Starting phenix.real_space_refine on Sat Dec 9 02:12:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/12_2023/6krd_0756.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/12_2023/6krd_0756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/12_2023/6krd_0756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/12_2023/6krd_0756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/12_2023/6krd_0756.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6krd_0756/12_2023/6krd_0756.pdb" } resolution = 4.38 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= 0.027 sd= 0.214 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 311 5.16 5 C 38287 2.51 5 N 10565 2.21 5 O 11842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "z ARG 15": "NH1" <-> "NH2" Residue "Z TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 61005 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3851 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 10, 'TRANS': 500} Chain breaks: 1 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3865 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 10, 'TRANS': 502} Chain breaks: 1 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: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3824 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 10, 'TRANS': 493} 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: "D" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3255 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 4 Chain: "e" Number of atoms: 3839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3839 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 1 Chain: "E" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3786 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 15, 'TRANS': 479} Chain breaks: 1 Chain: "g" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3769 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 19, 'TRANS': 473} Chain breaks: 1 Chain: "G" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3518 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 18, 'TRANS': 443} Chain breaks: 2 Chain: "q" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3978 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 18, 'TRANS': 505} Chain: "Q" Number of atoms: 3974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3974 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 18, 'TRANS': 504} Chain: "z" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4030 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 15, 'TRANS': 508} Chain breaks: 1 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: "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} Time building chain proxies: 22.89, per 1000 atoms: 0.38 Number of scatterers: 61005 At special positions: 0 Unit cell: (199.018, 199.018, 192.428, 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 311 16.00 O 11842 8.00 N 10565 7.00 C 38287 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: 16.51 Conformation dependent library (CDL) restraints added in 8.0 seconds 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14896 Finding SS restraints... Secondary structure from input PDB file: 321 helices and 90 sheets defined 53.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'a' and resid 22 through 41 removed outlier: 3.754A pdb=" N ARG a 26 " --> pdb=" O GLY a 22 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 66 through 73 removed outlier: 3.905A pdb=" N LEU a 70 " --> pdb=" O GLY a 66 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER a 71 " --> pdb=" O ALA a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 94 removed outlier: 3.671A pdb=" N ILE a 82 " --> pdb=" O PRO a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 111 removed outlier: 3.737A pdb=" N VAL a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU a 109 " --> pdb=" O ALA a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 118 removed outlier: 3.924A pdb=" N LEU a 115 " --> pdb=" O ARG a 111 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS a 117 " --> pdb=" O ASN a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 144 removed outlier: 3.605A pdb=" N ILE a 137 " --> pdb=" O LEU a 133 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE a 139 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL a 143 " --> pdb=" O PHE a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 removed outlier: 4.375A pdb=" N ALA a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS a 161 " --> pdb=" O ILE a 157 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR a 162 " --> pdb=" O ASN a 158 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER a 163 " --> pdb=" O ILE a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 171 Processing helix chain 'a' and resid 172 through 187 removed outlier: 4.576A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL a 187 " --> pdb=" O ALA a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.557A pdb=" N SER a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 277 through 292 removed outlier: 3.586A pdb=" N VAL a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU a 283 " --> pdb=" O GLY a 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG a 284 " --> pdb=" O ILE a 280 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE a 288 " --> pdb=" O ARG a 284 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE a 289 " --> pdb=" O VAL a 285 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 313 removed outlier: 3.792A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU a 312 " --> pdb=" O LYS a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 324 through 334 removed outlier: 4.300A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.584A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG a 400 " --> pdb=" O ASP a 396 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS a 403 " --> pdb=" O GLU a 399 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL a 409 " --> pdb=" O SER a 405 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 437 removed outlier: 3.810A pdb=" N ILE a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP a 434 " --> pdb=" O ASN a 430 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN a 435 " --> pdb=" O ILE a 431 " (cutoff:3.500A) Processing helix chain 'a' and resid 443 through 454 removed outlier: 4.124A pdb=" N ALA a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 466 removed outlier: 3.630A pdb=" N ASN a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 removed outlier: 3.529A pdb=" N TYR a 480 " --> pdb=" O LYS a 476 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN a 485 " --> pdb=" O HIS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 511 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.709A pdb=" N ALA a 537 " --> pdb=" O GLU a 533 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE a 538 " --> pdb=" O ALA a 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 42 removed outlier: 3.889A pdb=" N ARG A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.819A pdb=" N ILE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.748A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.655A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.639A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.953A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 4.260A pdb=" N ASP A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.833A pdb=" N SER A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 removed outlier: 3.536A pdb=" N ILE A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 4.184A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.573A pdb=" N ARG A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.532A pdb=" N LEU A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 441 removed outlier: 3.673A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.619A pdb=" N SER A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.550A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 35 removed outlier: 4.402A pdb=" N ALA b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL b 29 " --> pdb=" O GLY b 25 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER b 35 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 67 removed outlier: 3.542A pdb=" N ILE b 63 " --> pdb=" O ASP b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 88 removed outlier: 3.912A pdb=" N ASN b 79 " --> pdb=" O LYS b 75 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE b 80 " --> pdb=" O VAL b 76 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU b 87 " --> pdb=" O VAL b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 105 removed outlier: 3.801A pdb=" N THR b 96 " --> pdb=" O THR b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 removed outlier: 3.552A pdb=" N ALA b 130 " --> pdb=" O LEU b 126 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS b 137 " --> pdb=" O ASP b 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA b 138 " --> pdb=" O ALA b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.537A pdb=" N PHE b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU b 151 " --> pdb=" O THR b 147 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU b 153 " --> pdb=" O PHE b 149 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE b 154 " --> pdb=" O ARG b 150 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA b 157 " --> pdb=" O LEU b 153 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR b 159 " --> pdb=" O HIS b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 168 removed outlier: 3.593A pdb=" N GLN b 168 " --> pdb=" O ILE b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 183 removed outlier: 3.725A pdb=" N PHE b 173 " --> pdb=" O ASP b 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA b 177 " --> pdb=" O PHE b 173 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE b 181 " --> pdb=" O ALA b 177 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU b 182 " --> pdb=" O THR b 178 " (cutoff:3.500A) removed outlier: 3.748A 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 259 removed outlier: 3.528A pdb=" N LEU b 258 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA b 259 " --> pdb=" O THR b 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 254 through 259' Processing helix chain 'b' and resid 259 through 278 removed outlier: 3.503A pdb=" N GLU b 267 " --> pdb=" O LYS b 263 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS b 270 " --> pdb=" O ARG b 266 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN b 271 " --> pdb=" O GLU b 267 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS b 272 " --> pdb=" O LYS b 268 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS b 275 " --> pdb=" O ASN b 271 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE b 276 " --> pdb=" O LYS b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 302 removed outlier: 3.673A pdb=" N ASP b 300 " --> pdb=" O GLN b 296 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU b 301 " --> pdb=" O LEU b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 311 through 322 removed outlier: 3.587A pdb=" N ALA b 318 " --> pdb=" O VAL b 314 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 397 removed outlier: 3.765A pdb=" N LEU b 377 " --> pdb=" O THR b 373 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP b 386 " --> pdb=" O ARG b 382 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL b 390 " --> pdb=" O ASP b 386 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS b 396 " --> pdb=" O SER b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 removed outlier: 3.699A pdb=" N SER b 412 " --> pdb=" O GLU b 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 438 removed outlier: 3.618A pdb=" N ARG b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA b 436 " --> pdb=" O ALA b 432 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG b 438 " --> pdb=" O ALA b 434 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 448 Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.520A pdb=" N LEU b 455 " --> pdb=" O ASP b 451 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER b 461 " --> pdb=" O SER b 457 " (cutoff:3.500A) removed outlier: 4.130A 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: 3.717A pdb=" N VAL b 507 " --> pdb=" O GLU b 503 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 removed outlier: 3.536A pdb=" N ALA B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.999A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 3.521A pdb=" N THR B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 138 removed outlier: 4.424A pdb=" N ILE B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.726A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.670A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.904A pdb=" N PHE B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 255 through 268 removed outlier: 4.197A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.621A pdb=" N SER B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.567A pdb=" N PHE B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.562A pdb=" N VAL B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 397 removed outlier: 3.745A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.619A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 removed outlier: 3.659A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.810A pdb=" N THR B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 464 removed outlier: 3.516A pdb=" N SER B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 510 removed outlier: 3.692A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 37 removed outlier: 3.552A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR d 37 " --> pdb=" O ASP d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 68 Processing helix chain 'd' and resid 76 through 89 removed outlier: 4.046A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 113 removed outlier: 3.846A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU d 108 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG d 109 " --> pdb=" O GLY d 105 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU d 110 " --> pdb=" O ALA d 106 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.531A pdb=" N ILE d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 3.595A pdb=" N ALA d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 161 No H-bonds generated for 'chain 'd' and resid 159 through 161' Processing helix chain 'd' and resid 166 through 183 Proline residue: d 172 - end of helix removed outlier: 3.715A pdb=" N LYS d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP d 183 " --> pdb=" O LEU d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 194 removed outlier: 3.828A pdb=" N ASP d 193 " --> pdb=" O ASP d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 267 through 281 removed outlier: 3.676A pdb=" N ASN d 273 " --> pdb=" O ALA d 269 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE d 274 " --> pdb=" O TYR d 270 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE d 278 " --> pdb=" O ILE d 274 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA d 281 " --> pdb=" O LYS d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 309 removed outlier: 4.019A pdb=" N HIS d 303 " --> pdb=" O ASP d 299 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE d 304 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS d 307 " --> pdb=" O HIS d 303 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU d 308 " --> pdb=" O PHE d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 328 removed outlier: 4.353A pdb=" N GLU d 322 " --> pdb=" O ARG d 318 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY d 327 " --> pdb=" O PHE d 323 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU d 328 " --> pdb=" O LEU d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.767A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU d 389 " --> pdb=" O MET d 385 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP d 396 " --> pdb=" O ARG d 392 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE d 401 " --> pdb=" O ALA d 397 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU d 404 " --> pdb=" O VAL d 400 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL d 405 " --> pdb=" O ILE d 401 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS d 406 " --> pdb=" O ARG d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.683A pdb=" N SER d 422 " --> pdb=" O GLU d 418 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG d 424 " --> pdb=" O GLU d 420 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS d 427 " --> pdb=" O ARG d 423 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 432 No H-bonds generated for 'chain 'd' and resid 430 through 432' Processing helix chain 'd' and resid 435 through 447 removed outlier: 3.802A pdb=" N ILE d 439 " --> pdb=" O VAL d 435 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN d 441 " --> pdb=" O ALA d 437 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 removed outlier: 3.553A pdb=" N ALA d 458 " --> pdb=" O LEU d 454 " (cutoff:3.500A) Processing helix chain 'd' and resid 461 through 472 removed outlier: 3.592A pdb=" N LYS d 472 " --> pdb=" O GLU d 468 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 475 No H-bonds generated for 'chain 'd' and resid 473 through 475' Processing helix chain 'd' and resid 500 through 519 removed outlier: 4.080A pdb=" N SER d 504 " --> pdb=" O PRO d 500 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE d 508 " --> pdb=" O SER d 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.753A pdb=" N ARG D 21 " --> pdb=" O PRO D 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.551A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 113 removed outlier: 3.547A pdb=" N ILE D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.551A pdb=" N ILE D 120 " --> pdb=" O HIS D 116 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.158A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.816A pdb=" N SER D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.573A pdb=" N ALA D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 removed outlier: 3.535A pdb=" N HIS D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 4.572A pdb=" N GLU D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.935A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.736A pdb=" N ILE D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 434 through 447 removed outlier: 4.142A pdb=" N PHE D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP D 440 " --> pdb=" O GLN D 436 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.525A pdb=" N ALA D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.602A pdb=" N VAL D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.582A pdb=" N ILE D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing helix chain 'e' and resid 43 through 62 removed outlier: 3.662A pdb=" N LYS e 47 " --> pdb=" O GLY e 43 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU e 52 " --> pdb=" O LYS e 48 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE e 61 " --> pdb=" O VAL e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 93 Processing helix chain 'e' and resid 101 through 115 removed outlier: 4.154A pdb=" N VAL e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER e 110 " --> pdb=" O GLN e 106 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 removed outlier: 3.537A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU e 136 " --> pdb=" O GLN e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 3.628A pdb=" N ILE e 146 " --> pdb=" O HIS e 142 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP e 151 " --> pdb=" O ALA e 147 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU e 152 " --> pdb=" O ASN e 148 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER e 159 " --> pdb=" O LYS e 155 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS e 160 " --> pdb=" O LEU e 156 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 188 removed outlier: 3.649A pdb=" N LEU e 180 " --> pdb=" O PHE e 176 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS e 185 " --> pdb=" O LEU e 181 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR e 186 " --> pdb=" O ARG e 182 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 195 Processing helix chain 'e' and resid 196 through 211 removed outlier: 4.411A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET e 203 " --> pdb=" O ARG e 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA e 204 " --> pdb=" O PHE e 200 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL e 205 " --> pdb=" O ALA e 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA e 207 " --> pdb=" O MET e 203 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL e 208 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) Processing helix chain 'e' and resid 220 through 222 No H-bonds generated for 'chain 'e' and resid 220 through 222' Processing helix chain 'e' and resid 233 through 237 removed outlier: 3.767A pdb=" N ASP e 236 " --> pdb=" O SER e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 306 through 317 removed outlier: 3.631A pdb=" N ASP e 311 " --> pdb=" O LYS e 307 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 removed outlier: 3.774A pdb=" N LEU e 334 " --> pdb=" O GLU e 330 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU e 335 " --> pdb=" O ALA e 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN e 337 " --> pdb=" O HIS e 333 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN e 338 " --> pdb=" O LEU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 353 through 359 Processing helix chain 'e' and resid 412 through 436 removed outlier: 3.508A pdb=" N ARG e 421 " --> pdb=" O ASP e 417 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP e 436 " --> pdb=" O ASN e 432 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 458 removed outlier: 3.518A pdb=" N VAL e 448 " --> pdb=" O GLY e 444 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 477 removed outlier: 3.952A pdb=" N ALA e 468 " --> pdb=" O ILE e 464 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP e 477 " --> pdb=" O ALA e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 477 through 487 Processing helix chain 'e' and resid 490 through 502 Processing helix chain 'e' and resid 521 through 526 removed outlier: 3.866A pdb=" N GLU e 524 " --> pdb=" O ASP e 521 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'E' and resid 45 through 59 removed outlier: 3.732A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 4.219A pdb=" N THR E 63 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 65 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.779A pdb=" N ILE E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 4.039A pdb=" N VAL E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 139 removed outlier: 3.806A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 138 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 165 removed outlier: 3.541A pdb=" N ASP E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.793A pdb=" N ARG E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.700A pdb=" N THR E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.778A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 212 removed outlier: 4.090A pdb=" N GLU E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE E 209 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 211 " --> pdb=" O ALA E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 317 removed outlier: 3.596A pdb=" N VAL E 313 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS E 314 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 333 through 338 removed outlier: 3.847A pdb=" N GLN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 333 through 338' Processing helix chain 'E' and resid 351 through 358 removed outlier: 3.976A pdb=" N ALA E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 removed outlier: 3.505A pdb=" N ASP E 425 " --> pdb=" O ARG E 421 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS E 428 " --> pdb=" O HIS E 424 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 459 removed outlier: 3.563A pdb=" N VAL E 448 " --> pdb=" O GLY E 444 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 477 removed outlier: 