Starting phenix.real_space_refine on Sat Dec 9 17:49:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw4_9540/12_2023/5gw4_9540.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw4_9540/12_2023/5gw4_9540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw4_9540/12_2023/5gw4_9540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw4_9540/12_2023/5gw4_9540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw4_9540/12_2023/5gw4_9540.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gw4_9540/12_2023/5gw4_9540.pdb" } resolution = 4.7 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 ------------------------------------------------------------------------------- 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= 0.159 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 320 5.16 5 C 40466 2.51 5 N 11186 2.21 5 O 12572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 64544 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 4103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4103 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 11, 'TRANS': 531} Chain: "A" Number of atoms: 4103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4103 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 11, 'TRANS': 531} Chain: "b" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3930 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 10, 'TRANS': 506} Chain: "B" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3930 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 10, 'TRANS': 506} Chain: "d" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3985 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "D" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3985 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "e" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4068 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "E" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4068 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "g" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 19, 'TRANS': 498} Chain: "G" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 19, 'TRANS': 498} Chain: "h" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3969 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain: "H" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3969 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain: "q" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4125 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 19, 'TRANS': 523} Chain: "Q" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4125 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 19, 'TRANS': 523} Chain: "z" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4110 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain: "Z" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4110 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Time building chain proxies: 24.91, per 1000 atoms: 0.39 Number of scatterers: 64544 At special positions: 0 Unit cell: (196.382, 216.152, 197.7, 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 320 16.00 O 12572 8.00 N 11186 7.00 C 40466 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: 19.58 Conformation dependent library (CDL) restraints added in 9.6 seconds 16828 Ramachandran restraints generated. 8414 Oldfield, 0 Emsley, 8414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15724 Finding SS restraints... Secondary structure from input PDB file: 324 helices and 92 sheets defined 54.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'a' and resid 22 through 41 removed outlier: 3.591A pdb=" N ARG a 26 " --> pdb=" O GLY a 22 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 73 removed outlier: 3.601A pdb=" N SER a 71 " --> pdb=" O ALA a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 94 Processing helix chain 'a' and resid 97 through 118 removed outlier: 3.565A pdb=" N VAL a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU a 114 " --> pdb=" O LYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 144 removed outlier: 3.660A pdb=" N ARG a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN a 141 " --> pdb=" O ILE a 137 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 164 removed outlier: 3.654A pdb=" N ILE a 159 " --> pdb=" O THR a 155 " (cutoff:3.500A) removed outlier: 3.677A 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: 4.233A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL a 187 " --> pdb=" O ALA a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.543A pdb=" N SER a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 292 removed outlier: 3.606A pdb=" N LEU a 270 " --> pdb=" O ASP a 266 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA a 278 " --> pdb=" O ARG a 274 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE a 288 " --> pdb=" O ARG a 284 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 313 removed outlier: 3.818A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 334 removed outlier: 4.018A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.898A pdb=" N ASP a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL a 409 " --> pdb=" O SER a 405 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 439 removed outlier: 3.546A pdb=" N ILE a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN a 435 " --> pdb=" O ILE a 431 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR a 438 " --> pdb=" O ASP a 434 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR a 439 " --> pdb=" O ASN a 435 " (cutoff:3.500A) Processing helix chain 'a' and resid 444 through 454 Processing helix chain 'a' and resid 456 through 466 removed outlier: 3.512A pdb=" N ASN a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 removed outlier: 3.597A pdb=" N ALA a 475 " --> pdb=" O SER a 471 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS a 481 " --> pdb=" O LEU a 477 " (cutoff:3.500A) Processing helix chain 'a' and resid 512 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.581A pdb=" N ILE a 538 " --> pdb=" O ALA a 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 42 removed outlier: 3.718A pdb=" N ARG A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 97 through 118 removed outlier: 3.508A pdb=" N ILE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 143 removed outlier: 3.553A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 172 through 188 removed outlier: 4.170A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.669A pdb=" N GLU A 215 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 216' Processing helix chain 'A' and resid 266 through 290 removed outlier: 3.504A pdb=" N GLU A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 4.122A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 4.214A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.677A pdb=" N GLU A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.633A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.707A pdb=" N ASN A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.645A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 35 removed outlier: 3.590A pdb=" N ARG b 19 " --> pdb=" O ALA b 15 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU b 20 " --> pdb=" O GLU b 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 4.163A 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: 3.835A pdb=" N LEU b 77 " --> pdb=" O ALA b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 109 removed outlier: 3.969A pdb=" N LYS b 108 " --> pdb=" O ARG b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 Processing helix chain 'b' and resid 145 through 161 removed outlier: 3.608A pdb=" N GLU b 151 " --> pdb=" O THR b 147 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE b 154 " --> pdb=" O ARG b 150 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 168 removed outlier: 3.647A pdb=" N GLN b 168 " --> pdb=" O ILE b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 183 removed outlier: 3.804A pdb=" N PHE b 173 " --> pdb=" O ASP b 169 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE b 181 " --> pdb=" O ALA b 177 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG b 183 " --> pdb=" O ASN b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 191 No H-bonds generated for 'chain 'b' and resid 189 through 191' Processing helix chain 'b' and resid 202 through 206 Processing helix chain 'b' and resid 254 through 278 removed outlier: 3.557A pdb=" N LEU b 258 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU b 262 " --> pdb=" O LEU b 258 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS b 270 " --> pdb=" O ARG b 266 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN b 271 " --> pdb=" O GLU b 267 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS b 272 " --> pdb=" O LYS b 268 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS b 275 " --> pdb=" O ASN b 271 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 302 Processing helix chain 'b' and resid 311 through 322 Processing helix chain 'b' and resid 373 through 397 removed outlier: 3.508A pdb=" N LEU b 377 " --> pdb=" O THR b 373 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 Processing helix chain 'b' and resid 426 through 449 Proline residue: b 441 - end of helix removed outlier: 3.665A pdb=" N ALA b 448 " --> pdb=" O LEU b 444 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY b 449 " --> pdb=" O ALA b 445 " (cutoff:3.500A) Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.516A pdb=" N SER b 457 " --> pdb=" O SER b 453 " (cutoff:3.500A) removed