Starting phenix.real_space_refine on Sat Dec 9 06:22:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/12_2023/6ks7_0759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/12_2023/6ks7_0759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/12_2023/6ks7_0759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/12_2023/6ks7_0759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/12_2023/6ks7_0759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ks7_0759/12_2023/6ks7_0759.pdb" } resolution = 4.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.164 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 316 5.16 5 C 38930 2.51 5 N 10732 2.21 5 O 12044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 15": "NH1" <-> "NH2" 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" Residue "Z TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 62022 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3878 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 12, 'TRANS': 493} Chain: "a" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3879 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 10, 'TRANS': 503} Chain breaks: 1 Chain: "A" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3924 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 10, 'TRANS': 510} Chain breaks: 1 Chain: "b" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3833 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 10, 'TRANS': 494} Chain: "B" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3833 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 10, 'TRANS': 494} Chain: "d" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3687 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 470} Chain breaks: 2 Chain: "D" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3756 Classifications: {'peptide': 492} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 477} Chain breaks: 3 Chain: "e" Number of atoms: 3842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3842 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 1 Chain: "E" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 15, 'TRANS': 502} Chain: "g" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3722 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 18, 'TRANS': 468} Chain breaks: 2 Chain: "G" Number of atoms: 3905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3905 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 18, 'TRANS': 489} Chain breaks: 1 Chain: "h" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3658 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 12, 'TRANS': 467} Chain breaks: 1 Chain: "q" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3978 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 18, 'TRANS': 505} Chain: "Q" Number of atoms: 4005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4005 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 18, 'TRANS': 509} Chain: "z" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4070 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "Z" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4070 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Time building chain proxies: 23.78, per 1000 atoms: 0.38 Number of scatterers: 62022 At special positions: 0 Unit cell: (201.654, 204.29, 205.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 316 16.00 O 12044 8.00 N 10732 7.00 C 38930 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: 18.03 Conformation dependent library (CDL) restraints added in 8.6 seconds 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15136 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 88 sheets defined 54.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.683A pdb=" N ALA H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.534A pdb=" N LEU H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP H 74 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 94 Processing helix chain 'H' and resid 97 through 112 removed outlier: 3.944A pdb=" N THR H 102 " --> pdb=" O THR H 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 removed outlier: 3.907A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 144 removed outlier: 3.692A pdb=" N ILE H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS H 131 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU H 142 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 167 removed outlier: 4.449A pdb=" N LEU H 158 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA H 165 " --> pdb=" O CYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 4.194A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 186 " --> pdb=" O CYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 208 through 212 removed outlier: 3.596A pdb=" N GLU H 211 " --> pdb=" O ALA H 208 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 212 " --> pdb=" O MET H 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 208 through 212' Processing helix chain 'H' and resid 265 through 270 removed outlier: 4.417A pdb=" N ALA H 269 " --> pdb=" O GLU H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 272 No H-bonds generated for 'chain 'H' and resid 271 through 272' Processing helix chain 'H' and resid 273 through 277 Processing helix chain 'H' and resid 278 through 289 removed outlier: 4.066A pdb=" N GLN H 284 " --> pdb=" O GLU H 280 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 304 removed outlier: 3.857A pdb=" N ALA H 303 " --> pdb=" O GLY H 300 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR H 304 " --> pdb=" O ASP H 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 300 through 304' Processing helix chain 'H' and resid 305 through 310 removed outlier: 3.771A pdb=" N ASP H 309 " --> pdb=" O GLN H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 331 removed outlier: 3.566A pdb=" N MET H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN H 324 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG H 325 " --> pdb=" O ASP H 321 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL H 326 " --> pdb=" O ASP H 322 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE H 327 " --> pdb=" O MET H 323 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN H 328 " --> pdb=" O ASN H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 382 through 406 removed outlier: 3.597A pdb=" N GLU H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE H 399 " --> pdb=" O ASP H 395 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU H 404 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 431 removed outlier: 3.568A pdb=" N GLU H 419 " --> pdb=" O ALA H 415 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 424 " --> pdb=" O VAL H 420 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP H 426 " --> pdb=" O LYS H 422 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR H 430 " --> pdb=" O ASP H 426 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE H 431 " --> pdb=" O TYR H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 446 Processing helix chain 'H' and resid 447 through 457 Processing helix chain 'H' and resid 460 through 472 removed outlier: 3.728A pdb=" N ARG H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA H 471 " --> pdb=" O LYS H 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 519 removed outlier: 3.723A pdb=" N LEU H 507 " --> pdb=" O LYS H 503 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN H 508 " --> pdb=" O ILE H 504 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE H 517 " --> pdb=" O ALA H 513 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 41 removed outlier: 3.781A pdb=" N ARG a 26 " --> pdb=" O GLY a 22 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 66 through 73 removed outlier: 3.802A pdb=" N LEU a 70 " --> pdb=" O GLY a 66 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER a 71 " --> pdb=" O ALA a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 94 removed outlier: 3.571A pdb=" N ILE a 82 " --> pdb=" O PRO a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 111 removed outlier: 3.752A pdb=" N VAL a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU a 109 " --> pdb=" O ALA a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 118 removed outlier: 3.920A pdb=" N LEU a 115 " --> pdb=" O ARG a 111 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS a 117 " --> pdb=" O ASN a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 144 removed outlier: 3.555A pdb=" N ILE a 137 " --> pdb=" O LEU a 133 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE a 139 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL a 143 " --> pdb=" O PHE a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 removed outlier: 4.309A pdb=" N ALA a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS a 161 " --> pdb=" O ILE a 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR a 162 " --> pdb=" O ASN a 158 " (cutoff:3.500A) removed outlier: 4.060A 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: 4.446A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N MET a 179 " --> pdb=" O PHE a 175 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP a 182 " --> pdb=" O ASN a 178 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL a 187 " --> pdb=" O ALA a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.582A pdb=" N SER a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 274 through 292 removed outlier: 4.124A pdb=" N ALA a 278 " --> pdb=" O ARG a 274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU a 283 " --> pdb=" O GLY a 279 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG a 284 " --> pdb=" O ILE a 280 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE a 288 " --> pdb=" O ARG a 284 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE a 289 " --> pdb=" O VAL a 285 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 313 removed outlier: 3.836A pdb=" N GLU a 309 " --> pdb=" O LEU a 305 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE a 310 " --> pdb=" O CYS a 306 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU a 312 " --> pdb=" O LYS a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 324 through 334 removed outlier: 4.261A pdb=" N ARG a 328 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.520A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG a 400 " --> pdb=" O ASP a 396 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS a 403 " --> pdb=" O GLU a 399 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP a 404 " --> pdb=" O ARG a 400 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL a 408 " --> pdb=" O ASP a 404 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL a 409 " --> pdb=" O SER a 405 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 437 removed outlier: 3.802A pdb=" N ILE a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR a 432 " --> pdb=" O ALA a 428 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP a 434 " --> pdb=" O ASN a 430 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN a 435 " --> pdb=" O ILE a 431 " (cutoff:3.500A) Processing helix chain 'a' and resid 443 through 454 removed outlier: 4.063A pdb=" N ALA a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 466 removed outlier: 3.613A pdb=" N ASN a 465 " --> pdb=" O THR a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 removed outlier: 3.516A pdb=" N TYR a 480 " --> pdb=" O LYS a 476 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN a 485 " --> pdb=" O HIS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 511 through 516 Processing helix chain 'a' and resid 521 through 540 removed outlier: 3.695A pdb=" N ALA a 537 " --> pdb=" O GLU a 533 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE a 538 " --> pdb=" O ALA a 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 42 removed outlier: 4.008A pdb=" N ARG A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.777A pdb=" N ILE A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.764A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.567A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.714A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.964A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 4.243A pdb=" N ASP A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.848A pdb=" N SER