3.560A pdb=" N ALA E 468 " --> pdb=" O ILE E 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 487 Processing helix chain 'E' and resid 490 through 502 removed outlier: 3.607A pdb=" N THR E 497 " --> pdb=" O GLY E 493 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN E 502 " --> pdb=" O LEU E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 550 removed outlier: 3.549A pdb=" N GLN E 537 " --> pdb=" O GLY E 533 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 35 removed outlier: 4.110A pdb=" N VAL g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE g 35 " --> pdb=" O VAL g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 66 removed outlier: 3.535A pdb=" N ILE g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG g 66 " --> pdb=" O HIS g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 removed outlier: 4.003A pdb=" N LYS g 76 " --> pdb=" O HIS g 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER g 77 " --> pdb=" O PRO g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.534A pdb=" N VAL g 96 " --> pdb=" O GLY g 92 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA g 105 " --> pdb=" O GLY g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 112 Processing helix chain 'g' and resid 117 through 140 Processing helix chain 'g' and resid 149 through 156 removed outlier: 4.212A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 3.851A 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: 4.121A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 4.211A pdb=" N GLU g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU g 174 " --> pdb=" O LYS g 170 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA g 178 " --> pdb=" O LEU g 174 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL g 182 " --> pdb=" O ALA g 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 276 through 288 removed outlier: 3.622A pdb=" N VAL g 280 " --> pdb=" O GLU g 276 " (cutoff:3.500A) removed outlier: 3.817A 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: 3.516A pdb=" N GLN g 306 " --> pdb=" O SER g 302 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR g 308 " --> pdb=" O LEU g 304 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS g 311 " --> pdb=" O HIS g 307 " (cutoff:3.500A) Processing helix chain 'g' and resid 324 through 333 removed outlier: 3.583A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 385 through 409 removed outlier: 3.768A pdb=" N ARG g 394 " --> pdb=" O ASN g 390 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER g 409 " --> pdb=" O ASN g 405 " (cutoff:3.500A) Processing helix chain 'g' and resid 417 through 431 removed outlier: 3.561A pdb=" N SER g 424 " --> pdb=" O GLU g 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS g 426 " --> pdb=" O ALA g 422 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA g 428 " --> pdb=" O SER g 424 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU g 429 " --> pdb=" O VAL g 425 " (cutoff:3.500A) Processing helix chain 'g' and resid 438 through 450 removed outlier: 3.774A pdb=" N VAL g 445 " --> pdb=" O PRO g 441 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA g 446 " --> pdb=" O TYR g 442 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP g 447 " --> pdb=" O GLN g 443 " (cutoff:3.500A) Processing helix chain 'g' and resid 450 through 461 Processing helix chain 'g' and resid 463 through 478 removed outlier: 3.502A pdb=" N GLN g 470 " --> pdb=" O ARG g 466 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA g 473 " --> pdb=" O SER g 469 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS g 475 " --> pdb=" O LEU g 471 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA g 476 " --> pdb=" O ARG g 472 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN g 477 " --> pdb=" O ALA g 473 " (cutoff:3.500A) Processing helix chain 'g' and resid 503 through 523 removed outlier: 3.508A pdb=" N LEU g 521 " --> pdb=" O ALA g 517 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL g 523 " --> pdb=" O LEU g 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 35 removed outlier: 3.533A pdb=" N ILE G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 39 removed outlier: 3.860A pdb=" N LEU G 39 " --> pdb=" O ARG G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 36 through 39' Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.739A pdb=" N ARG G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.860A pdb=" N LYS G 76 " --> pdb=" O HIS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.621A pdb=" N VAL G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.954A 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: 3.779A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 157 removed outlier: 3.529A pdb=" N LYS G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.159A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.784A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.566A pdb=" N GLU G 197 " --> pdb=" O PRO G 194 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 194 through 198' Processing helix chain 'G' and resid 303 through 309 removed outlier: 4.239A pdb=" N HIS G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 332 removed outlier: 3.588A pdb=" N ALA G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 408 removed outlier: 3.713A pdb=" N GLU G 391 " --> pdb=" O ASP G 387 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG G 394 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL G 402 " --> pdb=" O ASP G 398 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 403 " --> pdb=" O ALA G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 432 removed outlier: 3.539A pdb=" N VAL G 423 " --> pdb=" O THR G 419 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER G 424 " --> pdb=" O GLU G 420 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU G 429 " --> pdb=" O VAL G 425 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 432 " --> pdb=" O ALA G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 450 removed outlier: 3.549A pdb=" N TYR G 442 " --> pdb=" O GLN G 438 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN G 443 " --> pdb=" O GLN G 439 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA G 444 " --> pdb=" O TRP G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 460 removed outlier: 3.616A pdb=" N LEU G 456 " --> pdb=" O ILE G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 478 removed outlier: 3.560A pdb=" N LEU G 468 " --> pdb=" O PRO G 464 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER G 469 " --> pdb=" O ILE G 465 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS G 475 " --> pdb=" O LEU G 471 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G 476 " --> pdb=" O ARG G 472 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN G 477 " --> pdb=" O ALA G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 522 removed outlier: 3.617A pdb=" N LEU G 521 " --> pdb=" O ALA G 517 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 44 removed outlier: 3.605A pdb=" N ILE q 32 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.660A pdb=" N ARG q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU q 74 " --> pdb=" O THR q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 95 removed outlier: 3.611A pdb=" N LYS q 83 " --> pdb=" O HIS q 79 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN q 92 " --> pdb=" O ALA q 88 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 121 removed outlier: 3.749A pdb=" N LEU q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN q 112 " --> pdb=" O GLY q 108 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS q 116 " --> pdb=" O ASN q 112 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU q 117 " --> pdb=" O VAL q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 123 through 142 removed outlier: 3.567A pdb=" N ILE q 127 " --> pdb=" O SER q 123 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 159 through 168 Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 176 through 190 removed outlier: 4.215A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU q 181 " --> pdb=" O ILE q 177 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER q 187 " --> pdb=" O SER q 183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS q 188 " --> pdb=" O GLU q 184 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL q 189 " --> pdb=" O ALA q 185 " (cutoff:3.500A) Processing helix chain 'q' and resid 270 through 294 removed outlier: 4.264A pdb=" N LEU q 274 " --> pdb=" O ALA q 270 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU q 290 " --> pdb=" O ALA q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 308 through 316 removed outlier: 3.962A pdb=" N TYR q 312 " --> pdb=" O LEU q 308 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU q 313 " --> pdb=" O ALA q 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN q 314 " --> pdb=" O LEU q 310 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) Processing helix chain 'q' and resid 325 through 334 removed outlier: 4.008A pdb=" N LEU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU q 332 " --> pdb=" O GLU q 328 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG q 334 " --> pdb=" O ARG q 330 " (cutoff:3.500A) Processing helix chain 'q' and resid 391 through 410 removed outlier: 3.685A pdb=" N ASP q 395 " --> pdb=" O GLN q 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP q 396 " --> pdb=" O ASN q 392 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP q 402 " --> pdb=" O GLU q 398 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP q 403 " --> pdb=" O ARG q 399 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA q 406 " --> pdb=" O ASP q 402 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA q 407 " --> pdb=" O ASP q 403 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL q 408 " --> pdb=" O GLY q 404 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS q 409 " --> pdb=" O VAL q 405 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 439 removed outlier: 3.579A pdb=" N ILE q 428 " --> pdb=" O GLY q 424 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE q 431 " --> pdb=" O GLU q 427 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER q 432 " --> pdb=" O ILE q 428 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG q 433 " --> pdb=" O GLU q 429 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR q 437 " --> pdb=" O ARG q 433 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU q 439 " --> pdb=" O THR q 435 " (cutoff:3.500A) Processing helix chain 'q' and resid 445 through 455 Processing helix chain 'q' and resid 457 through 467 Processing helix chain 'q' and resid 470 through 483 removed outlier: 3.560A pdb=" N LEU q 475 " --> pdb=" O VAL q 471 " (cutoff:3.500A) Proline residue: q 476 - end of helix removed outlier: 3.563A pdb=" N TYR q 479 " --> pdb=" O LEU q 475 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS q 482 " --> pdb=" O LEU q 478 " (cutoff:3.500A) Processing helix chain 'q' and resid 511 through 515 removed outlier: 3.688A pdb=" N GLU q 514 " --> pdb=" O ASP q 511 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 541 removed outlier: 3.679A pdb=" N ASN q 529 " --> pdb=" O LYS q 525 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL q 538 " --> pdb=" O ALA q 534 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 44 removed outlier: 3.765A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS Q 42 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 75 removed outlier: 3.671A pdb=" N MET Q 71 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 95 removed outlier: 4.091A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN Q 91 " --> pdb=" O MET Q 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 114 removed outlier: 3.954A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE Q 105 " --> pdb=" O ASN Q 101 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN Q 112 " --> pdb=" O GLY Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 120 Processing helix chain 'Q' and resid 123 through 142 removed outlier: 3.712A pdb=" N ILE Q 127 " --> pdb=" O SER Q 123 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS Q 136 " --> pdb=" O ASN Q 132 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE Q 137 " --> pdb=" O MET Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 168 Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 174 through 190 removed outlier: 4.280A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Q 182 " --> pdb=" O LEU Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 294 removed outlier: 4.034A pdb=" N LEU Q 274 " --> pdb=" O ALA Q 270 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP Q 275 " --> pdb=" O GLN Q 271 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU Q 281 " --> pdb=" O SER Q 277 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS Q 282 " --> pdb=" O LYS Q 278 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU Q 290 " --> pdb=" O ALA Q 286 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET Q 294 " --> pdb=" O GLU Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 316 removed outlier: 3.907A pdb=" N LEU Q 310 " --> pdb=" O GLY Q 306 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS Q 311 " --> pdb=" O GLU Q 307 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR Q 312 " --> pdb=" O LEU Q 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU Q 313 " --> pdb=" O ALA Q 309 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN Q 314 " --> pdb=" O LEU Q 310 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR Q 316 " --> pdb=" O TYR Q 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 306 through 316' Processing helix chain 'Q' and resid 326 through 333 removed outlier: 4.287A pdb=" N ARG Q 330 " --> pdb=" O LYS Q 326 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) removed outlier: 3.602A 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 407 removed outlier: 3.638A pdb=" N LEU Q 394 " --> pdb=" O THR Q 390 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP Q 396 " --> pdb=" O ASN Q 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA Q 407 " --> pdb=" O ASP Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 408 through 412 removed outlier: 3.703A pdb=" N MET Q 412 " --> pdb=" O LYS Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.701A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG Q 433 " --> pdb=" O GLU Q 429 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU Q 439 " --> pdb=" O THR Q 435 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 455 removed outlier: 4.424A 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 removed outlier: 3.624A pdb=" N VAL Q 474 " --> pdb=" O ASP Q 470 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU Q 475 " --> pdb=" O VAL Q 471 " (cutoff:3.500A) Proline residue: Q 476 - end of helix Processing helix chain 'Q' and resid 511 through 516 Processing helix chain 'Q' and resid 521 through 541 removed outlier: 3.522A pdb=" N PHE Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN Q 529 " --> pdb=" O LYS Q 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR Q 537 " --> pdb=" O GLU Q 533 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL Q 538 " --> pdb=" O ALA Q 534 " (cutoff:3.500A) Processing helix chain 'z' and resid 18 through 35 removed outlier: 3.632A pdb=" N VAL z 32 " --> pdb=" O GLY z 28 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR z 35 " --> pdb=" O SER z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 65 Processing helix chain 'z' and resid 71 through 86 removed outlier: 4.045A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE z 76 " --> pdb=" O THR z 72 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA z 81 " --> pdb=" O ALA z 77 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 108 removed outlier: 3.725A pdb=" N VAL z 95 " --> pdb=" O THR z 91 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG z 107 " --> pdb=" O ARG z 103 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 removed outlier: 3.856A pdb=" N LYS z 131 " --> pdb=" O LYS z 127 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE z 132 " --> pdb=" O GLU z 128 " (cutoff:3.500A) removed outlier: 3.628A 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: 4.123A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER z 156 " --> pdb=" O GLN z 152 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER z 157 " --> pdb=" O VAL z 153 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL z 162 " --> pdb=" O LEU z 158 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.937A pdb=" N VAL z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU z 179 " --> pdb=" O THR z 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 203 through 207 removed outlier: 3.528A pdb=" N THR z 207 " --> pdb=" O PRO z 204 " (cutoff:3.500A) Processing helix chain 'z' and resid 263 through 284 removed outlier: 4.779A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS z 273 " --> pdb=" O PHE z 269 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP z 279 " --> pdb=" O LYS z 275 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU z 280 " --> pdb=" O LYS z 276 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS z 281 " --> pdb=" O ILE z 277 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN z 282 " --> pdb=" O ILE z 278 " (cutoff:3.500A) Processing helix chain 'z' and resid 303 through 312 removed outlier: 4.374A pdb=" N ASP z 307 " --> pdb=" O PRO z 303 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL z 308 " --> pdb=" O MET z 304 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS z 311 " --> pdb=" O ASP z 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS z 312 " --> pdb=" O VAL z 308 " (cutoff:3.500A) Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.518A pdb=" N GLU z 326 " --> pdb=" O ARG z 322 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG z 327 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN z 329 " --> pdb=" O MET z 325 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 344 through 348 removed outlier: 3.745A pdb=" N LEU z 348 " --> pdb=" O PRO z 345 " (cutoff:3.500A) Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.717A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN z 404 " --> pdb=" O ARG z 400 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU z 406 " --> pdb=" O VAL z 402 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 3.545A pdb=" N ARG z 427 " --> pdb=" O SER z 423 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN z 430 " --> pdb=" O LEU z 426 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN z 432 " --> pdb=" O SER z 428 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.222A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA z 446 " --> pdb=" O THR z 442 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU z 451 " --> pdb=" O PHE z 447 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 462 removed outlier: 3.517A pdb=" N LYS z 456 " --> pdb=" O LEU z 452 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER z 462 " --> pdb=" O LEU z 458 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.874A pdb=" N ASP z 479 " --> pdb=" O ASP z 475 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP z 482 " --> pdb=" O ASP z 478 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER z 483 " --> pdb=" O ASP z 479 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 removed outlier: 3.656A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU z 528 " --> pdb=" O ALA z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 35 removed outlier: 3.539A pdb=" N LEU Z 29 " --> pdb=" O SER Z 25 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) 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) removed outlier: 3.529A pdb=" N THR Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 80 removed outlier: 3.840A pdb=" N LEU Z 75 " --> pdb=" O PRO Z 71 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE Z 76 " --> pdb=" O THR Z 72 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA Z 80 " --> pdb=" O ILE Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 87 removed outlier: 3.555A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.511A pdb=" N VAL Z 95 " --> pdb=" O THR Z 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Z 102 " --> pdb=" O VAL Z 98 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG Z 107 " --> pdb=" O ARG Z 103 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 removed outlier: 3.647A pdb=" N LYS Z 131 " --> pdb=" O LYS Z 127 " (cutoff:3.500A) removed outlier: 3.911A 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: 4.364A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL Z 153 " --> pdb=" O PHE Z 149 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER Z 156 " --> pdb=" O GLN Z 152 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER Z 157 " --> pdb=" O VAL Z 153 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS Z 161 " --> pdb=" O SER Z 157 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL Z 162 " --> pdb=" O LEU Z 158 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 182 Proline residue: Z 172 - end of helix removed outlier: 3.855A pdb=" N VAL Z 178 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Z 179 " --> pdb=" O THR Z 175 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER Z 180 " --> pdb=" O ASP Z 176 " (cutoff:3.500A) removed outlier: 4.086A 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: 3.557A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS Z 261 " --> pdb=" O ASP Z 257 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU Z 262 " --> pdb=" O GLN Z 258 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS Z 276 " --> pdb=" O ALA Z 272 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU Z 280 " --> pdb=" O LYS Z 276 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN Z 282 " --> pdb=" O ILE Z 278 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL Z 284 " --> pdb=" O LEU Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 304 through 312 removed outlier: 3.940A pdb=" N VAL Z 308 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS Z 311 " --> pdb=" O ASP Z 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 332 removed outlier: 3.919A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG Z 327 " --> pdb=" O ARG Z 323 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 348 removed outlier: 3.641A pdb=" N LEU Z 348 " --> pdb=" O PRO Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 385 through 408 removed outlier: 3.526A pdb=" N ALA Z 389 " --> pdb=" O HIS Z 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN Z 404 " --> pdb=" O ARG Z 400 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS Z 407 " --> pdb=" O ALA Z 403 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.504A pdb=" N SER Z 428 " --> pdb=" O ARG Z 424 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN Z 430 " --> pdb=" O LEU Z 426 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN Z 432 " --> pdb=" O SER Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 440 through 451 Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.526A pdb=" N LYS Z 456 " --> pdb=" O LEU Z 452 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 483 removed outlier: 3.559A pdb=" N VAL Z 469 " --> pdb=" O ASP Z 465 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP Z 479 " --> pdb=" O ASP Z 475 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.751A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Z 529 " --> pdb=" O SER Z 525 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 41 removed outlier: 3.865A pdb=" N ILE h 27 " --> pdb=" O LYS h 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS h 33 " --> pdb=" O ASN h 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA h 35 " --> pdb=" O ASN h 31 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL h 36 " --> pdb=" O ALA h 32 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU h 40 " --> pdb=" O VAL h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 72 removed outlier: 3.517A pdb=" N ILE h 69 " --> pdb=" O ASP h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 94 removed outlier: 4.158A pdb=" N LEU h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 112 removed outlier: 3.784A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU h 108 " --> pdb=" O LEU h 104 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET h 109 " --> pdb=" O ALA h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 117 removed outlier: 3.751A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.716A pdb=" N ILE h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG h 130 " --> pdb=" O MET h 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA h 132 " --> pdb=" O GLY h 128 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU h 135 " --> pdb=" O LYS h 131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU h 138 " --> pdb=" O SER h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 153 through 166 removed outlier: 3.833A pdb=" N LEU h 158 " --> pdb=" O GLY h 154 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG h 163 " --> pdb=" O GLU h 159 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA h 165 " --> pdb=" O CYS h 161 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 188 removed outlier: 3.564A pdb=" N PHE h 178 " --> pdb=" O ASN h 174 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP h 184 " --> pdb=" O LYS h 180 " (cutoff:3.500A) removed outlier: 3.803A 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 268 through 273 removed outlier: 3.614A pdb=" N VAL h 271 " --> pdb=" O GLN h 268 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA h 273 " --> pdb=" O ILE h 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 274 through 289 removed outlier: 3.687A pdb=" N ILE h 278 " --> pdb=" O GLU h 274 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG h 283 " --> pdb=" O PHE h 279 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU h 286 " --> pdb=" O LEU h 282 " (cutoff:3.500A) Processing helix chain 'h' and resid 302 through 307 removed outlier: 4.204A pdb=" N PHE h 306 " --> pdb=" O LEU h 302 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE h 307 " --> pdb=" O ALA h 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 302 through 307' Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.543A pdb=" N ASN h 324 " --> pdb=" O ALA h 320 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN h 328 " --> pdb=" O ASN h 324 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL h 330 " --> pdb=" O VAL h 326 " (cutoff:3.500A) Processing helix chain 'h' and resid 342 through 346 Processing helix chain 'h' and resid 382 through 406 removed outlier: 3.534A pdb=" N ILE h 386 " --> pdb=" O ALA h 382 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA h 396 " --> pdb=" O SER h 392 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU h 404 " --> pdb=" O VAL h 400 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN h 405 " --> pdb=" O LYS h 401 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN h 406 " --> pdb=" O ARG h 402 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 430 removed outlier: 3.643A pdb=" N SER h 421 " --> pdb=" O GLU h 417 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS h 422 " --> pdb=" O MET h 418 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS h 423 " --> pdb=" O GLU h 419 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP h 426 " --> pdb=" O LYS h 422 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 removed outlier: 3.575A pdb=" N ILE h 438 " --> pdb=" O LYS h 434 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 458 Processing helix chain 'h' and resid 460 through 473 removed outlier: 3.580A pdb=" N ILE h 464 " --> pdb=" O ASP h 460 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU h 465 " --> pdb=" O ALA h 461 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN h 466 " --> pdb=" O ILE h 462 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG h 469 " --> pdb=" O LEU h 465 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU h 470 " --> pdb=" O ASN h 466 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA h 471 " --> pdb=" O LYS h 467 " (cutoff:3.500A) removed outlier: 3.843A 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 518 removed outlier: 3.534A pdb=" N LEU h 507 " --> pdb=" O LYS h 503 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN h 508 " --> pdb=" O ILE h 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.685A pdb=" N ALA H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.556A pdb=" N LEU H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 94 removed outlier: 3.513A pdb=" N SER H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 112 removed outlier: 3.992A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.935A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU H 118 " --> pdb=" O PRO H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.640A pdb=" N ILE H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS H 131 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 166 removed outlier: 4.496A pdb=" N LEU H 158 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.719A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP H 184 " --> pdb=" O LYS H 180 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 185 " --> pdb=" O MET H 181 " (cutoff:3.500A) removed outlier: 3.692A 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: 3.590A pdb=" N GLU H 211 " --> pdb=" O ALA H 208 " (cutoff:3.500A) removed outlier: 3.630A 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 264 through 272 removed outlier: 3.741A pdb=" N GLN H 268 " --> pdb=" O GLU H 265 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA H 269 " --> pdb=" O ASP H 266 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE H 270 " --> pdb=" O TYR H 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL H 271 " --> pdb=" O GLN H 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP H 272 " --> pdb=" O ALA H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 281 through 287 removed outlier: 3.566A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 319 through 331 removed outlier: 3.537A pdb=" N MET H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN H 324 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL H 326 " --> pdb=" O ASP H 322 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE H 327 " --> pdb=" O MET H 323 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.646A pdb=" N GLU H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU H 404 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 431 removed outlier: 3.621A pdb=" N GLU H 419 " --> pdb=" O ALA H 415 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU H 424 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR H 430 " --> pdb=" O ASP H 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE H 431 " --> pdb=" O TYR H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 446 Processing helix chain 'H' and resid 447 through 458 Processing helix chain 'H' and resid 460 through 472 removed outlier: 3.735A pdb=" N ARG H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA H 471 " --> pdb=" O LYS H 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 519 removed outlier: 3.741A pdb=" N LEU H 507 " --> pdb=" O LYS H 503 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN H 508 " --> pdb=" O ILE H 504 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE H 517 " --> pdb=" O ALA H 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 19 through 21 removed outlier: 3.589A pdb=" N ILE a 20 " --> pdb=" O MET a 544 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS d 46 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE d 48 " --> pdb=" O ILE d 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE d 56 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 62 through 63 removed outlier: 4.389A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL g 527 " --> pdb=" O MET a 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 204 through 207 removed outlier: 6.023A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER a 384 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL a 219 " --> pdb=" O SER a 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 222 through 225 removed outlier: 7.668A pdb=" N GLY a 376 " --> pdb=" O ASP a 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 244 through 246 removed outlier: 3.659A pdb=" N LEU a 297 " --> pdb=" O ALA a 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.562A pdb=" N ILE A 20 " --> pdb=" O MET A 544 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 544 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 48 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.115A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 384 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 219 " --> pdb=" O SER A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 225 removed outlier: 3.783A pdb=" N LYS A 375 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 360 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.546A pdb=" N THR A 298 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AB4, first strand: chain 'b' and resid 55 through 57 removed outlier: 3.763A pdb=" N MET b 55 " --> pdb=" O LEU b 46 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU b 46 " --> pdb=" O MET b 55 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP b 43 " --> pdb=" O ILE d 521 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP d 523 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU b 45 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA d 525 " --> pdb=" O LEU b 45 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 193 through 198 removed outlier: 6.304A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 225 through 229 removed outlier: 6.954A pdb=" N ASP b 341 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS b 340 " --> pdb=" O CYS b 359 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS b 359 " --> pdb=" O CYS b 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 231 through 233 removed outlier: 7.297A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 400 through 402 Processing sheet with id=AB9, first strand: chain 'b' and resid 470 through 473 Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.639A pdb=" N MET B 55 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP B 43 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP D 523 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 45 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA D 525 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 47 " --> pdb=" O ALA D 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 193 through 199 removed outlier: 3.528A pdb=" N VAL B 368 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B 207 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.004A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 338 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC5, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AC6, first strand: chain 'B' and resid 470 through 473 Processing sheet with id=AC7, first strand: chain 'B' and resid 511 through 514 removed outlier: 8.027A pdb=" N ILE E 73 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE B 514 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N ILE E 75 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS E 72 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR E 84 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'd' and resid 197 through 200 removed outlier: 6.115A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.673A pdb=" N VAL d 213 " --> pdb=" O VAL d 363 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL d 363 " --> pdb=" O VAL d 213 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ARG d 362 " --> pdb=" O VAL d 350 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL d 350 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR d 364 " --> pdb=" O ASP d 348 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 234 through 237 removed outlier: 4.295A pdb=" N GLY d 235 " --> pdb=" O VAL d 285 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU d 287 " --> pdb=" O GLY d 235 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN d 289 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU d 286 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP d 315 " --> pdb=" O LEU d 286 