outlier: 3.789A 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: 3.595A pdb=" N VAL b 507 " --> pdb=" O GLU b 503 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 23 Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.982A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.063A 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 71 through 88 removed outlier: 3.523A pdb=" N VAL B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 3.513A pdb=" N GLN B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 138 removed outlier: 3.509A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.713A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.895A pdb=" N PHE B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 255 through 279 removed outlier: 3.727A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.683A pdb=" N VAL B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 397 removed outlier: 3.785A pdb=" N THR B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 Processing helix chain 'B' and resid 426 through 448 removed outlier: 3.572A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 451 through 465 removed outlier: 4.209A 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 Processing helix chain 'd' and resid 17 through 37 removed outlier: 3.633A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.832A 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 72 through 89 removed outlier: 3.671A pdb=" N MET d 77 " --> pdb=" O PRO d 73 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU d 78 " --> pdb=" O VAL d 74 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 113 removed outlier: 3.718A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG d 109 " --> pdb=" O GLY d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.723A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 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: 3.616A pdb=" N LYS d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP d 183 " --> pdb=" O LEU d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 192 No H-bonds generated for 'chain 'd' and resid 190 through 192' Processing helix chain 'd' and resid 258 through 281 removed outlier: 3.870A pdb=" N ALA d 281 " --> pdb=" O LYS d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 308 removed outlier: 3.605A pdb=" N HIS d 303 " --> pdb=" O ASP d 299 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE d 304 " --> pdb=" O LEU d 300 " (cutoff:3.500A) Processing helix chain 'd' and resid 317 through 328 removed outlier: 4.169A pdb=" N GLU d 322 " --> pdb=" O ARG d 318 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.645A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU d 391 " --> pdb=" O ILE d 387 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.943A pdb=" N LYS d 427 " --> pdb=" O ARG d 423 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 432 No H-bonds generated for 'chain 'd' and resid 430 through 432' Processing helix chain 'd' and resid 434 through 448 removed outlier: 4.210A pdb=" N PHE d 438 " --> pdb=" O GLY d 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE d 439 " --> pdb=" O VAL d 435 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN d 441 " --> pdb=" O ALA d 437 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU d 448 " --> pdb=" O ALA d 444 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 Processing helix chain 'd' and resid 461 through 473 Processing helix chain 'd' and resid 501 through 520 Processing helix chain 'D' and resid 16 through 37 removed outlier: 3.658A pdb=" N VAL D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.840A pdb=" N VAL D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.602A pdb=" N SER D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 3.970A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 183 removed outlier: 3.892A pdb=" N LEU D 170 " --> pdb=" O TYR D 166 " (cutoff:3.500A) Proline residue: D 172 - end of helix removed outlier: 3.534A pdb=" N LYS D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 194 Processing helix chain 'D' and resid 256 through 281 removed outlier: 3.537A pdb=" N ILE D 274 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 318 through 328 removed outlier: 4.408A pdb=" N GLU D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.790A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.581A pdb=" N ILE D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 434 through 447 removed outlier: 3.976A pdb=" N PHE D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.853A pdb=" N GLU D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 520 Processing helix chain 'e' and resid 42 through 62 removed outlier: 3.615A pdb=" N LYS e 47 " --> pdb=" O GLY e 43 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 93 Processing helix chain 'e' and resid 98 through 115 removed outlier: 3.699A pdb=" N LEU e 103 " --> pdb=" O GLU e 99 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 removed outlier: 3.555A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 3.564A pdb=" N SER e 159 " --> pdb=" O LYS e 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 189 removed outlier: 3.510A pdb=" N PHE e 176 " --> pdb=" O ASN e 172 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG e 177 " --> pdb=" O ASP e 173 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 195 removed outlier: 3.504A pdb=" N LYS e 195 " --> pdb=" O ILE e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 196 through 211 removed outlier: 3.792A pdb=" N PHE e 200 " --> pdb=" O ASP e 196 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL e 205 " --> pdb=" O ALA e 201 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL e 208 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 3.915A 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 Processing helix chain 'e' and resid 291 through 317 removed outlier: 3.641A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 removed outlier: 3.537A pdb=" N ASN e 332 " --> pdb=" O ASP e 328 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 358 removed outlier: 3.710A pdb=" N GLU e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS e 353 " --> pdb=" O GLN e 349 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA e 355 " --> pdb=" O LEU e 351 " (cutoff:3.500A) Processing helix chain 'e' and resid 412 through 436 Processing helix chain 'e' and resid 444 through 461 removed outlier: 3.969A pdb=" N ASP e 459 " --> pdb=" O SER e 455 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 477 removed outlier: 3.960A pdb=" N ALA e 468 " --> pdb=" O ILE e 464 " (cutoff:3.500A) removed outlier: 3.523A 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: 3.859A pdb=" N LEU e 525 " --> pdb=" O ASP e 521 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'E' and resid 44 through 62 removed outlier: 4.461A pdb=" N LYS E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.284A 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 100 through 115 removed outlier: 3.944A pdb=" N LEU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 138 removed outlier: 3.569A pdb=" N VAL E 122 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 165 Processing helix chain 'E' and resid 173 through 189 removed outlier: 3.787A pdb=" N ALA E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS E 185 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 212 removed outlier: 4.090A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 209 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN E 210 " --> pdb=" O GLU E 206 " (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 291 through 317 removed outlier: 3.533A pdb=" N MET E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL E 313 " --> pdb=" O MET E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 338 removed outlier: 3.588A pdb=" N ASN E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.506A pdb=" N ILE E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 412 through 436 Processing helix chain 'E' and resid 444 through 461 removed outlier: 3.774A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 477 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: 3.546A pdb=" N LEU E 525 " --> pdb=" O ASP E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 550 Processing helix chain 'g' and resid 17 through 36 removed outlier: 4.393A pdb=" N GLN g 21 " --> pdb=" O GLY g 17 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE g 35 " --> pdb=" O VAL g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 39 No H-bonds generated for 'chain 'g' and resid 37 through 39' Processing helix chain 'g' and resid 60 through 66 removed outlier: 3.516A pdb=" N LEU g 65 " --> pdb=" O GLY g 61 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG g 66 " --> pdb=" O HIS g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.601A pdb=" N VAL g 96 " --> pdb=" O GLY g 92 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (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 147 through 156 removed outlier: 3.536A pdb=" N LYS g 152 " --> pdb=" O ASP g 148 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 3.566A 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: 4.154A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 3.676A pdb=" N GLU g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA g 178 " --> pdb=" O LEU g 174 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR g 181 " --> pdb=" O ASP g 177 " (cutoff:3.500A) Processing helix chain 'g' and resid 267 through 288 removed outlier: 3.688A pdb=" N ARG g 271 " --> pdb=" O GLU g 267 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU g 277 " --> pdb=" O LEU g 273 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL g 280 " --> pdb=" O GLU g 276 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.560A pdb=" N HIS g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS g 311 " --> pdb=" O HIS g 307 " (cutoff:3.500A) Processing helix chain 'g' and resid 321 through 333 removed outlier: 3.702A pdb=" N ARG g 327 " --> pdb=" O SER g 323 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.620A pdb=" N SER g 409 " --> pdb=" O ASN g 405 " (cutoff:3.500A) Processing helix chain 'g' and resid 417 through 432 removed outlier: 3.523A pdb=" N SER g 424 " --> pdb=" O GLU g 420 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS g 432 " --> pdb=" O ALA g 428 " (cutoff:3.500A) Processing helix chain 'g' and resid 438 through 450 removed outlier: 3.772A pdb=" N ALA g 446 " --> pdb=" O TYR g 442 " (cutoff:3.500A) Processing helix chain 'g' and resid 450 through 461 Processing helix chain 'g' and resid 463 through 477 removed outlier: 3.551A pdb=" N ALA g 473 " --> pdb=" O SER g 469 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS g 475 " --> pdb=" O LEU g 471 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA g 476 " --> pdb=" O ARG g 472 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN g 477 " --> pdb=" O ALA g 473 " (cutoff:3.500A) Processing helix chain 'g' and resid 494 through 498 Processing helix chain 'g' and resid 503 through 523 removed outlier: 3.561A pdb=" N LEU g 520 " --> pdb=" O SER g 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL g 523 " --> pdb=" O LEU g 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 36 removed outlier: 3.518A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.525A pdb=" N ARG G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.597A pdb=" N GLU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.621A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.646A 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: 3.538A pdb=" N LYS G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 156 removed outlier: 3.652A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (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: 4.382A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.623A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 267 No H-bonds generated for 'chain 'G' and resid 265 through 267' Processing helix chain 'G' and resid 268 through 289 removed outlier: 4.193A pdb=" N ILE G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL G 280 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 287 " --> pdb=" O MET G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 removed outlier: 3.639A pdb=" N HIS G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.802A pdb=" N ARG G 327 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 3.946A 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 344 through 348 removed outlier: 3.684A pdb=" N ASP G 347 " --> pdb=" O LYS G 344 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 344 through 348' Processing helix chain 'G' and resid 385 through 408 Processing helix chain 'G' and resid 417 through 432 removed outlier: 3.529A pdb=" N SER G 424 " --> pdb=" O GLU G 420 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS G 432 " --> pdb=" O ALA G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 450 removed outlier: 3.523A pdb=" N GLN G 443 " --> pdb=" O GLN G 439 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 444 " --> pdb=" O TRP G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 460 Processing helix chain 'G' and resid 463 through 478 removed outlier: 3.585A pdb=" N LEU G 468 " --> pdb=" O PRO G 464 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS G 475 " --> pdb=" O LEU G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 522 removed outlier: 3.547A pdb=" N ALA G 513 " --> pdb=" O SER G 509 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 41 removed outlier: 4.157A pdb=" N ILE h 26 " --> pdb=" O GLY h 22 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 74 removed outlier: 4.369A pdb=" N ASP h 74 " --> pdb=" O LEU h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 94 removed outlier: 4.145A pdb=" N LEU h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 112 removed outlier: 4.001A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 118 removed outlier: 3.563A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.617A pdb=" N ILE h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU h 142 " --> pdb=" O GLU h 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 167 removed outlier: 3.971A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA h 165 " --> pdb=" O CYS h 161 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 188 removed outlier: 3.963A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS h 182 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL h 183 " --> pdb=" O VAL h 179 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL h 186 " --> pdb=" O CYS h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 208 through 212 removed outlier: 3.538A pdb=" N GLU h 211 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER h 212 " --> pdb=" O MET h 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 208 through 212' Processing helix chain 'h' and resid 263 through 289 removed outlier: 3.521A pdb=" N ILE h 270 " --> pdb=" O ASP h 266 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL h 271 " --> pdb=" O TYR h 267 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 removed outlier: 3.816A pdb=" N ASP h 309 " --> pdb=" O GLN h 305 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG h 310 " --> pdb=" O PHE h 306 " (cutoff:3.500A) Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.887A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) removed outlier: 3.894A 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 356 through 360 removed outlier: 3.837A pdb=" N GLU h 360 " --> pdb=" O ILE h 357 " (cutoff:3.500A) Processing helix chain 'h' and resid 382 through 406 removed outlier: 3.539A pdb=" N ALA h 396 " --> pdb=" O SER h 392 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG h 402 " --> pdb=" O MET h 398 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 430 removed outlier: 3.709A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 Processing helix chain 'h' and resid 447 through 458 Processing helix chain 'h' and resid 460 through 473 removed outlier: 3.763A pdb=" N ASN h 466 " --> pdb=" O ILE h 462 " (cutoff:3.500A) Processing helix chain 'h' and resid 491 through 495 Processing helix chain 'h' and resid 500 through 519 Processing helix chain 'H' and resid 22 through 41 removed outlier: 3.941A pdb=" N ILE H 26 " --> pdb=" O GLY H 22 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 77 through 94 removed outlier: 3.721A pdb=" N LEU H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 112 removed outlier: 4.027A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.532A pdb=" N LEU H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.530A pdb=" N ILE H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 167 removed outlier: 3.619A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 173 removed outlier: 4.397A pdb=" N ASN H 173 " --> pdb=" O LEU H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 4.133A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS H 182 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 185 " --> pdb=" O MET H 181 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL H 186 " --> pdb=" O CYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 289 removed outlier: 3.516A pdb=" N VAL H 271 " --> pdb=" O TYR H 267 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 310 removed outlier: 3.827A pdb=" N THR H 304 " --> pdb=" O GLY H 300 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP H 309 " --> pdb=" O GLN H 305 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG H 310 " --> pdb=" O PHE H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 331 Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 356 through 360 removed outlier: 3.713A pdb=" N GLU H 360 " --> pdb=" O ILE H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 406 removed outlier: 3.743A pdb=" N ASP H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG H 402 " --> pdb=" O MET H 398 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN H 406 " --> pdb=" O ARG H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 428 removed outlier: 3.605A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 446 removed outlier: 3.906A pdb=" N MET H 437 " --> pdb=" O GLY H 433 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE H 438 " --> pdb=" O LYS H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 457 removed outlier: 3.508A pdb=" N LEU H 453 " --> pdb=" O ILE H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 474 removed outlier: 3.554A pdb=" N LEU H 465 " --> pdb=" O ALA H 461 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN H 466 " --> pdb=" O ILE H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 491 through 495 Processing helix chain 'H' and resid 500 through 519 Processing helix chain 'q' and resid 22 through 25 removed outlier: 3.869A pdb=" N ASP q 25 " --> pdb=" O SER q 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 22 through 25' Processing helix chain 'q' and resid 26 through 44 removed outlier: 3.717A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.625A pdb=" N ARG