A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 290 removed outlier: 3.578A pdb=" N ILE A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.522A pdb=" N LYS A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.731A pdb=" N ARG A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.791A pdb=" N GLU A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.712A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 456 through 463 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.951A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.531A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 35 removed outlier: 3.511A pdb=" N GLY b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA b 28 " --> pdb=" O VAL b 24 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL b 29 " --> pdb=" O GLY b 25 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER b 35 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 67 removed outlier: 3.552A pdb=" N ILE b 63 " --> pdb=" O ASP b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 71 through 74 Processing helix chain 'b' and resid 75 through 88 removed outlier: 3.814A pdb=" N ASN b 79 " --> pdb=" O LYS b 75 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE b 80 " --> pdb=" O VAL b 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP b 86 " --> pdb=" O LYS b 82 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU b 87 " --> pdb=" O VAL b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 105 removed outlier: 3.862A pdb=" N THR b 96 " --> pdb=" O THR b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 138 removed outlier: 3.557A pdb=" N ALA b 130 " --> pdb=" O LEU b 126 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS b 137 " --> pdb=" O ASP b 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA b 138 " --> pdb=" O ALA b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.580A pdb=" N GLU b 151 " --> pdb=" O THR b 147 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP b 152 " --> pdb=" O MET b 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU b 153 " --> pdb=" O PHE b 149 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE b 154 " --> pdb=" O ARG b 150 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR b 159 " --> pdb=" O HIS b 155 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR b 160 " --> pdb=" O ILE b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 168 removed outlier: 3.564A pdb=" N GLN b 168 " --> pdb=" O ILE b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 183 removed outlier: 3.728A pdb=" N PHE b 173 " --> pdb=" O ASP b 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA b 177 " --> pdb=" O PHE b 173 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE b 181 " --> pdb=" O ALA b 177 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU b 182 " --> pdb=" O THR b 178 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG b 183 " --> pdb=" O ASN b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 191 No H-bonds generated for 'chain 'b' and resid 189 through 191' Processing helix chain 'b' and resid 202 through 206 Processing helix chain 'b' and resid 254 through 259 removed outlier: 3.834A pdb=" N ALA b 259 " --> pdb=" O THR b 255 " (cutoff:3.500A) Processing helix chain 'b' and resid 259 through 278 removed outlier: 4.161A pdb=" N LYS b 270 " --> pdb=" O ARG b 266 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN b 271 " --> pdb=" O GLU b 267 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS b 272 " --> pdb=" O LYS b 268 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS b 275 " --> pdb=" O ASN b 271 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE b 276 " --> pdb=" O LYS b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 302 removed outlier: 3.529A pdb=" N PHE b 298 " --> pdb=" O PRO b 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR b 299 " --> pdb=" O GLU b 295 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP b 300 " --> pdb=" O GLN b 296 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU b 301 " --> pdb=" O LEU b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 311 through 322 removed outlier: 3.647A pdb=" N ALA b 318 " --> pdb=" O VAL b 314 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 397 removed outlier: 3.725A pdb=" N LEU b 377 " --> pdb=" O THR b 373 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL b 390 " --> pdb=" O ASP b 386 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS b 396 " --> pdb=" O SER b 392 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 removed outlier: 3.734A pdb=" N SER b 412 " --> pdb=" O GLU b 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 438 removed outlier: 3.619A pdb=" N ARG b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA b 436 " --> pdb=" O ALA b 432 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG b 438 " --> pdb=" O ALA b 434 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 447 removed outlier: 3.624A pdb=" N ASN b 447 " --> pdb=" O ILE b 443 " (cutoff:3.500A) Processing helix chain 'b' and resid 451 through 465 removed outlier: 3.564A pdb=" N LEU b 455 " --> pdb=" O ASP b 451 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER b 461 " --> pdb=" O SER b 457 " (cutoff:3.500A) removed outlier: 4.091A 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: 3.718A pdb=" N VAL b 507 " --> pdb=" O GLU b 503 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 35 removed outlier: 3.639A pdb=" N GLY B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 3.999A 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: 3.519A pdb=" N LYS B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 removed outlier: 3.518A pdb=" N THR B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 138 removed outlier: 4.445A pdb=" N ILE B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 removed outlier: 3.719A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.664A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.880A pdb=" N PHE B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 255 through 268 removed outlier: 4.315A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 4.424A pdb=" N LYS B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.539A pdb=" N PHE B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.533A pdb=" N VAL B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 394 removed outlier: 3.753A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.517A pdb=" N SER B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 removed outlier: 3.640A pdb=" N PHE B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.808A pdb=" N THR B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 464 removed outlier: 3.504A pdb=" N SER B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 510 removed outlier: 3.713A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 37 removed outlier: 3.637A pdb=" N THR d 37 " --> pdb=" O ASP d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 68 Processing helix chain 'd' and resid 76 through 89 removed outlier: 3.998A pdb=" N GLU d 80 " --> pdb=" O ARG d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 107 removed outlier: 3.848A pdb=" N VAL d 97 " --> pdb=" O THR d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 113 removed outlier: 3.681A pdb=" N ASN d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 139 removed outlier: 3.546A pdb=" N ILE d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN d 125 " --> pdb=" O ALA d 121 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL d 132 " --> pdb=" O ALA d 128 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP d 133 " --> pdb=" O LYS d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 3.556A pdb=" N ARG d 152 " --> pdb=" O GLU d 148 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 161 No H-bonds generated for 'chain 'd' and resid 159 through 161' Processing helix chain 'd' and resid 166 through 183 Proline residue: d 172 - end of helix removed outlier: 3.714A pdb=" N LYS d 180 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE d 181 " --> pdb=" O SER d 177 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP d 183 " --> pdb=" O LEU d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 194 removed outlier: 3.824A pdb=" N ASP d 193 " --> pdb=" O ASP d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 281 removed outlier: 3.742A pdb=" N ASN d 273 " --> pdb=" O ALA d 269 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE d 274 " --> pdb=" O TYR d 270 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE d 278 " --> pdb=" O ILE d 274 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA d 281 " --> pdb=" O LYS d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 309 removed outlier: 3.968A pdb=" N HIS d 303 " --> pdb=" O ASP d 299 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE d 304 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS d 307 " --> pdb=" O HIS d 303 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU d 308 " --> pdb=" O PHE d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 328 removed outlier: 4.396A pdb=" N GLU d 322 " --> pdb=" O ARG d 318 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY d 327 " --> pdb=" O PHE d 323 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU d 328 " --> pdb=" O LEU d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 383 through 407 removed outlier: 3.814A pdb=" N ILE d 387 " --> pdb=" O ASN d 383 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU d 389 " --> pdb=" O MET d 385 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP d 396 " --> pdb=" O ARG d 392 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU d 404 " --> pdb=" O VAL d 400 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL d 405 " --> pdb=" O ILE d 401 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS d 406 " --> pdb=" O ARG d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 415 through 429 removed outlier: 3.677A pdb=" N SER d 422 " --> pdb=" O GLU d 418 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG d 424 " --> pdb=" O GLU d 420 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER d 426 " --> pdb=" O SER d 422 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS d 427 " --> pdb=" O ARG d 423 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU d 428 " --> pdb=" O ARG d 424 " (cutoff:3.500A) Processing helix chain 'd' and resid 430 through 432 No H-bonds generated for 'chain 'd' and resid 430 through 432' Processing helix chain 'd' and resid 435 through 448 removed outlier: 3.769A pdb=" N ILE d 439 " --> pdb=" O VAL d 435 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN d 441 " --> pdb=" O ALA d 437 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER d 445 " --> pdb=" O GLN d 441 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU d 448 " --> pdb=" O ALA d 444 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 removed outlier: 3.552A pdb=" N ALA d 458 " --> pdb=" O LEU d 454 " (cutoff:3.500A) Processing helix chain 'd' and resid 461 through 472 removed outlier: 3.554A pdb=" N LYS d 472 " --> pdb=" O GLU d 468 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 475 No H-bonds generated for 'chain 'd' and resid 473 through 475' Processing helix chain 'd' and resid 500 through 519 removed outlier: 4.092A pdb=" N SER d 504 " --> pdb=" O PRO d 500 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE d 508 " --> pdb=" O SER d 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.796A pdb=" N ARG D 21 " --> pdb=" O PRO D 17 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.602A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 113 removed outlier: 3.960A pdb=" N VAL D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.541A pdb=" N PHE D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.211A pdb=" N LEU D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.805A pdb=" N SER D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.551A pdb=" N ALA D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 281 removed outlier: 3.872A pdb=" N ILE D 274 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 removed outlier: 3.518A pdb=" N HIS D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 4.504A pdb=" N GLU D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 383 through 407 