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE d 288 " --> pdb=" O ASP d 315 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 196 through 200 removed outlier: 3.761A pdb=" N GLY D 381 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 213 through 214 removed outlier: 3.843A pdb=" N VAL D 363 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 360 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR D 364 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 285 through 287 removed outlier: 6.196A pdb=" N LEU D 286 " --> pdb=" O VAL D 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 410 through 411 Processing sheet with id=AD6, first strand: chain 'e' and resid 72 through 75 removed outlier: 3.631A pdb=" N LYS e 72 " --> pdb=" O THR e 84 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR e 84 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR e 82 " --> pdb=" O LEU e 74 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'e' and resid 166 through 167 removed outlier: 3.632A pdb=" N ASP e 166 " --> pdb=" O VAL e 439 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 224 through 230 removed outlier: 6.492A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL e 408 " --> pdb=" O LYS e 225 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN e 227 " --> pdb=" O VAL e 408 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY e 410 " --> pdb=" O GLN e 227 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'e' and resid 342 through 343 removed outlier: 7.231A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL e 320 " --> pdb=" O LYS e 268 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE e 322 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY e 375 " --> pdb=" O LEU e 269 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 381 through 382 removed outlier: 4.144A pdb=" N TYR e 381 " --> pdb=" O ILE e 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'e' and resid 551 through 554 removed outlier: 4.110A pdb=" N ILE e 551 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU h 52 " --> pdb=" O ILE e 551 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN e 553 " --> pdb=" O LEU h 52 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL h 54 " --> pdb=" O ASN e 553 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE h 53 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR h 61 " --> pdb=" O ILE h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AE4, first strand: chain 'E' and resid 224 through 230 removed outlier: 6.252A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N GLY E 410 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG E 229 " --> pdb=" O GLY E 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 269 through 272 removed outlier: 6.152A pdb=" N ALA E 270 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 380 through 382 Processing sheet with id=AE7, first strand: chain 'E' and resid 554 through 556 removed outlier: 7.096A pdb=" N ILE E 555 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 53 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR H 61 " --> pdb=" O ILE H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'g' and resid 55 through 56 Processing sheet with id=AE9, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AF1, first strand: chain 'g' and resid 207 through 208 removed outlier: 3.790A pdb=" N GLU g 207 " --> pdb=" O ILE g 379 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU g 381 " --> pdb=" O GLU g 207 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'g' and resid 224 through 225 removed outlier: 3.729A pdb=" N LEU g 225 " --> pdb=" O SER g 366 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'g' and resid 294 through 296 Processing sheet with id=AF4, first strand: chain 'g' and resid 482 through 484 removed outlier: 3.675A pdb=" N VAL g 492 " --> pdb=" O GLY g 483 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 55 through 56 removed outlier: 4.201A pdb=" N VAL G 56 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 48 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AF7, first strand: chain 'G' and resid 206 through 208 Processing sheet with id=AF8, first strand: chain 'G' and resid 294 through 296 Processing sheet with id=AF9, first strand: chain 'G' and resid 482 through 484 Processing sheet with id=AG1, first strand: chain 'q' and resid 53 through 56 removed outlier: 4.010A pdb=" N LYS q 53 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE q 55 " --> pdb=" O ILE q 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE q 63 " --> pdb=" O ILE q 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'q' and resid 207 through 213 removed outlier: 3.679A pdb=" N ILE q 212 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY q 388 " --> pdb=" O ILE q 212 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR q 383 " --> pdb=" O ILE q 223 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE q 223 " --> pdb=" O THR q 383 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.500A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N LEU q 341 " --> pdb=" O VAL q 247 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL q 249 " --> pdb=" O LEU q 341 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.500A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'q' and resid 360 through 362 Processing sheet with id=AG6, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AG7, first strand: chain 'q' and resid 544 through 545 removed outlier: 4.139A pdb=" N ILE q 545 " --> pdb=" O MET z 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Q' and resid 62 through 63 removed outlier: 5.707A pdb=" N ILE Q 54 " --> pdb=" O ILE H 524 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 210 through 213 removed outlier: 3.749A pdb=" N VAL Q 210 " --> pdb=" O ILE Q 384 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU Q 386 " --> pdb=" O VAL Q 210 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE Q 212 " --> pdb=" O LEU Q 386 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 319 through 322 removed outlier: 3.523A pdb=" N LEU Q 321 " --> pdb=" O ILE Q 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N LEU Q 341 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL Q 249 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 319 through 322 removed outlier: 3.523A pdb=" N LEU Q 321 " --> pdb=" O ILE Q 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 357 through 363 removed outlier: 3.847A pdb=" N THR Q 357 " --> pdb=" O LYS Q 372 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS Q 372 " --> pdb=" O THR Q 357 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS Q 359 " --> pdb=" O VAL Q 370 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP Q 366 " --> pdb=" O ILE Q 363 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 419 through 421 Processing sheet with id=AH5, first strand: chain 'Q' and resid 544 through 545 removed outlier: 6.239A pdb=" N ILE Q 545 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS Z 54 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AH7, first strand: chain 'z' and resid 195 through 199 removed outlier: 6.416A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'z' and resid 227 through 228 Processing sheet with id=AH9, first strand: chain 'z' and resid 231 through 234 removed outlier: 5.882A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AI2, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AI3, first strand: chain 'Z' and resid 194 through 197 removed outlier: 6.116A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Z' and resid 227 through 228 Processing sheet with id=AI5, first strand: chain 'Z' and resid 292 through 295 removed outlier: 6.033A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'Z' and resid 490 through 491 Processing sheet with id=AI7, first strand: chain 'h' and resid 145 through 146 removed outlier: 3.580A pdb=" N VAL h 145 " --> pdb=" O ILE h 409 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE h 409 " --> pdb=" O VAL h 145 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 199 through 200 removed outlier: 5.831A pdb=" N GLY h 200 " --> pdb=" O LEU h 376 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 203 through 205 removed outlier: 6.405A pdb=" N ILE h 204 " --> pdb=" O GLY h 380 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'h' and resid 235 through 236 removed outlier: 4.142A pdb=" N PHE h 352 " --> pdb=" O PHE h 236 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 313 through 315 removed outlier: 3.562A pdb=" N ALA h 315 " --> pdb=" O VAL h 293 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS h 240 " --> pdb=" O ILE h 292 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU h 294 " --> pdb=" O LYS h 240 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU h 242 " --> pdb=" O LEU h 294 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N GLN h 335 " --> pdb=" O ILE h 241 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER h 243 " --> pdb=" O GLN h 335 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 313 through 315 removed outlier: 3.562A pdb=" N ALA h 315 " --> pdb=" O VAL h 293 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS h 240 " --> pdb=" O ILE h 292 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU h 294 " --> pdb=" O LYS h 240 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU h 242 " --> pdb=" O LEU h 294 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.923A pdb=" N GLY h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 145 through 146 removed outlier: 3.754A pdb=" N VAL H 145 " --> pdb=" O ILE H 409 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE H 409 " --> pdb=" O VAL H 145 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'H' and resid 199 through 204 removed outlier: 6.532A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR H 375 " --> pdb=" O ILE H 215 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'H' and resid 241 through 244 removed outlier: 3.674A pdb=" N LEU H 294 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 351 through 355 removed outlier: 3.603A pdb=" N GLU H 353 " --> pdb=" O LEU H 364 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 479 through 481 removed outlier: 3.810A pdb=" N GLY H 489 " --> pdb=" O GLY H 480 " (cutoff:3.500A) 2424 hydrogen bonds defined for protein. 