q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) Processing helix chain 'q' and resid 79 through 95 removed outlier: 3.667A pdb=" N LYS q 83 " --> pdb=" O HIS q 79 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN q 92 " --> pdb=" O ALA q 88 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 121 removed outlier: 3.751A pdb=" N LYS q 116 " --> pdb=" O ASN q 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU q 117 " --> pdb=" O VAL q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 123 through 145 removed outlier: 3.505A pdb=" N GLU q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP q 143 " --> pdb=" O LEU q 139 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU q 144 " --> pdb=" O LYS q 140 " (cutoff:3.500A) Processing helix chain 'q' and resid 155 through 168 removed outlier: 3.890A pdb=" N LYS q 161 " --> pdb=" O ASN q 157 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 174 through 190 removed outlier: 3.918A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA q 185 " --> pdb=" O LEU q 181 " (cutoff:3.500A) Processing helix chain 'q' and resid 269 through 294 removed outlier: 3.518A pdb=" N ASP q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) Processing helix chain 'q' and resid 306 through 316 removed outlier: 3.810A pdb=" N LEU q 310 " --> pdb=" O GLY q 306 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS q 311 " --> pdb=" O GLU q 307 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR q 312 " --> pdb=" O LEU q 308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN q 314 " --> pdb=" O LEU q 310 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) Processing helix chain 'q' and resid 325 through 334 removed outlier: 3.525A pdb=" N LEU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG q 334 " --> pdb=" O ARG q 330 " (cutoff:3.500A) Processing helix chain 'q' and resid 390 through 410 removed outlier: 3.552A pdb=" N ASP q 402 " --> pdb=" O GLU q 398 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP q 403 " --> pdb=" O ARG q 399 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY q 410 " --> pdb=" O ALA q 406 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 439 removed outlier: 3.596A pdb=" N ILE q 428 " --> pdb=" O GLY q 424 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE q 431 " --> pdb=" O GLU q 427 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER q 432 " --> pdb=" O ILE q 428 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG q 433 " --> pdb=" O GLU q 429 " (cutoff:3.500A) removed outlier: 3.727A 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: 3.511A 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 removed outlier: 4.423A pdb=" N GLU q 515 " --> pdb=" O ASP q 511 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 541 removed outlier: 3.526A pdb=" N ASN q 529 " --> pdb=" O LYS q 525 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 25 Processing helix chain 'Q' and resid 26 through 44 removed outlier: 4.096A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS Q 42 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 75 removed outlier: 3.541A pdb=" N MET Q 71 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 95 removed outlier: 3.991A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 120 removed outlier: 4.100A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE Q 105 " --> pdb=" O ASN Q 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS Q 116 " --> pdb=" O ASN Q 112 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU Q 117 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 143 removed outlier: 3.790A pdb=" N ASP Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 168 removed outlier: 3.941A pdb=" N LYS Q 161 " --> pdb=" O ASN Q 157 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 174 through 190 removed outlier: 3.882A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 216 through 220 Processing helix chain 'Q' and resid 269 through 294 removed outlier: 3.543A pdb=" N MET Q 273 " --> pdb=" O ASN Q 269 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET Q 294 " --> pdb=" O GLU Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 317 removed outlier: 3.661A pdb=" N LEU Q 310 " --> pdb=" O GLY Q 306 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS Q 311 " --> pdb=" O GLU Q 307 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR Q 312 " --> pdb=" O LEU Q 308 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN Q 314 " --> pdb=" O LEU Q 310 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 333 removed outlier: 3.805A pdb=" N LEU Q 329 " --> pdb=" O SER Q 325 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG Q 330 " --> pdb=" O LYS Q 326 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 352 Processing helix chain 'Q' and resid 390 through 410 removed outlier: 3.637A pdb=" N LEU Q 394 " --> pdb=" O THR Q 390 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP Q 396 " --> pdb=" O ASN Q 392 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL Q 408 " --> pdb=" O GLY Q 404 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Q 409 " --> pdb=" O VAL Q 405 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY Q 410 " --> pdb=" O ALA Q 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.833A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU Q 429 " --> pdb=" O ALA Q 425 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU Q 439 " --> pdb=" O THR Q 435 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 455 removed outlier: 4.492A 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: 3.578A pdb=" N VAL Q 474 " --> pdb=" O ASP Q 470 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU Q 475 " --> pdb=" O VAL Q 471 " (cutoff:3.500A) Proline residue: Q 476 - end of helix Processing helix chain 'Q' and resid 511 through 515 removed outlier: 3.519A pdb=" N GLU Q 514 " --> pdb=" O ASP Q 511 " (cutoff:3.500A) Processing helix chain 'Q' and resid 521 through 541 removed outlier: 3.511A pdb=" N PHE Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN Q 529 " --> pdb=" O LYS Q 525 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL Q 538 " --> pdb=" O ALA Q 534 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.619A pdb=" N LEU z 29 " --> pdb=" O SER z 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR z 35 " --> pdb=" O SER z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 65 removed outlier: 3.509A pdb=" N LEU z 63 " --> pdb=" O GLY z 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 70 through 87 removed outlier: 3.690A pdb=" N VAL z 74 " --> pdb=" O SER z 70 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 112 removed outlier: 3.836A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN z 110 " --> pdb=" O HIS z 106 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU z 111 " --> pdb=" O ARG z 107 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 Processing helix chain 'z' and resid 143 through 145 No H-bonds generated for 'chain 'z' and resid 143 through 145' Processing helix chain 'z' and resid 146 through 162 removed outlier: 3.679A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.578A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 190 through 192 No H-bonds generated for 'chain 'z' and resid 190 through 192' Processing helix chain 'z' and resid 203 through 207 removed outlier: 3.523A pdb=" N THR z 207 " --> pdb=" O PRO z 204 " (cutoff:3.500A) Processing helix chain 'z' and resid 255 through 284 removed outlier: 3.596A pdb=" N ASP z 260 " --> pdb=" O ALA z 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS z 261 " --> pdb=" O ASP z 257 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU z 266 " --> pdb=" O LEU z 262 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU z 280 " --> pdb=" O LYS z 276 " (cutoff:3.500A) Processing helix chain 'z' and resid 302 through 312 removed outlier: 3.530A pdb=" N LEU z 306 " --> pdb=" O ASP z 302 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP z 307 " --> pdb=" O PRO z 303 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS z 312 " --> pdb=" O VAL z 308 " (cutoff:3.500A) Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.611A pdb=" N ARG z 327 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 339 through 343 Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.627A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN z 404 " --> pdb=" O ARG z 400 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 3.675A pdb=" N ASN z 430 " --> pdb=" O LEU z 426 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) Processing helix chain 'z' and resid 440 through 450 Processing helix chain 'z' and resid 452 through 462 removed outlier: 3.574A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER z 462 " --> pdb=" O LEU z 458 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 removed outlier: 3.705A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU z 528 " --> pdb=" O ALA z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 35 removed outlier: 4.171A pdb=" N THR Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 removed outlier: 3.565A pdb=" N LEU Z 62 " --> pdb=" O ASP Z 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU Z 65 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 80 Processing helix chain 'Z' and resid 80 through 85 removed outlier: 3.646A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.563A pdb=" N ARG Z 107 " --> pdb=" O ARG Z 103 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 removed outlier: 3.553A pdb=" N GLU Z 135 " --> pdb=" O