removed outlier: 3.936A pdb=" N ILE D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.725A pdb=" N ILE D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 434 through 447 removed outlier: 4.145A pdb=" N PHE D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP D 440 " --> pdb=" O GLN D 436 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.567A pdb=" N ALA D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.510A pdb=" N VAL D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.651A pdb=" N ILE D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 62 removed outlier: 3.544A pdb=" N LYS e 47 " --> pdb=" O GLY e 43 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS e 48 " --> pdb=" O LEU e 44 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU e 52 " --> pdb=" O LYS e 48 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) removed outlier: 4.004A 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 98 through 115 removed outlier: 3.532A pdb=" N LYS e 102 " --> pdb=" O ASN e 98 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU e 103 " --> pdb=" O GLU e 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU e 104 " --> pdb=" O ILE e 100 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER e 110 " --> pdb=" O GLN e 106 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 139 removed outlier: 3.547A pdb=" N VAL e 124 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU e 136 " --> pdb=" O GLN e 132 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN e 138 " --> pdb=" O LEU e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 3.746A pdb=" N ILE e 146 " --> pdb=" O HIS e 142 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP e 151 " --> pdb=" O ALA e 147 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU e 152 " --> pdb=" O ASN e 148 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER e 159 " --> pdb=" O LYS e 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS e 160 " --> pdb=" O LEU e 156 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 174 through 188 removed outlier: 4.465A pdb=" N ASP e 178 " --> pdb=" O GLU e 174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU e 180 " --> pdb=" O PHE e 176 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA e 184 " --> pdb=" O LEU e 180 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS e 185 " --> pdb=" O LEU e 181 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR e 186 " --> pdb=" O ARG e 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 195 Processing helix chain 'e' and resid 196 through 211 removed outlier: 3.558A pdb=" N PHE e 200 " --> pdb=" O ASP e 196 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU e 202 " --> pdb=" O ASP e 198 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET e 203 " --> pdb=" O ARG e 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA e 204 " --> pdb=" O PHE e 200 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL e 205 " --> pdb=" O ALA e 201 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL e 208 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 237 removed outlier: 3.799A pdb=" N ASP e 236 " --> pdb=" O SER e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 302 through 317 removed outlier: 3.601A pdb=" N ASP e 311 " --> pdb=" O LYS e 307 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL e 313 " --> pdb=" O MET e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 removed outlier: 4.046A pdb=" N ASN e 332 " --> pdb=" O ASP e 328 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS e 333 " --> pdb=" O ASP e 329 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN e 337 " --> pdb=" O HIS e 333 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN e 338 " --> pdb=" O LEU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 349 through 358 removed outlier: 4.351A pdb=" N HIS e 353 " --> pdb=" O GLN e 349 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE e 354 " --> pdb=" O GLU e 350 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA e 355 " --> pdb=" O LEU e 351 " (cutoff:3.500A) Processing helix chain 'e' and resid 412 through 436 removed outlier: 3.616A pdb=" N ASP e 436 " --> pdb=" O ASN e 432 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 458 removed outlier: 3.551A pdb=" N VAL e 448 " --> pdb=" O GLY e 444 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL e 454 " --> pdb=" O MET e 450 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 477 removed outlier: 3.949A pdb=" N ALA e 468 " --> pdb=" O ILE e 464 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG e 470 " --> pdb=" O GLN e 466 " (cutoff:3.500A) removed outlier: 3.697A 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: 3.862A pdb=" N GLU e 524 " --> pdb=" O ASP e 521 " (cutoff:3.500A) Processing helix chain 'e' and resid 531 through 550 removed outlier: 3.545A pdb=" N ILE e 538 " --> pdb=" O LYS e 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 59 removed outlier: 3.753A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 4.209A pdb=" N THR E 63 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 65 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.746A pdb=" N ILE E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.978A pdb=" N VAL E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER E 110 " --> pdb=" O GLN E 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 139 removed outlier: 3.795A pdb=" N VAL E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 138 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 165 removed outlier: 3.575A pdb=" N ASP E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.883A pdb=" N ARG E 177 " --> pdb=" O ASP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.702A pdb=" N THR E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.725A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 212 removed outlier: 4.166A pdb=" N GLU E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE E 209 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 293 No H-bonds generated for 'chain 'E' and resid 291 through 293' Processing helix chain 'E' and resid 294 through 304 removed outlier: 3.583A pdb=" N GLN E 299 " --> pdb=" O TYR E 295 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR E 300 " --> pdb=" O GLN E 296 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN E 303 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP E 304 " --> pdb=" O THR E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 317 removed outlier: 4.117A pdb=" N MET E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP E 312 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL E 313 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 332 removed outlier: 4.130A pdb=" N ASN E 332 " --> pdb=" O ASP E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 332' Processing helix chain 'E' and resid 333 through 338 removed outlier: 3.907A pdb=" N GLN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 333 through 338' Processing helix chain 'E' and resid 349 through 358 removed outlier: 4.387A pdb=" N HIS E 353 " --> pdb=" O GLN E 349 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 removed outlier: 3.582A pdb=" N VAL E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 459 removed outlier: 3.662A pdb=" N VAL E 448 " --> pdb=" O GLY E 444 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 477 removed outlier: 3.542A pdb=" N ALA E 468 " --> pdb=" O ILE E 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 487 Processing helix chain 'E' and resid 490 through 502 removed outlier: 3.592A pdb=" N THR E 497 " --> pdb=" O GLY E 493 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 502 " --> pdb=" O LEU E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 550 Processing helix chain 'g' and resid 18 through 33 removed outlier: 3.518A pdb=" N ILE g 25 " --> pdb=" O GLN g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 39 removed outlier: 3.980A pdb=" N LEU g 39 " --> pdb=" O ARG g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 66 removed outlier: 3.511A pdb=" N ILE g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG g 66 " --> pdb=" O HIS g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 89 removed outlier: 4.028A pdb=" N LYS g 76 " --> pdb=" O HIS g 72 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER g 77 " --> pdb=" O PRO g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 107 removed outlier: 3.556A pdb=" N VAL g 96 " --> pdb=" O GLY g 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA g 105 " --> pdb=" O GLY g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 113 Processing helix chain 'g' and resid 117 through 140 Processing helix chain 'g' and resid 149 through 156 removed outlier: 4.201A pdb=" N LYS g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) removed outlier: 3.811A 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: 4.136A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 removed outlier: 4.109A pdb=" N GLU g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA g 178 " --> pdb=" O LEU g 174 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL g 182 " --> pdb=" O ALA g 178 " (cutoff:3.500A) Processing helix chain 'g' and resid 277 through 289 removed outlier: 3.559A pdb=" N GLN g 286 " --> pdb=" O LEU g 282 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE g 287 " --> pdb=" O MET g 283 " (cutoff:3.500A) Processing helix chain 'g' and resid 302 through 309 removed outlier: 3.597A pdb=" N GLN g 306 " --> pdb=" O SER g 302 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS g 307 " --> pdb=" O ASP g 303 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR g 308 " --> pdb=" O LEU g 304 " (cutoff:3.500A) Processing helix chain 'g' and resid 324 through 333 removed outlier: 3.631A 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 445 through 469 removed outlier: 3.839A pdb=" N ARG g 454 " --> pdb=" O ASN g 450 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER g 469 " --> pdb=" O ASN g 465 " (cutoff:3.500A) Processing helix chain 'g' and resid 477 through 491 removed outlier: 3.581A pdb=" N SER g 484 " --> pdb=" O GLU g 480 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS g 486 " --> pdb=" O ALA g 482 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA g 488 " --> pdb=" O SER g 484 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU g 489 " --> pdb=" O VAL g 485 " (cutoff:3.500A) Processing helix chain 'g' and resid 498 through 510 removed outlier: 3.706A pdb=" N VAL g 505 " --> pdb=" O PRO g 501 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA g 506 " --> pdb=" O TYR g 502 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP g 507 " --> pdb=" O GLN g 503 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA g 508 " --> pdb=" O ALA g 504 " (cutoff:3.500A) Processing helix chain 'g' and resid 510 through 521 Processing helix chain 'g' and resid 523 through 538 removed outlier: 3.512A pdb=" N GLN g 530 " --> pdb=" O ARG g 526 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA g 533 " --> pdb=" O SER g 529 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS g 535 " --> pdb=" O LEU g 531 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA g 536 " --> pdb=" O ARG g 532 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN g 537 " --> pdb=" O ALA g 533 " (cutoff:3.500A) Processing helix chain 'g' and resid 563 through 583 removed outlier: 3.827A pdb=" N VAL g 583 " --> pdb=" O LEU g 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 3.757A pdb=" N ALA G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 39 removed outlier: 3.856A pdb=" N LEU G 39 " --> pdb=" O ARG G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 36 through 39' Processing helix chain 'G' and resid 60 through 68 removed outlier: 3.743A pdb=" N ARG G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.886A pdb=" N LYS G 76 " --> pdb=" O HIS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 107 removed outlier: 3.620A pdb=" N VAL G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.736A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 157 removed outlier: 3.670A pdb=" N LYS G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.165A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 removed outlier: 3.833A pdb=" N GLU G 173 