7026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.27 Time building geometry restraints manager: 18.28 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: 20646 1.34 - 1.46: 11267 1.46 - 1.58: 29254 1.58 - 1.70: 0 1.70 - 1.81: 504 Bond restraints: 61671 Sorted by residual: bond pdb=" C ARG d 372 " pdb=" N PRO d 373 " ideal model delta sigma weight residual 1.334 1.441 -0.107 2.34e-02 1.83e+03 2.09e+01 bond pdb=" C ALA q 346 " pdb=" N PRO q 347 " ideal model delta sigma weight residual 1.334 1.425 -0.091 2.34e-02 1.83e+03 1.51e+01 bond pdb=" C ALA Q 346 " pdb=" N PRO Q 347 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.77e+00 bond pdb=" C SER G 409 " pdb=" N PRO G 410 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.43e+00 bond pdb=" CA ILE E 479 " pdb=" CB ILE E 479 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.30e+00 ... (remaining 61666 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.29: 1399 107.29 - 113.97: 36861 113.97 - 120.64: 24827 120.64 - 127.31: 19720 127.31 - 133.98: 376 Bond angle restraints: 83183 Sorted by residual: angle pdb=" N GLY h 228 " pdb=" CA GLY h 228 " pdb=" C GLY h 228 " ideal model delta sigma weight residual 116.01 121.21 -5.20 1.64e+00 3.72e-01 1.00e+01 angle pdb=" N HIS e 353 " pdb=" CA HIS e 353 " pdb=" C HIS e 353 " ideal model delta sigma weight residual 110.80 117.05 -6.25 2.13e+00 2.20e-01 8.61e+00 angle pdb=" C PHE H 229 " pdb=" N GLU H 230 " pdb=" CA GLU H 230 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.63e+00 angle pdb=" C ILE e 244 " pdb=" N LEU e 245 " pdb=" CA LEU e 245 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.15e+00 angle pdb=" C GLY B 466 " pdb=" N ILE B 467 " pdb=" CA ILE B 467 " ideal model delta sigma weight residual 121.97 126.74 -4.77 1.80e+00 3.09e-01 7.02e+00 ... (remaining 83178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 37702 15.98 - 31.96: 322 31.96 - 47.94: 190 47.94 - 63.91: 57 63.91 - 79.89: 6 Dihedral angle restraints: 38277 sinusoidal: 15299 harmonic: 22978 Sorted by residual: 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 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP H 272 " pdb=" C ASP H 272 " pdb=" N ALA H 273 " pdb=" CA ALA H 273 " ideal model delta harmonic sigma weight residual -180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA VAL H 271 " pdb=" C VAL H 271 " pdb=" N ASP H 272 " pdb=" CA ASP H 272 " ideal model delta harmonic sigma weight residual -180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 38274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 7332 0.038 - 0.075: 1925 0.075 - 0.113: 640 0.113 - 0.150: 119 0.150 - 0.188: 2 Chirality restraints: 10018 Sorted by residual: chirality pdb=" CA GLU h 230 " pdb=" N GLU h 230 " pdb=" C GLU h 230 " pdb=" CB GLU h 230 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CB ILE e 244 " pdb=" CA ILE e 244 " pdb=" CG1 ILE e 244 " pdb=" CG2 ILE e 244 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA HIS e 353 " pdb=" N HIS e 353 " pdb=" C HIS e 353 " pdb=" CB HIS e 353 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 10015 not shown) Planarity restraints: 10682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 372 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO D 373 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS e 280 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO e 281 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO e 281 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO e 281 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 278 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO E 279 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 279 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 279 " 0.022 5.00e-02 4.00e+02 ... (remaining 10679 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 9385 2.76 - 3.30: 57069 3.30 - 3.83: 90633 3.83 - 4.37: 107636 4.37 - 4.90: 185213 Nonbonded interactions: 449936 Sorted by model distance: nonbonded pdb=" O LEU E 223 " pdb=" OG1 THR E 403 " model vdw 2.226 2.440 nonbonded pdb=" O LEU H 198 " pdb=" OG1 THR H 373 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR Z 182 " pdb=" O GLN Z 185 " model vdw 2.260 2.440 nonbonded pdb=" O VAL Z 367 " pdb=" ND2 ASN Z 370 " model vdw 2.265 2.520 nonbonded pdb=" O LEU h 198 " pdb=" OG1 THR h 373 " model vdw 2.269 2.440 ... (remaining 449931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 256 or resid 276 through 547)) selection = chain 'a' } ncs_group { reference = (chain 'B' and resid 19 through 520) selection = chain 'b' } ncs_group { reference = (chain 'D' and (resid 17 through 479 or resid 492 through 528)) selection = (chain 'd' and (resid 17 through 233 or resid 282 through 289 or resid 298 throu \ gh 328 or resid 347 through 528)) } ncs_group { reference = (chain 'E' and resid 42 through 560) selection = (chain 'e' and (resid 42 through 281 or resid 308 through 560)) } ncs_group { reference = (chain 'G' and resid 17 through 530) selection = (chain 'g' and (resid 17 through 246 or resid 290 through 335 or resid 349 throu \ gh 530)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = (chain 'q' and resid 27 through 549) } ncs_group { reference = (chain 'Z' and (resid 8 through 254 or resid 262 through 538)) selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 4.290 Check model and map are aligned: 0.660 Set scattering table: 0.430 Process input model: 116.860 Find NCS groups from input model: 5.310 Set up NCS constraints: 0.350 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5251 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 0.107 61671 Z= 0.088 Angle : 0.390 8.276 83183 Z= 0.221 Chirality : 0.039 0.188 10018 Planarity : 0.002 0.058 10682 Dihedral : 7.152 79.892 23381 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % 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: -3.58 (0.07), residues: 7946 helix: -3.61 (0.05), residues: 3509 sheet: -0.90 (0.20), residues: 483 loop : -1.19 (0.08), residues: 3954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP h 275 HIS 0.006 0.000 HIS e 353 PHE 0.025 0.001 PHE E 276 TYR 0.007 0.000 TYR G 442 ARG 0.003 0.000 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2378 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2378 time to evaluate : 5.027 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 outliers start: 0 outliers final: 0 residues processed: 2378 average time/residue: 0.6153 time to fit residues: 2409.1978 Evaluate side-chains 1218 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1218 time to evaluate : 4.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 10.0000 chunk 602 optimal weight: 6.9990 chunk 334 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 406 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 623 optimal weight: 9.9990 chunk 241 optimal weight: 0.6980 chunk 378 optimal weight: 3.9990 chunk 463 optimal weight: 4.9990 chunk 721 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 38 ASN a 88 GLN a 89 GLN ** a 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS a 430 ASN ** a 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 77 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS A 485 GLN b 142 ASN b 155 HIS b 222 GLN b 286 ASN ** b 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS d 149 GLN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 289 GLN d 395 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN D 289 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 ASN e 337 GLN e 349 GLN e 397 GLN e 474 GLN e 502 GLN e 536 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 432 ASN ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN g 397 GLN ** g 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN Q 79 HIS ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 GLN Q 446 GLN ** z 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 329 GLN Z 185 GLN Z 200 GLN Z 329 GLN Z 337 GLN Z 356 GLN Z 430 ASN ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 172 HIS ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 HIS H 216 ASN H 231 GLN H 405 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 61671 Z= 0.243 Angle : 0.647 11.942 83183 Z= 0.339 Chirality : 0.046 0.500 10018 Planarity : 0.005 0.157 10682 Dihedral : 3.778 26.825 8441 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 0.12 % Allowed : 2.75 % Favored : 97.13 % 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: -1.54 (0.08), residues: 7946 helix: -0.99 (0.08), residues: 3634 sheet: -0.50 (0.19), residues: 602 loop : -1.00 (0.09), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 167 HIS 0.030 0.002 HIS d 62 PHE 0.024 0.002 PHE B 218 TYR 0.022 0.002 TYR H 479 ARG 0.018 0.001 ARG e 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1630 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1622 time to evaluate : 5.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 1624 average time/residue: 0.5604 time to fit residues: 1550.5115 Evaluate side-chains 1141 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1140 time to evaluate : 5.013 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4095 time to fit residues: 7.9540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 1.9990 chunk 224 optimal weight: 30.0000 chunk 600 optimal weight: 8.9990 chunk 491 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 723 optimal weight: 5.9990 chunk 781 optimal weight: 0.8980 chunk 644 optimal weight: 4.9990 chunk 717 optimal weight: 20.0000 chunk 246 optimal weight: 0.2980 chunk 580 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 465 ASN B 260 GLN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS d 496 HIS ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 HIS D 499 GLN ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** g 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN G 439 GLN G 475 HIS ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN q 451 GLN q 516 ASN Q 39 HIS Q 66 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 22 ASN ** z 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN h 305 GLN h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 505 ASN H 90 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 61671 Z= 0.196 Angle : 0.568 13.269 83183 Z= 0.292 Chirality : 0.043 0.194 10018 Planarity : 0.003 0.063 10682 Dihedral : 3.798 26.683 8441 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.83 % 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: -0.78 (0.09), residues: 7946 helix: -0.11 (0.08), residues: 3705 sheet: -0.29 (0.20), residues: 600 loop : -0.88 (0.09), residues: 3641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP g 167 HIS 0.015 0.001 HIS E 50 PHE 0.035 0.002 PHE e 249 TYR 0.017 0.001 TYR H 479 ARG 0.010 0.001 ARG z 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1450 time to evaluate : 5.275 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: 5 outliers final: 0 residues processed: 1454 average time/residue: 0.5620 time to fit residues: 1390.3067 Evaluate side-chains 1100 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1100 time to evaluate : 5.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 0.0970 chunk 543 optimal weight: 8.9990 chunk 375 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 345 optimal weight: 0.0870 chunk 485 optimal weight: 5.9990 chunk 725 optimal weight: 2.9990 chunk 768 optimal weight: 0.8980 chunk 379 optimal weight: 9.9990 chunk 687 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 141 ASN a 514 HIS A 29 ASN A 77 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 125 GLN d 395 HIS d 496 HIS d 499 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 72 HIS g 166 HIS ** g 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 356 GLN ** Z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 ASN ** h 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 61671 Z= 0.153 Angle : 0.517 10.256 83183 Z= 0.264 Chirality : 0.042 0.255 10018 Planarity : 0.003 0.045 10682 Dihedral : 3.689 24.629 8441 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.64 % Favored : 97.28 % Rotamer: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % 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: -0.40 (0.09), residues: 7946 helix: 0.31 (0.08), residues: 3715 sheet: -0.30 (0.20), residues: 620 loop : -0.78 (0.09), residues: 3611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 167 HIS 0.011 0.001 HIS D 62 PHE 0.034 0.001 PHE h 307 TYR 0.024 0.001 TYR Q 201 ARG 0.009 0.000 ARG d 520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1401 time to evaluate : 5.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1402 average time/residue: 0.5648 time to fit residues: 1363.2707 Evaluate side-chains 1093 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1093 time to evaluate : 5.058 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 6.9990 chunk 436 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 572 optimal weight: 0.9990 chunk 317 optimal weight: 10.0000 chunk 655 optimal weight: 5.9990 chunk 531 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 392 optimal weight: 0.6980 chunk 689 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 29 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 393 GLN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 496 HIS ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 553 ASN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** g 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 39 HIS ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS Q 472 ASN ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 430 ASN ** Z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN ** h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 216 ASN h 456 ASN h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 61671 Z= 0.188 Angle : 0.564 13.002 83183 Z= 0.289 Chirality : 0.043 0.245 10018 Planarity : 0.003 0.065 10682 Dihedral : 3.915 26.901 8441 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 0.03 % Allowed : 1.96 % Favored : 98.01 % 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: 7946 helix: 0.51 (0.08), residues: 3722 sheet: -0.30 (0.21), residues: 617 loop : -0.75 (0.10), residues: 3607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP g 167 HIS 0.008 0.001 HIS D 62 PHE 0.023 0.002 PHE E 179 TYR 0.035 0.001 TYR h 226 ARG 0.010 0.000 ARG Z 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1384 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1382 time to evaluate : 5.