LYS Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 146 through 162 removed outlier: 4.053A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER Z 157 " --> pdb=" O VAL Z 153 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS Z 161 " --> pdb=" O SER Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 182 Proline residue: Z 172 - end of helix removed outlier: 3.588A pdb=" N VAL Z 178 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL Z 181 " --> pdb=" O ALA Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 192 No H-bonds generated for 'chain 'Z' and resid 190 through 192' Processing helix chain 'Z' and resid 203 through 207 Processing helix chain 'Z' and resid 255 through 284 removed outlier: 3.510A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS Z 276 " --> pdb=" O ALA Z 272 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU Z 280 " --> pdb=" O LYS Z 276 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 312 removed outlier: 3.687A pdb=" N LEU Z 306 " --> pdb=" O ASP Z 302 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP Z 307 " --> pdb=" O PRO Z 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL Z 308 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 332 removed outlier: 3.751A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG Z 327 " --> pdb=" O ARG Z 323 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 348 Processing helix chain 'Z' and resid 384 through 408 removed outlier: 3.734A pdb=" N LEU Z 388 " --> pdb=" O THR Z 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR Z 391 " --> pdb=" O ALA Z 387 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.955A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) Processing helix chain 'Z' and resid 439 through 451 removed outlier: 4.309A pdb=" N GLY Z 443 " --> pdb=" O LYS Z 439 " (cutoff:3.500A) Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.635A pdb=" N VAL Z 459 " --> pdb=" O PRO Z 455 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 483 Processing helix chain 'Z' and resid 500 through 505 Processing helix chain 'Z' and resid 510 through 529 Processing sheet with id=AA1, first strand: chain 'a' and resid 18 through 21 removed outlier: 3.968A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS d 46 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE d 48 " --> pdb=" O ILE d 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 62 through 63 removed outlier: 3.728A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 204 through 207 removed outlier: 6.565A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER a 384 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE a 386 " --> pdb=" O LEU a 217 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU a 217 " --> pdb=" O ILE a 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 222 through 225 removed outlier: 3.676A pdb=" N LYS a 375 " --> pdb=" O GLU a 360 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU a 360 " --> pdb=" O LYS a 375 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR a 377 " --> pdb=" O CYS a 358 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N CYS a 358 " --> pdb=" O THR a 377 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR a 298 " --> pdb=" O VAL a 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 418 through 420 Processing sheet with id=AA6, first strand: chain 'a' and resid 500 through 503 removed outlier: 3.585A pdb=" N VAL a 510 " --> pdb=" O GLY a 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.083A pdb=" N ILE A 541 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET D 47 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.544A pdb=" N THR A 63 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.587A pdb=" N ILE A 386 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 217 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 225 removed outlier: 3.720A pdb=" N LYS A 375 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 360 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 361 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 237 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 316 through 318 removed outlier: 3.884A pdb=" N ILE A 244 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 356 " --> pdb=" O ILE A 244 " (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: 3.582A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP b 43 " --> pdb=" O ILE d 521 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP d 523 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU b 45 " --> pdb=" O ASP d 523 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 193 through 198 removed outlier: 6.168A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL b 368 " --> pdb=" O PHE b 207 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE b 207 " --> pdb=" O VAL b 368 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 304 through 307 removed outlier: 7.112A pdb=" N THR b 283 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS b 230 " --> pdb=" O THR b 283 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE b 285 " --> pdb=" O LYS b 230 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP b 341 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS b 230 " --> pdb=" O GLU b 339 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU b 339 " --> pdb=" O LYS b 230 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS b 340 " --> pdb=" O CYS b 359 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS b 359 " --> pdb=" O CYS b 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 400 through 402 Processing sheet with id=AB8, first strand: chain 'b' and resid 470 through 473 Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.767A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 43 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP D 523 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 45 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 525 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 193 through 199 removed outlier: 6.352A pdb=" N GLN B 194 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 369 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE B 196 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLY B 371 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 198 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 207 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.092A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 338 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AC4, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AC5, first strand: chain 'B' and resid 470 through 473 removed outlier: 3.588A pdb=" N ALA B 480 " --> pdb=" O GLY B 471 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 511 through 514 removed outlier: 8.149A pdb=" N ILE E 73 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE B 514 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N ILE E 75 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS E 72 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 84 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 194 through 200 removed outlier: 6.175A pdb=" N ARG d 195 " --> pdb=" O VAL d 377 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE d 379 " --> pdb=" O ARG d 195 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.550A pdb=" N GLU d 351 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER d 346 " --> pdb=" O LYS d 233 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS d 233 " --> pdb=" O SER d 346 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY d 235 " --> pdb=" O VAL d 285 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU d 286 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASP d 315 " --> pdb=" O LEU d 286 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE d 288 " --> pdb=" O ASP d 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.550A pdb=" N GLU d 351 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER d 346 " --> pdb=" O LYS d 233 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS d 233 " --> pdb=" O SER d 346 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N ILE d 333 " --> pdb=" O ILE d 234 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU d 236 " --> pdb=" O ILE d 333 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 410 through 411 Processing sheet with id=AD2, first strand: chain 'd' and resid 480 through 483 removed outlier: 3.716A pdb=" N GLY d 481 " --> pdb=" O THR d 490 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR d 490 " --> pdb=" O GLY d 481 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 195 through 200 removed outlier: 5.801A pdb=" N ARG D 195 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE D 379 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL D 197 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY D 381 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS D 199 " --> pdb=" O GLY D 381 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 378 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU D 208 " --> pdb=" O VAL D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 213 through 214 removed outlier: 3.623A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR D 364 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP D 348 " --> pdb=" O LYS D 231 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 311 through 316 removed outlier: 9.664A pdb=" N LEU D 286 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE D 316 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE D 288 