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.590A pdb=" N GLU G 197 " --> pdb=" O PRO G 194 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 194 through 198' Processing helix chain 'G' and resid 265 through 267 No H-bonds generated for 'chain 'G' and resid 265 through 267' Processing helix chain 'G' and resid 268 through 288 removed outlier: 3.938A pdb=" N ILE G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 280 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN G 286 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE G 287 " --> pdb=" O MET G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 309 removed outlier: 4.191A pdb=" N HIS G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 332 removed outlier: 3.529A pdb=" N ALA G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.669A pdb=" N ASP G 347 " --> pdb=" O LYS G 344 " (cutoff:3.500A) removed outlier: 3.743A 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 445 through 468 removed outlier: 3.715A pdb=" N GLU G 451 " --> pdb=" O ASP G 447 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG G 454 " --> pdb=" O ASN G 450 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL G 462 " --> pdb=" O ASP G 458 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G 463 " --> pdb=" O ALA G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 492 removed outlier: 3.575A pdb=" N VAL G 483 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 486 " --> pdb=" O ALA G 482 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 489 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS G 492 " --> pdb=" O ALA G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 510 removed outlier: 3.549A pdb=" N TYR G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN G 503 " --> pdb=" O GLN G 499 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA G 504 " --> pdb=" O TRP G 500 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 520 removed outlier: 3.628A pdb=" N LEU G 516 " --> pdb=" O ILE G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 538 removed outlier: 3.574A pdb=" N LEU G 528 " --> pdb=" O PRO G 524 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 529 " --> pdb=" O ILE G 525 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS G 535 " --> pdb=" O LEU G 531 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA G 536 " --> pdb=" O ARG G 532 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN G 537 " --> pdb=" O ALA G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 582 removed outlier: 3.616A pdb=" N LEU G 581 " --> pdb=" O ALA G 577 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 41 removed outlier: 3.519A pdb=" N ILE h 27 " --> pdb=" O LYS h 23 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS h 33 " --> pdb=" O ASN h 29 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL h 36 " --> pdb=" O ALA h 32 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 72 Processing helix chain 'h' and resid 80 through 94 removed outlier: 3.962A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 112 removed outlier: 3.981A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA h 112 " --> pdb=" O LEU h 108 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 118 removed outlier: 3.803A pdb=" N LEU h 116 " --> pdb=" O ALA h 112 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU h 117 " --> pdb=" O LYS h 113 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU h 118 " --> pdb=" O PRO h 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 112 through 118' Processing helix chain 'h' and resid 121 through 144 removed outlier: 3.749A pdb=" N ILE h 125 " --> pdb=" O SER h 121 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU h 138 " --> pdb=" O SER h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 162 removed outlier: 4.179A pdb=" N CYS h 161 " --> pdb=" O LEU h 157 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA h 162 " --> pdb=" O LEU h 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 162 through 167 Processing helix chain 'h' and resid 174 through 188 removed outlier: 4.004A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS h 182 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL h 183 " --> pdb=" O VAL h 179 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP h 184 " --> pdb=" O LYS h 180 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA h 185 " --> pdb=" O MET h 181 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL h 186 " --> pdb=" O CYS h 182 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER h 188 " --> pdb=" O ASP h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 208 through 212 removed outlier: 3.589A pdb=" N GLU h 211 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER h 212 " --> pdb=" O MET h 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 208 through 212' Processing helix chain 'h' and resid 279 through 289 removed outlier: 3.502A pdb=" N VAL h 285 " --> pdb=" O LYS h 281 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 removed outlier: 3.696A pdb=" N THR h 304 " --> pdb=" O GLY h 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE h 306 " --> pdb=" O LEU h 302 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP h 309 " --> pdb=" O GLN h 305 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG h 310 " --> pdb=" O PHE h 306 " (cutoff:3.500A) Processing helix chain 'h' and resid 319 through 331 removed outlier: 3.572A pdb=" N ASN h 324 " --> pdb=" O ALA h 320 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG h 325 " --> pdb=" O ASP h 321 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE h 327 " --> pdb=" O MET h 323 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN h 328 " --> pdb=" O ASN h 324 " (cutoff:3.500A) Processing helix chain 'h' and resid 342 through 346 Processing helix chain 'h' and resid 382 through 406 removed outlier: 3.505A pdb=" N ILE h 386 " --> pdb=" O ALA h 382 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA h 396 " --> pdb=" O SER h 392 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL h 400 " --> pdb=" O ALA h 396 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG h 402 " --> pdb=" O MET h 398 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA h 403 " --> pdb=" O ILE h 399 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN h 405 " --> pdb=" O LYS h 401 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN h 406 " --> pdb=" O ARG h 402 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 429 removed outlier: 3.678A pdb=" N ARG h 425 " --> pdb=" O SER h 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP h 426 " --> pdb=" O LYS h 422 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 removed outlier: 3.541A pdb=" N ILE h 438 " --> pdb=" O LYS h 434 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 458 removed outlier: 3.511A pdb=" N LEU h 453 " --> pdb=" O ILE h 449 " (cutoff:3.500A) Processing helix chain 'h' and resid 460 through 473 removed outlier: 3.681A pdb=" N ASN h 466 " --> pdb=" O ILE h 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA h 471 " --> pdb=" O LYS h 467 " (cutoff:3.500A) Processing helix chain 'h' and resid 491 through 495 Processing helix chain 'h' and resid 500 through 519 removed outlier: 3.520A pdb=" N ILE h 517 " --> pdb=" O ALA h 513 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 44 removed outlier: 3.724A pdb=" N ILE q 32 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS q 42 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 removed outlier: 3.958A pdb=" N ARG q 73 " --> pdb=" O ALA q 69 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU q 74 " --> pdb=" O THR q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 95 removed outlier: 4.169A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN q 92 " --> pdb=" O ALA q 88 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS q 93 " --> pdb=" O THR q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 121 removed outlier: 3.794A pdb=" N LEU q 111 " --> pdb=" O ALA q 107 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN q 112 " --> pdb=" O GLY q 108 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS q 116 " --> pdb=" O ASN q 112 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU q 117 " --> pdb=" O VAL q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 123 through 142 removed outlier: 3.531A pdb=" N ILE q 127 " --> pdb=" O SER q 123 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 159 through 168 Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 176 through 190 removed outlier: 4.252A pdb=" N GLU q 180 " --> pdb=" O ASP q 176 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU q 181 " --> pdb=" O ILE q 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA q 185 " --> pdb=" O LEU q 181 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER q 187 " --> pdb=" O SER q 183 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS q 188 " --> pdb=" O GLU q 184 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL q 189 " --> pdb=" O ALA q 185 " (cutoff:3.500A) Processing helix chain 'q' and resid 270 through 294 removed outlier: 4.286A pdb=" N LEU q 274 " --> pdb=" O ALA q 270 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU q 290 " --> pdb=" O ALA q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 308 through 316 removed outlier: 3.970A pdb=" N TYR q 312 " --> pdb=" O LEU q 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU q 313 " --> pdb=" O ALA q 309 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN q 314 " --> pdb=" O LEU q 310 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG q 315 " --> pdb=" O HIS q 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR q 316 " --> pdb=" O TYR q 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 308 through 316' Processing helix chain 'q' and resid 325 through 334 removed outlier: 4.010A pdb=" N LEU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG q 331 " --> pdb=" O PHE q 327 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG q 334 " --> pdb=" O ARG q 330 " (cutoff:3.500A) Processing helix chain 'q' and resid 390 through 410 removed outlier: 3.659A pdb=" N ASP q 395 " --> pdb=" O GLN q 391 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP q 402 " --> pdb=" O GLU q 398 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP q 403 " --> pdb=" O ARG q 399 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY q 404 " --> pdb=" O ALA q 400 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA q 406 " --> pdb=" O ASP q 402 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA q 407 " --> pdb=" O ASP q 403 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL q 408 " --> pdb=" O GLY q 404 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS q 409 " --> pdb=" O VAL q 405 " (cutoff:3.500A) Processing helix chain 'q' and resid 424 through 439 removed outlier: 3.518A pdb=" N ILE q 428 " --> pdb=" O GLY q 424 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE q 431 " --> pdb=" O GLU q 427 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER q 432 " --> pdb=" O ILE q 428 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG q 433 " --> pdb=" O GLU q 429 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR q 437 " --> pdb=" O ARG q 433 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.551A pdb=" N LEU q 475 " --> pdb=" O VAL q 471 " (cutoff:3.500A) Proline residue: q 476 - end of helix removed outlier: 3.628A pdb=" N HIS q 482 " --> pdb=" O LEU q 478 " (cutoff:3.500A) Processing helix chain 'q' and resid 521 through 541 removed outlier: 3.690A pdb=" N ASN q 529 " --> pdb=" O LYS q 525 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL q 538 " --> pdb=" O ALA q 534 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 25 Processing helix chain 'Q' and resid 26 through 44 removed outlier: 3.681A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS Q 42 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 75 removed outlier: 3.728A pdb=" N MET Q 71 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 95 removed outlier: 4.007A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN Q 91 " --> pdb=" O MET Q 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 114 removed outlier: 3.899A pdb=" N MET Q 104 " --> pdb=" O THR Q 