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1382 average time/residue: 0.5656 time to fit residues: 1348.6972 Evaluate side-chains 1098 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1098 time to evaluate : 5.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 0.8980 chunk 692 optimal weight: 0.9990 chunk 151 optimal weight: 0.0770 chunk 451 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 769 optimal weight: 5.9990 chunk 638 optimal weight: 10.0000 chunk 356 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 chunk 403 optimal weight: 4.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 29 ASN A 77 HIS A 90 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 395 HIS d 496 HIS ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 GLN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 258 ASN z 114 HIS z 404 ASN z 430 ASN ** Z 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 356 GLN h 29 ASN h 291 ASN ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 61671 Z= 0.145 Angle : 0.534 10.527 83183 Z= 0.269 Chirality : 0.042 0.235 10018 Planarity : 0.003 0.139 10682 Dihedral : 3.762 26.626 8441 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.04 % Rotamer: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.63 % 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: -0.09 (0.09), residues: 7946 helix: 0.66 (0.09), residues: 3727 sheet: -0.25 (0.21), residues: 628 loop : -0.72 (0.10), residues: 3591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP g 167 HIS 0.009 0.001 HIS q 39 PHE 0.022 0.001 PHE e 200 TYR 0.025 0.001 TYR h 226 ARG 0.013 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1372 time to evaluate : 5.128 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 outliers start: 3 outliers final: 0 residues processed: 1374 average time/residue: 0.5662 time to fit residues: 1345.6940 Evaluate side-chains 1096 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1096 time to evaluate : 5.081 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 438 optimal weight: 3.9990 chunk 561 optimal weight: 0.0570 chunk 435 optimal weight: 2.9990 chunk 647 optimal weight: 0.6980 chunk 429 optimal weight: 4.9990 chunk 766 optimal weight: 6.9990 chunk 479 optimal weight: 1.9990 chunk 467 optimal weight: 20.0000 chunk 353 optimal weight: 10.0000 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 209 HIS a 514 HIS A 38 ASN A 77 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 447 ASN d 284 ASN d 395 HIS ** d 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 536 GLN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 477 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 30 GLN ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 152 GLN z 356 GLN z 430 ASN Z 201 HIS ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 305 GLN h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 61671 Z= 0.153 Angle : 0.542 10.239 83183 Z= 0.274 Chirality : 0.042 0.200 10018 Planarity : 0.003 0.069 10682 Dihedral : 3.749 26.904 8441 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 0.01 % Allowed : 1.16 % Favored : 98.83 % 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: -0.03 (0.09), residues: 7946 helix: 0.72 (0.09), residues: 3737 sheet: -0.23 (0.21), residues: 627 loop : -0.70 (0.10), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 167 HIS 0.009 0.001 HIS E 50 PHE 0.025 0.001 PHE Z 136 TYR 0.020 0.001 TYR h 226 ARG 0.012 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1371 time to evaluate : 5.098 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 outliers start: 1 outliers final: 0 residues processed: 1371 average time/residue: 0.5561 time to fit residues: 1319.0400 Evaluate side-chains 1087 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1087 time to evaluate : 5.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 457 optimal weight: 0.0370 chunk 230 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 487 optimal weight: 0.2980 chunk 522 optimal weight: 10.0000 chunk 378 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 602 optimal weight: 4.9990 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 29 ASN A 77 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 288 GLN d 284 ASN d 395 HIS ** d 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 HIS ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 30 GLN ** z 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 430 ASN ** Z 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 61671 Z= 0.157 Angle : 0.552 10.282 83183 Z= 0.278 Chirality : 0.043 0.200 10018 Planarity : 0.003 0.053 10682 Dihedral : 3.804 28.603 8441 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 0.01 % Allowed : 0.85 % Favored : 99.14 % 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: -0.01 (0.09), residues: 7946 helix: 0.76 (0.09), residues: 3743 sheet: -0.29 (0.20), residues: 655 loop : -0.70 (0.10), residues: 3548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP g 167 HIS 0.007 0.001 HIS E 142 PHE 0.027 0.001 PHE Z 136 TYR 0.022 0.001 TYR a 354 ARG 0.008 0.000 ARG b 435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1403 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 outliers start: 1 outliers final: 0 residues processed: 1403 average time/residue: 0.5682 time to fit residues: 1376.7885 Evaluate side-chains 1109 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1109 time to evaluate : 5.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 0.3980 chunk 734 optimal weight: 10.0000 chunk 669 optimal weight: 0.6980 chunk 714 optimal weight: 0.3980 chunk 733 optimal weight: 2.9990 chunk 429 optimal weight: 5.9990 chunk 311 optimal weight: 4.9990 chunk 560 optimal weight: 1.9990 chunk 219 optimal weight: 0.0870 chunk 645 optimal weight: 0.0000 chunk 675 optimal weight: 0.5980 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 29 ASN a 191 ASN a 514 HIS A 77 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 284 ASN d 395 HIS d 496 HIS D 67 GLN ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS g 475 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 451 GLN q 477 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS z 30 GLN z 114 HIS ** z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 430 ASN ** Z 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 356 GLN ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 ASN ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 216 ASN h 472 HIS ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 61671 Z= 0.142 Angle : 0.548 9.085 83183 Z= 0.274 Chirality : 0.042 0.161 10018 Planarity : 0.003 0.090 10682 Dihedral : 3.690 26.366 8441 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Rotamer: Outliers : 0.03 % 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: 0.09 (0.09), residues: 7946 helix: 0.85 (0.09), residues: 3747 sheet: -0.16 (0.20), residues: 643 loop : -0.69 (0.10), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 167 HIS 0.011 0.001 HIS d 395 PHE 0.028 0.001 PHE q 137 TYR 0.017 0.001 TYR h 226 ARG 0.013 0.000 ARG a 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1396 time to evaluate : 5.085 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 outliers start: 2 outliers final: 0 residues processed: 1396 average time/residue: 0.5668 time to fit residues: 1379.7592 Evaluate side-chains 1111 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1111 time to evaluate : 5.153 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 10.0000 chunk 468 optimal weight: 9.9990 chunk 755 optimal weight: 9.9990 chunk 460 optimal weight: 0.5980 chunk 358 optimal weight: 10.0000 chunk 524 optimal weight: 0.0980 chunk 792 optimal weight: 9.9990 chunk 728 optimal weight: 2.9990 chunk 630 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 487 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 141 ASN a 514 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 284 ASN d 395 HIS ** d 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN g 21 GLN g 166 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 451 GLN q 477 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 451 GLN z 30 GLN z 152 GLN z 430 ASN ** Z 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 GLN h 216 ASN h 291 ASN ** h 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN H 363 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.7905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 61671 Z= 0.195 Angle : 0.604 11.597 83183 Z= 0.306 Chirality : 0.044 0.214 10018 Planarity : 0.003 0.052 10682 Dihedral : 3.983 30.611 8441 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 0.01 % Allowed : 0.24 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 7946 helix: 0.79 (0.09), residues: 3748 sheet: -0.30 (0.21), residues: 612 loop : -0.75 (0.10), residues: 3586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 167 HIS 0.009 0.001 HIS d 395 PHE 0.028 0.002 PHE q 137 TYR 0.019 0.002 TYR a 432 ARG 0.015 0.001 ARG z 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15892 Ramachandran restraints generated. 7946 Oldfield, 0 Emsley, 7946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1400 time to evaluate : 5.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1401 average time/residue: 0.5714 time to fit residues: 1396.0510 Evaluate side-chains 1117 residues out of total 6736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1117 time to evaluate : 5.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 6.9990 chunk 500 optimal weight: 0.0050 chunk 671 optimal weight: 9.9990 chunk 193 optimal weight: 0.0570 chunk 581 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 175 optimal weight: 0.0970 chunk 631 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 648 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 overall best weight: 0.3912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 514 HIS A 77 HIS ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 284 ASN ** d 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 HIS ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 405 ASN G 459 ASN ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 477 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS Q 314 ASN Q 451 GLN z 30 GLN z 114 HIS ** z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 430 ASN ** Z 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 356 GLN ** h 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN ** H 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.232510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.220837 restraints weight = 154306.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.217730 restraints weight = 211665.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.215444 restraints weight = 242165.854| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 61671 Z= 0.152 Angle : 0.568 9.711 83183 Z= 0.283 Chirality : 0.043 0.203 10018 Planarity : 0.003 0.086 10682 Dihedral : 3.786 28.838 8441 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 0.01 % Allowed : 0.25 % Favored : 99.73 % 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: 0.08 (0.09), residues: 7946 helix: 0.88 (0.09), residues: 3753 sheet: -0.29 (0.21), residues: 624 loop : -0.72 (0.10), residues: 3569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 167 HIS 0.012 0.001 HIS d 395 PHE 0.028 0.001 PHE B 218 TYR 0.016 0.001 TYR h 226 ARG 0.007 0.000 ARG D 520 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19388.97 seconds wall clock time: 338 minutes 9.92 seconds (20289.92 seconds total)