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N ILE D 333 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU D 236 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AD7, first strand: chain 'D' and resid 481 through 483 removed outlier: 3.599A pdb=" N GLY D 488 " --> pdb=" O SER D 483 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 39 through 40 removed outlier: 4.073A pdb=" N ILE e 551 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU h 52 " --> pdb=" O ILE e 551 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN e 553 " --> pdb=" O LEU h 52 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL h 54 " --> pdb=" O ASN e 553 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE e 555 " --> pdb=" O VAL h 54 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE h 51 " --> pdb=" O SER h 63 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER h 63 " --> pdb=" O ILE h 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 72 through 75 Processing sheet with id=AE1, first strand: chain 'e' and resid 166 through 167 Processing sheet with id=AE2, first strand: chain 'e' and resid 224 through 230 removed outlier: 6.310A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL e 408 " --> pdb=" O LYS e 225 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN e 227 " --> pdb=" O VAL e 408 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N GLY e 410 " --> pdb=" O GLN e 227 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'e' and resid 257 through 258 removed outlier: 3.980A pdb=" N ILE e 380 " --> pdb=" O VAL e 258 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG e 379 " --> pdb=" O GLU e 396 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU e 396 " --> pdb=" O ARG e 379 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'e' and resid 342 through 343 removed outlier: 3.803A pdb=" N VAL e 320 " --> pdb=" O LYS e 268 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 39 through 42 removed outlier: 3.948A pdb=" N LYS E 39 " --> pdb=" O ILE E 556 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE E 556 " --> pdb=" O LYS E 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN E 41 " --> pdb=" O VAL E 554 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 554 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN E 553 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL H 54 " --> pdb=" O ASN E 553 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE E 555 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 53 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AE7, first strand: chain 'E' and resid 224 through 230 removed outlier: 6.176A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N GLY E 410 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ARG E 229 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 240 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 257 through 258 removed outlier: 4.297A pdb=" N ILE E 380 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG E 379 " --> pdb=" O GLU E 396 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 342 through 343 removed outlier: 6.203A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 320 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'g' and resid 55 through 56 Processing sheet with id=AF2, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AF3, first strand: chain 'g' and resid 207 through 209 removed outlier: 3.573A pdb=" N GLU g 207 " --> pdb=" O ILE g 379 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU g 381 " --> pdb=" O GLU g 207 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 224 through 225 Processing sheet with id=AF5, first strand: chain 'g' and resid 294 through 296 Processing sheet with id=AF6, first strand: chain 'g' and resid 482 through 484 Processing sheet with id=AF7, first strand: chain 'G' and resid 55 through 56 Processing sheet with id=AF8, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AF9, first strand: chain 'G' and resid 206 through 209 removed outlier: 3.803A pdb=" N LEU G 220 " --> pdb=" O THR G 378 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 224 through 225 removed outlier: 3.674A pdb=" N LEU G 225 " --> pdb=" O SER G 366 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 245 through 246 removed outlier: 3.680A pdb=" N LEU G 246 " --> pdb=" O ILE G 296 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 482 through 484 Processing sheet with id=AG4, first strand: chain 'h' and resid 201 through 205 removed outlier: 3.980A pdb=" N GLY h 380 " --> pdb=" O ILE h 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU h 377 " --> pdb=" O LEU h 213 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU h 213 " --> pdb=" O LEU h 377 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'h' and resid 219 through 220 removed outlier: 3.514A pdb=" N ASN h 363 " --> pdb=" O PHE h 220 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU h 364 " --> pdb=" O GLU h 353 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU h 353 " --> pdb=" O LEU h 364 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN h 366 " --> pdb=" O LEU h 351 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU h 351 " --> pdb=" O GLN h 366 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 241 through 243 removed outlier: 6.240A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 409 through 411 Processing sheet with id=AG8, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.591A pdb=" N GLY h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 200 through 205 removed outlier: 6.261A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY H 380 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 204 " --> pdb=" O GLY H 380 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 219 through 220 removed outlier: 3.600A pdb=" N ASN H 363 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU H 364 " --> pdb=" O GLU H 353 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU H 353 " --> pdb=" O LEU H 364 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN H 366 " --> pdb=" O LEU H 351 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU H 351 " --> pdb=" O GLN H 366 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 241 through 243 removed outlier: 6.851A pdb=" N LEU H 242 " --> pdb=" O LEU H 294 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL H 293 " --> pdb=" O ALA H 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'H' and resid 409 through 411 Processing sheet with id=AH4, first strand: chain 'H' and resid 479 through 481 Processing sheet with id=AH5, first strand: chain 'H' and resid 523 through 525 removed outlier: 6.889A pdb=" N ILE H 524 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS Q 53 " --> pdb=" O THR Q 65 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'q' and resid 20 through 21 removed outlier: 3.715A pdb=" N ILE q 545 " --> pdb=" O MET z 45 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS z 54 " --> pdb=" O LEU z 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 53 through 56 removed outlier: 3.539A pdb=" N LYS q 53 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 207 through 213 removed outlier: 6.538A pdb=" N ARG q 208 " --> pdb=" O ILE q 384 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU q 386 " --> pdb=" O ARG q 208 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL q 210 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N GLY q 388 " --> pdb=" O VAL q 210 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE q 212 " --> pdb=" O GLY q 388 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'q' and resid 227 through 228 removed outlier: 3.968A pdb=" N ASP q 366 " --> pdb=" O ILE q 363 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'q' and resid 319 through 322 removed outlier: 6.477A pdb=" N LYS q 246 " --> pdb=" O CYS q 298 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL q 300 " --> pdb=" O LYS q 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA q 248 " --> pdb=" O VAL q 300 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N LEU q 341 " --> pdb=" O VAL q 247 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL q 249 " --> pdb=" O LEU q 341 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'q' and resid 319 through 322 removed outlier: 6.477A pdb=" N LYS q 246 " --> pdb=" O CYS q 298 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL q 300 " --> pdb=" O LYS q 246 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA q 248 " --> pdb=" O VAL q 300 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AI4, first strand: chain 'Q' and resid 19 through 21 removed outlier: 3.995A pdb=" N ASN Q 19 " --> pdb=" O MET Q 546 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET Q 546 " --> pdb=" O ASN Q 19 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR Q 21 " --> pdb=" O ILE Q 544 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE Q 544 " --> pdb=" O TYR Q 21 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE Q 545 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS Z 44 " --> pdb=" O THR Z 56 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS Z 54 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 207 through 213 removed outlier: 3.778A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR Q 221 " --> pdb=" O ILE Q 385 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 319 through 322 removed outlier: 6.787A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N LEU Q 341 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL Q 249 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Q' and