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE Q 105 " --> pdb=" O ASN Q 101 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN Q 112 " --> pdb=" O GLY Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 120 Processing helix chain 'Q' and resid 123 through 142 removed outlier: 3.752A pdb=" N ILE Q 127 " --> pdb=" O SER Q 123 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS Q 136 " --> pdb=" O ASN Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 168 Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 174 through 190 removed outlier: 4.265A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU Q 181 " --> pdb=" O ILE Q 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER Q 187 " --> pdb=" O SER Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 294 removed outlier: 4.138A pdb=" N LEU Q 274 " --> pdb=" O ALA Q 270 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP Q 275 " --> pdb=" O GLN Q 271 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU Q 281 " --> pdb=" O SER Q 277 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS Q 282 " --> pdb=" O LYS Q 278 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET Q 294 " --> pdb=" O GLU Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 317 removed outlier: 3.829A pdb=" N LEU Q 310 " --> pdb=" O GLY Q 306 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS Q 311 " --> pdb=" O GLU Q 307 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR Q 312 " --> pdb=" O LEU Q 308 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN Q 314 " --> pdb=" O LEU Q 310 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG Q 315 " --> pdb=" O HIS Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 326 through 333 removed outlier: 4.147A pdb=" N ARG Q 330 " --> pdb=" O LYS Q 326 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS Q 333 " --> pdb=" O LEU Q 329 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 352 Processing helix chain 'Q' and resid 390 through 406 removed outlier: 3.597A pdb=" N LEU Q 394 " --> pdb=" O THR Q 390 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP Q 396 " --> pdb=" O ASN Q 392 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP Q 402 " --> pdb=" O GLU Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 407 through 412 removed outlier: 3.697A pdb=" N MET Q 412 " --> pdb=" O LYS Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 441 removed outlier: 3.737A pdb=" N ILE Q 428 " --> pdb=" O GLY Q 424 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER Q 432 " --> pdb=" O ILE Q 428 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG Q 433 " --> pdb=" O GLU Q 429 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU Q 439 " --> pdb=" O THR Q 435 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG Q 440 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 455 removed outlier: 4.387A 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: 3.629A pdb=" N VAL Q 474 " --> pdb=" O ASP Q 470 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU Q 475 " --> pdb=" O VAL Q 471 " (cutoff:3.500A) Proline residue: Q 476 - end of helix Processing helix chain 'Q' and resid 511 through 516 Processing helix chain 'Q' and resid 521 through 541 removed outlier: 3.548A pdb=" N PHE Q 526 " --> pdb=" O ALA Q 522 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN Q 529 " --> pdb=" O LYS Q 525 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Q 530 " --> pdb=" O PHE Q 526 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL Q 538 " --> pdb=" O ALA Q 534 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 35 removed outlier: 3.502A pdb=" N ALA z 26 " --> pdb=" O ASN z 22 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL z 32 " --> pdb=" O GLY z 28 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR z 35 " --> pdb=" O SER z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 65 removed outlier: 3.501A pdb=" N LEU z 63 " --> pdb=" O GLY z 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 71 through 86 removed outlier: 4.044A pdb=" N LEU z 75 " --> pdb=" O PRO z 71 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE z 76 " --> pdb=" O THR z 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA z 81 " --> pdb=" O ALA z 77 " (cutoff:3.500A) Processing helix chain 'z' and resid 90 through 112 removed outlier: 3.708A pdb=" N VAL z 95 " --> pdb=" O THR z 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN z 104 " --> pdb=" O GLU z 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG z 107 " --> pdb=" O ARG z 103 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE z 108 " --> pdb=" O GLN z 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE z 109 " --> pdb=" O ALA z 105 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN z 110 " --> pdb=" O HIS z 106 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU z 111 " --> pdb=" O ARG z 107 " (cutoff:3.500A) Processing helix chain 'z' and resid 114 through 137 removed outlier: 3.860A pdb=" N LYS z 131 " --> pdb=" O LYS z 127 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE z 132 " --> pdb=" O GLU z 128 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU z 135 " --> pdb=" O LYS z 131 " (cutoff:3.500A) Processing helix chain 'z' and resid 143 through 145 No H-bonds generated for 'chain 'z' and resid 143 through 145' Processing helix chain 'z' and resid 146 through 162 removed outlier: 4.199A pdb=" N GLN z 152 " --> pdb=" O GLU z 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER z 156 " --> pdb=" O GLN z 152 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER z 157 " --> pdb=" O VAL z 153 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU z 158 " --> pdb=" O ALA z 154 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL z 162 " --> pdb=" O LEU z 158 " (cutoff:3.500A) Processing helix chain 'z' and resid 166 through 182 Proline residue: z 172 - end of helix removed outlier: 3.920A pdb=" N VAL z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU z 179 " --> pdb=" O THR z 175 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL z 181 " --> pdb=" O ALA z 177 " (cutoff:3.500A) Processing helix chain 'z' and resid 203 through 207 removed outlier: 3.525A pdb=" N THR z 207 " --> pdb=" O PRO z 204 " (cutoff:3.500A) Processing helix chain 'z' and resid 255 through 263 removed outlier: 4.281A pdb=" N ASP z 260 " --> pdb=" O ALA z 256 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS z 261 " --> pdb=" O ASP z 257 " (cutoff:3.500A) Processing helix chain 'z' and resid 263 through 284 removed outlier: 4.743A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS z 273 " --> pdb=" O PHE z 269 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS z 276 " --> pdb=" O ALA z 272 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP z 279 " --> pdb=" O LYS z 275 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU z 280 " --> pdb=" O LYS z 276 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS z 281 " --> pdb=" O ILE z 277 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN z 282 " --> pdb=" O ILE z 278 " (cutoff:3.500A) Processing helix chain 'z' and resid 303 through 312 removed outlier: 4.427A pdb=" N ASP z 307 " --> pdb=" O PRO z 303 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL z 308 " --> pdb=" O MET z 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS z 311 " --> pdb=" O ASP z 307 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS z 312 " --> pdb=" O VAL z 308 " (cutoff:3.500A) Processing helix chain 'z' and resid 321 through 332 removed outlier: 3.535A pdb=" N GLU z 326 " --> pdb=" O ARG z 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG z 327 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN z 329 " --> pdb=" O MET z 325 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU z 330 " --> pdb=" O GLU z 326 " (cutoff:3.500A) Processing helix chain 'z' and resid 344 through 348 removed outlier: 3.734A pdb=" N LEU z 348 " --> pdb=" O PRO z 345 " (cutoff:3.500A) Processing helix chain 'z' and resid 384 through 408 removed outlier: 3.734A pdb=" N LEU z 388 " --> pdb=" O THR z 384 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN z 404 " --> pdb=" O ARG z 400 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL z 405 " --> pdb=" O ALA z 401 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU z 406 " --> pdb=" O VAL z 402 " (cutoff:3.500A) Processing helix chain 'z' and resid 416 through 434 removed outlier: 3.516A pdb=" N ARG z 427 " --> pdb=" O SER z 423 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER z 428 " --> pdb=" O ARG z 424 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN z 430 " --> pdb=" O LEU z 426 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) Processing helix chain 'z' and resid 439 through 451 removed outlier: 4.238A pdb=" N GLY z 443 " --> pdb=" O LYS z 439 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA z 446 " --> pdb=" O THR z 442 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE z 447 " --> pdb=" O GLY z 443 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU z 451 " --> pdb=" O PHE z 447 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 462 removed outlier: 3.525A pdb=" N LYS z 456 " --> pdb=" O LEU z 452 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL z 459 " --> pdb=" O PRO z 455 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER z 462 " --> pdb=" O LEU z 458 " (cutoff:3.500A) Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.895A pdb=" N ASP z 479 " --> pdb=" O ASP z 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA z 480 " --> pdb=" O GLU z 476 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP z 482 " --> pdb=" O ASP z 478 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER z 483 " --> pdb=" O ASP z 479 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 removed outlier: 3.544A pdb=" N ILE z 517 " --> pdb=" O LEU z 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR z 518 " --> pdb=" O ARG z 514 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY z 522 " --> pdb=" O THR z 518 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU z 527 " --> pdb=" O ILE z 523 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU z 528 " --> pdb=" O ALA z 524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 18 No H-bonds generated for 'chain 'Z' and resid 16 through 18' Processing helix chain 'Z' and resid 19 through 35 removed outlier: 3.521A pdb=" N VAL Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU Z 29 " --> pdb=" O SER Z 25 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 65 removed outlier: 3.577A pdb=" N LEU Z 62 " --> pdb=" O ASP Z 58 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU Z 65 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 80 removed outlier: 3.668A pdb=" N VAL Z 74 " --> pdb=" O SER Z 70 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU Z 75 " --> pdb=" O PRO Z 71 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE Z 76 " --> pdb=" O THR Z 72 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA Z 80 " --> pdb=" O ILE Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 85 removed outlier: 3.555A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.509A pdb=" N LEU Z 102 " --> pdb=" O VAL Z 98 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG Z 107 " --> pdb=" O ARG Z 103 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE Z 108 " --> pdb=" O GLN Z 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU Z 111 " --> pdb=" O ARG Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 137 removed outlier: 3.508A pdb=" N GLU Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS Z 131 " --> pdb=" O LYS Z 127 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU Z 135 " --> pdb=" O LYS Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 143 through 145 No H-bonds generated for 'chain 'Z' and resid 143 through 145' Processing helix chain 'Z' and resid 146 through 162 removed outlier: 4.388A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL Z 153 " --> pdb=" O PHE Z 149 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER Z 156 " --> pdb=" O GLN Z 152 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER Z 157 " --> pdb=" O VAL Z 153 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS Z 161 " --> pdb=" O SER Z 157 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL Z 162 " --> pdb=" O LEU Z 158 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 182 Proline residue: Z 172 - end of helix removed outlier: 3.890A pdb=" N VAL Z 178 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Z 179 " --> pdb=" O THR Z 175 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER Z 180 " --> pdb=" O ASP Z 176 " (cutoff:3.500A) removed outlier: 4.190A 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: 3.593A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS Z 261 " --> pdb=" O ASP Z 257 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS Z 276 " --> pdb=" O ALA Z 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP Z 279 " --> pdb=" O LYS Z 275 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU Z 280 " --> pdb=" O LYS Z 276 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS Z 281 " --> pdb=" O ILE Z 277 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN Z 282 " --> pdb=" O ILE Z 278 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL Z 284 " --> pdb=" O LEU Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 304 through 312 removed outlier: 3.925A pdb=" N VAL Z 308 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS Z 311 " --> pdb=" O ASP Z 307 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 333 removed outlier: 3.841A pdb=" N GLU Z 326 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG Z 327 " --> pdb=" O ARG Z 323 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 348 removed outlier: 3.625A pdb=" N LEU Z 348 " --> pdb=" O PRO Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 385 through 408 removed outlier: 3.531A pdb=" N ALA Z 389 " --> pdb=" O HIS Z 385 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR Z 391 " --> pdb=" O ALA Z 387 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN Z 404 " --> pdb=" O ARG Z 400 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL Z 405 " --> pdb=" O ALA Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 434 removed outlier: 3.574A pdb=" N SER Z 428 " --> pdb=" O ARG Z 424 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN Z 430 " --> pdb=" O LEU Z 426 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET Z 431 " --> pdb=" O ARG Z 427 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN Z 432 " --> pdb=" O SER Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 440 through 451 removed outlier: 3.515A pdb=" N LEU Z 451 " --> pdb=" O PHE Z 447 " (cutoff:3.500A) Processing helix chain 'Z' and resid 452 through 463 removed outlier: 3.570A pdb=" N LYS Z 456 " --> pdb=" O LEU Z 452 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL Z 459 " --> pdb=" O PRO Z 455 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 483 removed outlier: 3.520A pdb=" N VAL Z 469 " --> pdb=" O ASP Z 465 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP Z 478 " --> pdb=" O GLU Z 474 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP Z 479 " --> pdb=" O ASP Z 475 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP Z 482 " --> pdb=" O ASP Z 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 505 Processing helix chain 'Z' and resid 510 through 529 removed outlier: 3.815A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Z 529 " --> pdb=" O SER Z 525 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.854A pdb=" N THR H 61 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 53 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER H 63 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE H 51 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 555 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 199 through 205 removed outlier: 6.550A pdb=" N GLY H 200 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU H 378 " --> pdb=" O GLY H 200 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS H 202 " --> pdb=" O LEU H 378 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY H 380 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE H 204 " --> pdb=" O GLY H 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 241 through 244 removed outlier: 3.996A pdb=" N LEU H 294 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 351 through 355 removed outlier: 3.711A pdb=" N GLU H 353 " --> pdb=" O LEU H 364 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 364 " --> pdb=" O GLU H 353 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 409 through 411 Processing sheet with id=AA6, first strand: chain 'H' and resid 479 through 481 removed outlier: 3.810A pdb=" N GLY H 489 " --> pdb=" O GLY H 480 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 523 through 525 Processing sheet with id=AA8, first strand: chain 'a' and resid 19 through 20 removed outlier: 4.002A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS d 46 " --> pdb=" O SER d 58 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER d 58 " --> pdb=" O LYS d 46 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE d 48 " --> pdb=" O ILE d 56 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE d 56 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 62 through 63 removed outlier: 4.358A pdb=" N THR a 63 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS a 51 " --> pdb=" O THR a 63 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL g 587 " --> pdb=" O MET a 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 204 through 207 removed outlier: 5.998A pdb=" N ASN a 204 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU a 387 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU a 206 " --> pdb=" O LEU a 387 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER a 384 " --> pdb=" O VAL a 219 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL a 219 " --> pdb=" O SER a 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'a' and resid 222 through 225 removed outlier: 7.819A pdb=" N GLY a 376 " --> pdb=" O ASP a 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 244 through 246 removed outlier: 3.735A pdb=" N LEU a 297 " --> pdb=" O ALA a 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.140A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS D 46 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER D 58 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 48 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.095A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 384 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 219 " --> pdb=" O SER A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 222 through 225 removed outlier: 3.667A pdb=" N LYS A 375 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 360 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.612A pdb=" N LEU A 247 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 298 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AC2, first strand: chain 'b' and resid 55 through 57 removed outlier: 3.832A pdb=" N MET b 55 " --> pdb=" O LEU b 46 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU b 46 " --> pdb=" O MET b 55 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR b 57 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS b 44 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP b 43 " --> pdb=" O ILE d 521 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASP d 523 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU b 45 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA d 525 " --> pdb=" O LEU b 45 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 193 through 198 removed outlier: 6.210A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 225 through 229 removed outlier: 7.125A pdb=" N ASP b 341 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N CYS b 340 " --> pdb=" O CYS b 359 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS b 359 " --> pdb=" O CYS b 340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 231 through 233 removed outlier: 7.320A pdb=" N LEU b 232 " --> pdb=" O ILE b 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 400 through 402 Processing sheet with id=AC7, first strand: chain 'b' and resid 470 through 473 removed outlier: 3.568A pdb=" N THR b 478 " --> pdb=" O ASP b 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.687A pdb=" N MET B 55 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 57 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS B 44 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP B 43 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP D 523 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 45 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 525 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 193 through 199 removed outlier: 3.631A pdb=" N VAL B 368 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE B 207 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 212 through 215 removed outlier: 6.032A pdb=" N CYS B 359 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS B 340 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 338 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 212 through 215 Processing sheet with id=AD3, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AD4, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AD5, first strand: chain 'B' and resid 470 through 473 Processing sheet with id=AD6, first strand: chain 'B' and resid 511 through 514 removed outlier: 7.951A pdb=" N ILE E 73 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE B 514 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ILE E 75 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS E 72 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 84 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 197 through 200 removed outlier: 6.291A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'd' and resid 213 through 214 removed outlier: 3.690A pdb=" N VAL d 213 " --> pdb=" O VAL d 363 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL d 363 " --> pdb=" O VAL d 213 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE d 360 " --> pdb=" O ILE d 353 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU d 351 " --> pdb=" O ARG d 362 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR d 364 " --> pdb=" O LEU d 349 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU d 349 " --> pdb=" O THR d 364 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 234 through 237 removed outlier: 4.301A pdb=" N GLY d 235 " --> pdb=" O VAL d 285 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU d 287 " --> pdb=" O GLY d 235 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN d 289 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU d 286 " --> pdb=" O VAL d 313 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP d 315 " --> pdb=" O LEU d 286 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE d 288 " --> pdb=" O ASP d 315 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 196 through 200 removed outlier: 3.738A pdb=" N GLY D 381 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 213 through 214 removed outlier: 3.849A pdb=" N VAL D 363 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 360 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 351 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR D 364 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU D 349 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP D 348 " --> pdb=" O LYS D 231 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 285 through 289 removed outlier: 10.011A pdb=" N LEU D 286 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ILE D 316 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE D 288 " --> pdb=" O ILE D 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 410 through 411 Processing sheet with id=AE5, first strand: chain 'e' and resid 72 through 75 removed outlier: 3.625A pdb=" N LYS e 72 " --> pdb=" O THR e 84 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR e 84 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR e 82 " --> pdb=" O LEU e 74 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 166 through 167 removed outlier: 3.705A pdb=" N ASP e 166 " --> pdb=" O VAL e 439 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'e' and resid 224 through 230 removed outlier: 6.417A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL e 408 " --> pdb=" O LYS e 225 