010 0.001 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1302 time to evaluate : 5.241 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 outliers start: 1 outliers final: 0 residues processed: 1303 average time/residue: 0.5732 time to fit residues: 1298.6734 Evaluate side-chains 1024 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1024 time to evaluate : 5.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 474 optimal weight: 30.0000 chunk 763 optimal weight: 1.9990 chunk 466 optimal weight: 7.9990 chunk 362 optimal weight: 9.9990 chunk 530 optimal weight: 20.0000 chunk 800 optimal weight: 4.9990 chunk 737 optimal weight: 6.9990 chunk 637 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 492 optimal weight: 7.9990 chunk 391 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 89 GLN ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 172 HIS ** b 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 353 HIS ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN E 353 HIS E 383 GLN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 499 GLN g 530 GLN ** g 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 298 GLN Z 22 ASN Z 312 HIS ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.8935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 62618 Z= 0.236 Angle : 0.677 15.115 84459 Z= 0.349 Chirality : 0.046 0.308 10166 Planarity : 0.004 0.116 10848 Dihedral : 4.327 28.251 8568 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.09), residues: 8065 helix: 0.26 (0.08), residues: 3945 sheet: -0.58 (0.20), residues: 665 loop : -0.74 (0.10), residues: 3455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 500 HIS 0.011 0.001 HIS d 303 PHE 0.046 0.002 PHE Q 137 TYR 0.038 0.002 TYR e 381 ARG 0.011 0.001 ARG H 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16130 Ramachandran restraints generated. 8065 Oldfield, 0 Emsley, 8065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1301 time to evaluate : 5.372 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 outliers start: 0 outliers final: 0 residues processed: 1301 average time/residue: 0.5751 time to fit residues: 1301.4005 Evaluate side-chains 1007 residues out of total 6843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1007 time to evaluate : 5.304 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 506 optimal weight: 6.9990 chunk 679 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 588 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 638 optimal weight: 0.8980 chunk 267 optimal weight: 20.0000 chunk 655 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 485 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 375 GLN b 447 ASN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 ASN d 259 GLN ** d 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 461 ASN e 142 HIS ** e 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 530 GLN ** g 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 HIS ** G 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 GLN ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 430 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.127108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.102697 restraints weight = 329043.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.103931 restraints weight = 258325.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.104529 restraints weight = 220420.314| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.8983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 62618 Z= 0.177 Angle : 0.637 11.464 84459 Z= 0.323 Chirality : 0.045 0.286 10166 Planarity : 0.004 0.171 10848 Dihedral : 4.155 25.421 8568 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 0.01 % Allowed : 0.22 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8065 helix: 0.37 (0.08), residues: 3940 sheet: -0.43 (0.20), residues: 648 loop : -0.69 (0.10), residues: 3477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 275 HIS 0.012 0.001 HIS d 473 PHE 0.035 0.002 PHE Q 137 TYR 0.025 0.001 TYR Q 496 ARG 0.029 0.001 ARG Q 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19716.41 seconds wall clock time: 344 minutes 23.51 seconds (20663.51 seconds total)