resid 319 through 322 removed outlier: 6.787A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL Q 247 " --> pdb=" O GLY Q 353 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 357 through 363 removed outlier: 3.839A pdb=" N THR Q 357 " --> pdb=" O LYS Q 372 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 419 through 420 Processing sheet with id=AJ1, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AJ2, first strand: chain 'z' and resid 194 through 199 Processing sheet with id=AJ3, first strand: chain 'z' and resid 214 through 215 removed outlier: 3.610A pdb=" N LEU z 215 " --> pdb=" O THR z 365 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR z 365 " --> pdb=" O LEU z 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'z' and resid 227 through 228 Processing sheet with id=AJ5, first strand: chain 'z' and resid 231 through 234 removed outlier: 6.260A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AJ7, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 194 through 199 removed outlier: 6.375A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE Z 380 " --> pdb=" O GLU Z 195 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET Z 197 " --> pdb=" O ILE Z 380 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU Z 379 " --> pdb=" O THR Z 208 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR Z 208 " --> pdb=" O LEU Z 379 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Z' and resid 214 through 215 removed outlier: 3.922A pdb=" N THR Z 365 " --> pdb=" O LEU Z 215 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE Z 364 " --> pdb=" O GLU Z 357 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR Z 366 " --> pdb=" O TYR Z 355 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR Z 355 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 315 through 316 removed outlier: 3.725A pdb=" N LEU Z 315 " --> pdb=" O PHE Z 293 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Z' and resid 490 through 491 3196 hydrogen bonds defined for protein. 9255 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: 27.76 Time building geometry restraints manager: 21.60 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: 21913 1.34 - 1.46: 12010 1.46 - 1.58: 30823 1.58 - 1.70: 0 1.70 - 1.82: 518 Bond restraints: 65264 Sorted by residual: bond pdb=" C ALA Q 346 " pdb=" N PRO Q 347 " ideal model delta sigma weight residual 1.334 1.446 -0.112 2.34e-02 1.83e+03 2.29e+01 bond pdb=" C ALA q 346 " pdb=" N PRO q 347 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.42e+01 bond pdb=" CA THR B 398 " pdb=" CB THR B 398 " ideal model delta sigma weight residual 1.541 1.559 -0.018 1.20e-02 6.94e+03 2.32e+00 bond pdb=" CA THR b 398 " pdb=" CB THR b 398 " ideal model delta sigma weight residual 1.541 1.558 -0.017 1.20e-02 6.94e+03 2.04e+00 bond pdb=" N THR B 398 " pdb=" CA THR B 398 " ideal model delta sigma weight residual 1.456 1.473 -0.016 1.23e-02 6.61e+03 1.80e+00 ... (remaining 65259 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.94: 1291 106.94 - 113.70: 37990 113.70 - 120.46: 25452 120.46 - 127.21: 22902 127.21 - 133.97: 403 Bond angle restraints: 88038 Sorted by residual: angle pdb=" C SER Q 505 " pdb=" CA SER Q 505 " pdb=" CB SER Q 505 " ideal model delta sigma weight residual 116.63 110.19 6.44 1.16e+00 7.43e-01 3.08e+01 angle pdb=" C ASP q 493 " pdb=" CA ASP q 493 " pdb=" CB ASP q 493 " ideal model delta sigma weight residual 117.23 111.28 5.95 1.36e+00 5.41e-01 1.92e+01 angle pdb=" N ASN B 142 " pdb=" CA ASN B 142 " pdb=" C ASN B 142 " ideal model delta sigma weight residual 113.02 108.16 4.86 1.20e+00 6.94e-01 1.64e+01 angle pdb=" N THR b 398 " pdb=" CA THR b 398 " pdb=" C THR b 398 " ideal model delta sigma weight residual 113.28 107.18 6.10 1.57e+00 4.06e-01 1.51e+01 angle pdb=" N THR B 398 " pdb=" CA THR B 398 " pdb=" C THR B 398 " ideal model delta sigma weight residual 113.28 107.34 5.94 1.57e+00 4.06e-01 1.43e+01 ... (remaining 88033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 39908 16.16 - 32.32: 358 32.32 - 48.47: 205 48.47 - 64.63: 60 64.63 - 80.79: 3 Dihedral angle restraints: 40534 sinusoidal: 16262 harmonic: 24272 Sorted by residual: dihedral pdb=" CA VAL H 246 " pdb=" C VAL H 246 " pdb=" N GLU H 247 " pdb=" CA GLU H 247 " ideal model delta harmonic sigma weight residual 180.00 147.84 32.16 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA GLU g 193 " pdb=" C GLU g 193 " pdb=" N PRO g 194 " pdb=" CA PRO g 194 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLU H 247 " pdb=" C GLU H 247 " pdb=" N LEU H 248 " pdb=" CA LEU H 248 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 40531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 7659 0.036 - 0.072: 2052 0.072 - 0.108: 585 0.108 - 0.144: 243 0.144 - 0.180: 3 Chirality restraints: 10542 Sorted by residual: chirality pdb=" CB ILE e 244 " pdb=" CA ILE e 244 " pdb=" CG1 ILE e 244 " pdb=" CG2 ILE e 244 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ILE b 422 " pdb=" N ILE b 422 " pdb=" C ILE b 422 " pdb=" CB ILE b 422 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 10539 not shown) Planarity restraints: 11350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG d 372 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO d 373 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO d 373 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO d 373 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 18 " -0.007 2.00e-02 2.50e+03 6.65e-03 8.84e-01 pdb=" CG TYR Q 18 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 18 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 18 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 18 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR Q 18 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR Q 18 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE e 244 " -0.005 2.00e-02 2.50e+03 9.30e-03 8.65e-01 pdb=" C ILE e 244 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE e 244 " -0.006 2.00e-02 2.50e+03 pdb=" N LEU e 245 " -0.005 2.00e-02 2.50e+03 ... (remaining 11347 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2376 2.73 - 3.27: 66059 3.27 - 3.81: 97458 3.81 - 4.36: 121565 4.36 - 4.90: 205605 Nonbonded interactions: 493063 Sorted by model distance: nonbonded pdb=" O LEU H 198 " pdb=" OG1 THR H 373 " model vdw 2.187 2.440 nonbonded pdb=" O SER B 462 " pdb=" OG SER B 468 " model vdw 2.188 2.440 nonbonded pdb=" OD2 ASP B 512 " pdb=" OG1 THR E 63 " model vdw 2.232 2.440 nonbonded pdb=" O LEU E 223 " pdb=" OG1 THR E 403 " model vdw 2.234 2.440 nonbonded pdb=" O LEU Z 328 " pdb=" OG1 THR Z 332 " model vdw 2.241 2.440 ... (remaining 493058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'b' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'd' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'e' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'g' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'h' } pdb_interpretation.ncs_group { reference = chain 'Q' selection = chain 'q' } pdb_interpretation.ncs_group { reference = chain 'Z' selection = chain 'z' } Set refine NCS operators NCS operators will be refined. 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: 0.800 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: 0.050 Extract box with map and model: 6.420 Check model and map are aligned: 0.800 Set scattering table: 0.490 Process input model: 136.680 Find NCS groups from input model: 5.830 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 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 0.112 65264 Z= 0.097 Angle : 0.424 6.614 88038 Z= 0.249 Chirality : 0.039 0.180 10542 Planarity : 0.001 0.025 11350 Dihedral : 7.259 80.788 24810 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.07), residues: 8414 helix: -3.18 (0.05), residues: 4103 sheet: -1.03 (0.16), residues: 779 loop : -1.39 (0.09), residues: 3532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 167 HIS 0.008 0.001 HIS Q 494 PHE 0.015 0.001 PHE d 239 TYR 0.017 0.001 TYR Q 18 ARG 0.003 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16828 Ramachandran restraints generated. 8414 Oldfield, 0 Emsley, 8414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16828 Ramachandran restraints generated. 8414 Oldfield, 0 Emsley, 8414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1666 time to fit residues: 33.7734 Evaluate side-chains 79 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5054 Evaluate side-chains 135 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1572 time to fit residues: 25.1773 Evaluate side-chains 71 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4786 Evaluate side-chains 162 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1649 time to fit residues: 31.4529 Evaluate side-chains 79 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5110 Evaluate side-chains 156 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1590 time to fit residues: 29.4771 Evaluate side-chains 73 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5352 Evaluate side-chains 169 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1693 time to fit residues: 33.4565 Evaluate side-chains 92 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4859 Evaluate side-chains 127 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1631 time to fit residues: 24.4952 Evaluate side-chains 57 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4736 Evaluate side-chains 195 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1514 time to fit residues: 35.3308 Evaluate side-chains 105 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4908 Evaluate side-chains 194 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1622 time to fit residues: 37.3406 Evaluate side-chains 114 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 10.0000 chunk 633 optimal weight: 4.9990 chunk 351 optimal weight: 0.4980 chunk 216 optimal weight: 0.8980 chunk 427 optimal weight: 1.9990 chunk 338 optimal weight: 0.0870 chunk 655 optimal weight: 20.0000 chunk 253 optimal weight: 2.9990 chunk 398 optimal weight: 5.9990 chunk 487 optimal weight: 4.9990 chunk 759 optimal weight: 3.