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN e 227 " --> pdb=" O VAL e 408 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N GLY e 410 " --> pdb=" O GLN e 227 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 342 through 343 removed outlier: 6.511A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL e 320 " --> pdb=" O LYS e 268 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'e' and resid 379 through 382 removed outlier: 4.378A pdb=" N ARG e 379 " --> pdb=" O GLU e 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU e 396 " --> pdb=" O ARG e 379 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR e 381 " --> pdb=" O ILE e 394 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 554 through 556 removed outlier: 7.199A pdb=" N ILE e 555 " --> pdb=" O VAL h 54 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE h 51 " --> pdb=" O SER h 63 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER h 63 " --> pdb=" O ILE h 51 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE h 53 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR h 61 " --> pdb=" O ILE h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 224 through 230 removed outlier: 6.322A pdb=" N LYS E 225 " --> pdb=" O CYS E 406 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL E 408 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN E 227 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLY E 410 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG E 229 " --> pdb=" O GLY E 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 269 through 272 removed outlier: 6.307A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 380 through 382 Processing sheet with id=AF5, first strand: chain 'g' and resid 55 through 56 Processing sheet with id=AF6, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AF7, first strand: chain 'g' and resid 206 through 208 removed outlier: 3.800A pdb=" N GLU g 207 " --> pdb=" O ILE g 439 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU g 441 " --> pdb=" O GLU g 207 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 224 through 225 removed outlier: 3.789A pdb=" N LEU g 225 " --> pdb=" O SER g 366 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 294 through 296 Processing sheet with id=AG1, first strand: chain 'g' and resid 542 through 544 removed outlier: 3.722A pdb=" N VAL g 552 " --> pdb=" O GLY g 543 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 55 through 56 removed outlier: 4.259A pdb=" N VAL G 56 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU G 48 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AG4, first strand: chain 'G' and resid 206 through 208 Processing sheet with id=AG5, first strand: chain 'G' and resid 294 through 296 Processing sheet with id=AG6, first strand: chain 'G' and resid 542 through 544 removed outlier: 3.502A pdb=" N VAL G 552 " --> pdb=" O GLY G 543 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 201 through 205 removed outlier: 3.691A pdb=" N LEU h 378 " --> pdb=" O LYS h 202 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY h 380 " --> pdb=" O ILE h 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR h 375 " --> pdb=" O ILE h 215 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE h 215 " --> pdb=" O THR h 375 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU h 377 " --> pdb=" O LEU h 213 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU h 213 " --> pdb=" O LEU h 377 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 241 through 243 removed outlier: 6.211A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'h' and resid 351 through 355 removed outlier: 3.696A pdb=" N LEU h 351 " --> pdb=" O GLN h 366 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN h 366 " --> pdb=" O LEU h 351 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU h 353 " --> pdb=" O LEU h 364 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU h 364 " --> pdb=" O GLU h 353 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 409 through 411 Processing sheet with id=AH2, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.887A pdb=" N GLY h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 53 through 56 removed outlier: 3.682A pdb=" N LYS q 53 " --> pdb=" O THR q 65 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR q 65 " --> pdb=" O LYS q 53 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE q 55 " --> pdb=" O ILE q 63 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'q' and resid 207 through 213 removed outlier: 3.508A pdb=" N VAL q 210 " --> pdb=" O ILE q 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE q 212 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY q 388 " --> pdb=" O ILE q 212 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR q 383 " --> pdb=" O ILE q 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE q 223 " --> pdb=" O THR q 383 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.427A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N LEU q 341 " --> pdb=" O VAL q 247 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL q 249 " --> pdb=" O LEU q 341 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'q' and resid 319 through 322 removed outlier: 7.427A pdb=" N GLU q 297 " --> pdb=" O LEU q 319 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU q 321 " --> pdb=" O GLU q 297 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE q 299 " --> pdb=" O LEU q 321 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS q 246 " --> pdb=" O VAL q 296 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 360 through 363 removed outlier: 4.006A pdb=" N ASP q 366 " --> pdb=" O ILE q 363 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AH9, first strand: chain 'q' and resid 544 through 545 removed outlier: 4.028A pdb=" N ILE q 545 " --> pdb=" O MET z 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'Q' and resid 207 through 213 removed outlier: 3.911A pdb=" N ILE Q 384 " --> pdb=" O ARG Q 208 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL Q 210 " --> pdb=" O ILE Q 384 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU Q 386 " --> pdb=" O VAL Q 210 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE Q 212 " --> pdb=" O LEU Q 386 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY Q 388 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE Q 385 " --> pdb=" O THR Q 221 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR Q 221 " --> pdb=" O ILE Q 385 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 319 through 322 removed outlier: 3.551A pdb=" N LEU Q 321 " --> pdb=" O ILE Q 299 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N LEU Q 341 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL Q 249 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 319 through 322 removed outlier: 3.551A pdb=" N LEU Q 321 " --> pdb=" O ILE Q 299 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 357 through 363 removed outlier: 3.962A pdb=" N THR Q 357 " --> pdb=" O LYS Q 372 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS Q 372 " --> pdb=" O THR Q 357 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS Q 359 " --> pdb=" O VAL Q 370 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP Q 366 " --> pdb=" O ILE Q 363 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 419 through 421 Processing sheet with id=AI6, first strand: chain 'Q' and resid 544 through 545 removed outlier: 6.196A pdb=" N ILE Q 545 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS Z 54 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AI8, first strand: chain 'z' and resid 194 through 199 removed outlier: 6.452A pdb=" N GLU z 195 " --> pdb=" O ILE z 378 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE z 380 " --> pdb=" O GLU z 195 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET z 197 " --> pdb=" O ILE z 380 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'z' and resid 227 through 228 Processing sheet with id=AJ1, first strand: chain 'z' and resid 231 through 234 removed outlier: 5.963A pdb=" N TYR z 232 " --> pdb=" O VAL z 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AJ3, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AJ4, first strand: chain 'Z' and resid 194 through 197 removed outlier: 6.235A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Z' and resid 227 through 228 Processing sheet with id=AJ6, first strand: chain 'Z' and resid 292 through 295 removed outlier: 6.032A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'Z' and resid 490 through 491 2511 hydrogen bonds defined for protein. 7281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.13 Time building geometry restraints manager: 19.94 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: 20992 1.34 - 1.46: 11340 1.46 - 1.58: 29853 1.58 - 1.69: 0 1.69 - 1.81: 512 Bond restraints: 62697 Sorted by residual: bond pdb=" C ALA q 346 " pdb=" N PRO q 347 " ideal model delta sigma weight residual 1.334 1.433 -0.100 2.34e-02 1.83e+03 1.81e+01 bond pdb=" C VAL a 219 " pdb=" N PRO a 220 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.16e+00 bond pdb=" C SER G 469 " pdb=" N PRO G 470 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.80e+00 bond pdb=" CA ARG Z 15 " pdb=" C ARG Z 15 " ideal model delta sigma weight residual 1.520 1.532 -0.012 1.16e-02 7.43e+03 1.02e+00 bond pdb=" CA ARG Z 14 " pdb=" CB ARG Z 14 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.54e-02 4.22e+03 8.85e-01 ... (remaining 62692 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.23: 1380 107.23 - 113.91: 37313 113.91 - 120.60: 25118 120.60 - 127.28: 20361 127.28 - 133.96: 388 Bond angle restraints: 84560 Sorted by residual: angle pdb=" C SER Z 12 " pdb=" CA SER Z 12 " pdb=" CB SER Z 12 " ideal model delta sigma weight residual 115.79 109.77 6.02 1.19e+00 7.06e-01 2.56e+01 angle pdb=" C ASP Z 187 " pdb=" CA ASP Z 187 " pdb=" CB ASP Z 187 " ideal model delta sigma weight residual 116.54 110.98 5.56 1.15e+00 7.56e-01 2.33e+01 angle pdb=" CA ASP Z 187 " pdb=" C ASP Z 187 " pdb=" N ASN Z 188 " ideal model delta sigma weight residual 119.52 116.67 2.85 7.90e-01 1.60e+00 1.30e+01 angle pdb=" C LEU Z 13 " pdb=" N ARG Z 14 " pdb=" CA ARG Z 14 " ideal model delta sigma weight residual 122.08 127.36 -5.28 1.47e+00 4.63e-01 1.29e+01 angle pdb=" N GLU Z 11 " pdb=" CA GLU Z 11 " pdb=" C GLU Z 11 " ideal model delta sigma weight residual 108.38 112.73 -4.35 1.35e+00 5.49e-01 1.04e+01 ... (remaining 84555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 38344 16.18 - 32.36: 334 32.36 - 48.54: 199 48.54 - 64.72: 59 64.72 - 80.90: 3 Dihedral angle restraints: 38939 sinusoidal: 15590 harmonic: 23349 Sorted by residual: dihedral pdb=" CA PHE E 276 " pdb=" C PHE E 276 " pdb=" N GLU E 277 " pdb=" CA GLU E 277 " ideal model delta harmonic sigma weight residual -180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ALA H 273 " pdb=" C ALA H 273 " pdb=" N GLU H 274 " pdb=" CA GLU H 274 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASP H 272 " pdb=" C ASP H 272 " pdb=" N ALA H 273 " pdb=" CA ALA H 273 " ideal model delta harmonic sigma weight residual 180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 38936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 7152 0.034 - 0.069: 2193 0.069 - 0.103: 490 0.103 - 0.138: 335 0.138 - 0.172: 5 Chirality restraints: 10175 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 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CB ILE A 196 " pdb=" CA ILE A 196 " pdb=" CG1 ILE A 196 " pdb=" CG2 ILE A 196 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 10172 not shown) Planarity restraints: 10863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 276 " 0.016 2.00e-02 2.50e+03 1.46e-02 3.72e+00 pdb=" CG PHE E 276 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE E 276 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 276 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 276 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 276 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 372 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO D 373 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 270 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C ILE H 270 " 0.018 2.00e-02 2.50e+03 pdb=" O ILE H 270 