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 88 GLN a 90 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 ASN D 125 GLN D 140 HIS D 250 ASN D 284 ASN D 499 GLN Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS E 324 GLN E 397 GLN E 486 ASN E 536 GLN Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 21 GLN G 188 GLN G 226 ASN G 237 HIS G 459 ASN Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 25 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 HIS ** H 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 394 HIS Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 373 GLN ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 GLN Z 142 ASN Z 145 ASN Z 192 HIS ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 297 ASN Z 356 GLN Z 385 HIS ** Z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 515 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 1.0393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 65264 Z= 0.275 Angle : 0.817 21.084 88038 Z= 0.448 Chirality : 0.049 0.543 10542 Planarity : 0.006 0.256 11350 Dihedral : 4.604 43.310 8928 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 2.92 % Favored : 96.65 % Rotamer: Outliers : 0.31 % Allowed : 3.34 % Favored : 96.35 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.18 (0.08), residues: 8414 helix: -0.40 (0.07), residues: 4292 sheet: -0.19 (0.17), residues: 830 loop : -1.31 (0.10), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP g 440 HIS 0.017 0.002 HIS E 50 PHE 0.029 0.002 PHE Z 464 TYR 0.035 0.002 TYR b 124 ARG 0.031 0.001 ARG G 522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16668 Ramachandran restraints generated. 8334 Oldfield, 0 Emsley, 8334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16668 Ramachandran restraints generated. 8334 Oldfield, 0 Emsley, 8334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 0.375 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 outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1553 time to fit residues: 26.5319 Evaluate side-chains 77 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5096 Evaluate side-chains 89 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1282 time to fit residues: 14.1199 Evaluate side-chains 54 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4820 Evaluate side-chains 104 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.397 Fit side-chains 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: 104 average time/residue: 0.1494 time to fit residues: 18.8237 Evaluate side-chains 71 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4896 Evaluate side-chains 96 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 95 average time/residue: 0.1111 time to fit residues: 13.6183 Evaluate side-chains 65 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0559 time to fit residues: 0.5831 Evaluate side-chains 109 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.1444 time to fit residues: 18.7504 Evaluate side-chains 74 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5249 Evaluate side-chains 72 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1248 time to fit residues: 11.3748 Evaluate side-chains 51 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4768 Evaluate side-chains 125 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.368 Fit side-chains 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: 125 average time/residue: 0.1375 time to fit residues: 21.2185 Evaluate side-chains 82 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4953 Evaluate side-chains 120 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1423 time to fit residues: 20.8690 Evaluate side-chains 88 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 631 optimal weight: 3.9990 chunk 516 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 760 optimal weight: 0.9990 chunk 821 optimal weight: 10.0000 chunk 677 optimal weight: 4.9990 chunk 754 optimal weight: 0.0970 chunk 259 optimal weight: 10.0000 chunk 610 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 209 HIS ** a 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 485 GLN ** a 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 217 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 HIS ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** G 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN ** H 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 101 ASN Q 268 HIS Q 373 GLN ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 HIS Z 142 ASN ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 356 GLN ** Z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 1.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.546 65264 Z= 0.518 Angle : 1.310 52.986 88038 Z= 0.665 Chirality : 0.081 3.109 10542 Planarity : 0.011 0.205 11350 Dihedral : 5.274 45.250 8928 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.87 % Favored : 95.84 % Rotamer: Outliers : 1.74 % Allowed : 4.18 % Favored : 94.08 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.40 (0.08), residues: 8414 helix: -0.55 (0.07), residues: 4280 sheet: -0.32 (0.16), residues: 894 loop : -1.47 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 440 HIS 0.112 0.004 HIS A 403 PHE 0.201 0.005 PHE a 175 TYR 0.131 0.005 TYR a 432 ARG 0.094 0.003 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16668 Ramachandran restraints generated. 8334 Oldfield, 0 Emsley, 8334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16668 Ramachandran restraints generated. 8334 Oldfield, 0 Emsley, 8334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 102 time to evaluate : 0.374 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 outliers start: 53 outliers final: 14 residues processed: 126 average time/residue: 0.1541 time to fit residues: 23.4272 Evaluate side-chains 91 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0767 time to fit residues: 1.9531 Evaluate side-chains 67 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.1003 time to fit residues: 9.0084 Evaluate side-chains 54 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4792 Evaluate side-chains 89 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1313 time to fit residues: 14.6728 Evaluate side-chains 68 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4922 Evaluate side-chains 75 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.0923 time to fit residues: 9.5424 Evaluate side-chains 58 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5030 Evaluate side-chains 93 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.1034 time to fit residues: 12.4371 Evaluate side-chains 72 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0307 time to fit residues: 0.5476 Evaluate side-chains 60 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 58 average time/residue: 0.1262 time to fit residues: 9.3453 Evaluate side-chains 45 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4720 Evaluate side-chains 107 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1174 time to fit residues: 15.9526 Evaluate side-chains 70 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4931 Evaluate side-chains 99 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1018 time to fit residues: 13.2272 Evaluate side-chains 81 residues out of total 451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3546 > 50: distance: 0 - 1: 7.971 distance: 1 - 2: 5.785 distance: 1 - 7: 4.800 distance: 4 - 6: 10.315 distance: 7 - 8: 4.570 distance: 8 - 9: 6.561 distance: 8 - 11: 6.300 distance: 9 - 10: 13.270 distance: 9 - 15: 17.272 distance: 11 - 12: 4.765 distance: 12 - 13: 6.902 distance: 12 - 14: 3.167 distance: 15 - 16: 5.760 distance: 16 - 17: 8.198 distance: 16 - 19: 12.705 distance: 17 - 18: 11.456 distance: 17 - 20: 9.905 distance: 20 - 21: 8.429 distance: 21 - 22: 14.875 distance: 22 - 23: 5.687 distance: 22 - 24: 13.937 distance: 24 - 25: 15.852 distance: 25 - 26: 18.103 distance: 25 - 28: 12.101 distance: 26 - 27: 16.705 distance: 26 - 29: 11.091 distance: 29 - 30: 4.369 distance: 30 - 31: 14.813 distance: 30 - 33: 13.562 distance: 31 - 32: 13.457 distance: 31 - 38: 8.698 distance: 33 - 34: 21.120 distance: 34 - 35: 19.409 distance: 35 - 36: 32.067 distance: 35 - 37: 20.471 distance: 38 - 39: 3.166 distance: 39 - 40: 6.789 distance: 39 - 42: 10.106 distance: 40 - 41: 6.542 distance: 40 - 45: 8.975 distance: 42 - 43: 25.656 distance: 42 - 44: 14.233 distance: 45 - 46: 8.304 distance: 46 - 47: 4.358 distance: 46 - 49: 15.764 distance: 47 - 48: 22.307 distance: 47 - 52: 5.044 distance: 49 - 50: 12.404 distance: 49 - 51: 7.432 distance: 52 - 53: 6.117 distance: 53 - 54: 18.616 distance: 53 - 56: 9.159 distance: 54 - 55: 21.078 distance: 54 - 60: 18.783 distance: 56 - 57: 12.346 distance: 57 - 58: 14.400 distance: 57 - 59: 16.862 distance: 61 - 62: 5.389 distance: 61 - 64: 13.440 distance: 62 - 63: 8.734 distance: 64 - 65: 9.635 distance: 64 - 66: 12.904 distance: 67 - 68: 14.970