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL H 271 " -0.006 2.00e-02 2.50e+03 ... (remaining 10860 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 11351 2.77 - 3.30: 57385 3.30 - 3.84: 91825 3.84 - 4.37: 108870 4.37 - 4.90: 187043 Nonbonded interactions: 456474 Sorted by model distance: nonbonded pdb=" O LEU H 198 " pdb=" OG1 THR H 373 " model vdw 2.241 2.440 nonbonded pdb=" O ILE H 62 " pdb=" NH1 ARG H 391 " model vdw 2.267 2.520 nonbonded pdb=" O VAL Z 367 " pdb=" ND2 ASN Z 370 " model vdw 2.274 2.520 nonbonded pdb=" O ILE E 354 " pdb=" OG1 THR E 358 " model vdw 2.279 2.440 nonbonded pdb=" O PRO q 421 " pdb=" OG1 THR q 426 " model vdw 2.280 2.440 ... (remaining 456469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 256 or resid 273 through 547)) selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'D' and (resid 17 through 246 or resid 263 through 479 or resid 492 throu \ gh 528)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 43 through 281 or resid 301 through 560)) selection = (chain 'e' and resid 43 through 560) } ncs_group { reference = (chain 'G' and (resid 18 through 253 or resid 276 through 590)) selection = (chain 'g' and resid 18 through 590) } ncs_group { reference = (chain 'H' and (resid 23 through 250 or resid 278 through 528)) selection = (chain 'h' and resid 23 through 528) } ncs_group { reference = (chain 'Q' and resid 26 through 549) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.190 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 122.010 Find NCS groups from input model: 5.600 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 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 0.100 62697 Z= 0.082 Angle : 0.391 9.163 84560 Z= 0.222 Chirality : 0.039 0.172 10175 Planarity : 0.001 0.036 10863 Dihedral : 7.113 80.896 23803 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.07), residues: 8076 helix: -3.60 (0.04), residues: 3560 sheet: -0.82 (0.20), residues: 528 loop : -1.11 (0.08), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP E 325 HIS 0.003 0.000 HIS Q 39 PHE 0.034 0.001 PHE E 276 TYR 0.008 0.001 TYR G 502 ARG 0.002 0.000 ARG a 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2816 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2816 time to evaluate : 5.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2816 average time/residue: 0.6519 time to fit residues: 2989.3234 Evaluate side-chains 1399 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1399 time to evaluate : 5.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 8.9990 chunk 610 optimal weight: 6.9990 chunk 338 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 411 optimal weight: 10.0000 chunk 325 optimal weight: 1.9990 chunk 630 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 383 optimal weight: 10.0000 chunk 469 optimal weight: 5.9990 chunk 731 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 90 GLN H 291 ASN H 356 GLN ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 452 GLN a 64 ASN a 88 GLN a 191 ASN ** a 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 252 GLN A 261 GLN A 403 HIS b 118 GLN b 222 GLN b 260 GLN b 286 ASN b 385 HIS b 393 GLN B 304 ASN d 112 ASN ** d 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 499 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 284 ASN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 HIS ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 383 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 502 GLN ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN ** E 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 279 GLN g 503 GLN g 535 HIS G 156 GLN G 166 HIS G 188 GLN G 519 ASN G 530 GLN ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN h 90 GLN h 345 HIS h 394 HIS ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 GLN q 91 GLN ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 311 HIS q 451 GLN q 482 HIS Q 58 HIS Q 66 ASN Q 91 GLN Q 92 GLN Q 258 ASN ** z 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 ASN Z 145 ASN Z 185 GLN Z 297 ASN ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 515 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 62697 Z= 0.248 Angle : 0.681 12.687 84560 Z= 0.359 Chirality : 0.046 0.216 10175 Planarity : 0.005 0.074 10863 Dihedral : 3.761 20.927 8578 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.40 % Rotamer: Outliers : 0.22 % Allowed : 3.04 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.08), residues: 8076 helix: -0.98 (0.07), residues: 3719 sheet: -0.58 (0.18), residues: 670 loop : -0.81 (0.09), residues: 3687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 478 HIS 0.008 0.001 HIS E 50 PHE 0.030 0.002 PHE e 179 TYR 0.031 0.002 TYR Z 425 ARG 0.017 0.001 ARG Z 323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1795 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1780 time to evaluate : 5.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 1787 average time/residue: 0.5889 time to fit residues: 1780.4880 Evaluate side-chains 1291 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1288 time to evaluate : 5.435 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4726 time to fit residues: 10.0597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 608 optimal weight: 8.9990 chunk 497 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 732 optimal weight: 1.9990 chunk 791 optimal weight: 0.9990 chunk 652 optimal weight: 9.9990 chunk 726 optimal weight: 3.9990 chunk 249 optimal weight: 0.0970 chunk 587 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 ASN H 472 HIS A 261 GLN b 228 ASN b 286 ASN d 62 HIS d 112 ASN d 289 GLN D 238 GLN D 284 ASN D 473 HIS e 138 GLN e 537 GLN ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 457 GLN g 503 GLN G 519 ASN ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 GLN h 90 GLN h 345 HIS q 66 ASN q 91 GLN q 92 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN ** z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 62697 Z= 0.193 Angle : 0.582 12.012 84560 Z= 0.300 Chirality : 0.044 0.234 10175 Planarity : 0.004 0.071 10863 Dihedral : 3.661 20.268 8578 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 0.09 % Allowed : 2.44 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 8076 helix: -0.08 (0.08), residues: 3736 sheet: -0.44 (0.19), residues: 664 loop : -0.70 (0.10), residues: 3676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 560 HIS 0.010 0.001 HIS Q 188 PHE 0.043 0.002 PHE A 129 TYR 0.028 0.002 TYR h 427 ARG 0.017 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1630 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1624 time to evaluate : 5.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 1627 average time/residue: 0.5944 time to fit residues: 1657.0416 Evaluate side-chains 1242 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1242 time to evaluate : 5.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.9990 chunk 550 optimal weight: 1.9990 chunk 380 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 349 optimal weight: 5.9990 chunk 491 optimal weight: 1.9990 chunk 734 optimal weight: 7.9990 chunk 778 optimal weight: 0.7980 chunk 383 optimal weight: 0.7980 chunk 696 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 209 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN b 286 ASN B 192 HIS D 59 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN D 441 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN g 24 ASN g 503 GLN G 166 HIS ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN h 345 HIS q 91 GLN q 392 ASN ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 145 ASN ** z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 62697 Z= 0.159 Angle : 0.548 8.698 84560 Z= 0.281 Chirality : 0.043 0.205 10175 Planarity : 0.003 0.051 10863 Dihedral : 3.653 20.252 8578 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8076 helix: 0.29 (0.08), residues: 3745 sheet: -0.33 (0.20), residues: 633 loop : -0.58 (0.10), residues: 3698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP g 560 HIS 0.010 0.001 HIS b 155 PHE 0.030 0.001 PHE d 124 TYR 0.028 0.001 TYR b 124 ARG 0.009 0.000 ARG Q 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1590 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1587 time to evaluate : 5.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1588 average time/residue: 0.5714 time to fit residues: 1552.5033 Evaluate side-chains 1242 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1242 time to evaluate : 5.436 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 6.9990 chunk 441 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 579 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 chunk 664 optimal weight: 3.9990 chunk 537 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 1.9990 chunk 698 optimal weight: 0.6980 chunk 196 optimal weight: 0.0470 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 261 GLN b 286 ASN B 168 GLN D 284 ASN D 395 HIS D 473 HIS e 138 GLN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN E 85 ASN E 424 HIS E 466 GLN E 543 GLN g 503 GLN G 535 HIS ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 GLN ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN h 345 HIS ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 GLN q 451 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 62697 Z= 0.160 Angle : 0.549 9.485 84560 Z= 0.281 Chirality : 0.043 0.194 10175 Planarity : 0.003 0.063 10863 Dihedral : 3.692 21.265 8578 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.09), residues: 8076 helix: 0.49 (0.08), residues: 3770 sheet: -0.22 (0.20), residues: 631 loop : -0.52 (0.10), residues: 3675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP h 497 HIS 0.012 0.001 HIS E 424 PHE 0.029 0.001 PHE z 122 TYR 0.035 0.001 TYR h 427 ARG 0.009 0.000 ARG d 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1557 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1555 time to evaluate : 5.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1556 average time/residue: 0.5799 time to fit residues: 1552.2814 Evaluate side-chains 1214 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1214 time to evaluate : 5.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 2.9990 chunk 700 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 456 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 778 optimal weight: 6.9990 chunk 646 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 408 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 90 GLN ** H 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN A 261 GLN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 286 ASN B 304 ASN d 441 GLN D 59 ASN ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN E 424 HIS ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 GLN g 24 ASN ** g 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN G 123 GLN G 166 HIS ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 GLN h 90 GLN h 345 HIS ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 515 ASN ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 91 GLN ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 62697 Z= 0.202 Angle : 0.609 12.713 84560 Z= 0.314 Chirality : 0.044 0.197 10175 Planarity : 0.004 0.063 10863 Dihedral : 4.006 25.171 8578 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 0.04 % Allowed : 1.84 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 8076 helix: 0.53 (0.08), residues: 3804 sheet: -0.43 (0.19), residues: 661 loop : -0.62 (0.10), residues: 3611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP g 560 HIS 0.011 0.001 HIS E 424 PHE 0.030 0.002 PHE q 526 TYR 0.022 0.002 TYR b 124 ARG 0.014 0.001 ARG d 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1548 time to evaluate : 5.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1549 average time/residue: 0.5900 time to fit residues: 1571.0923 Evaluate side-chains 1180 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1180 time to evaluate : 5.503 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 443 optimal weight: 0.3980 chunk 568 optimal weight: 0.0670 chunk 440 optimal weight: 0.9990 chunk 655 optimal weight: 0.8980 chunk 434 optimal weight: 8.9990 chunk 775 optimal weight: 7.9990 chunk 485 optimal weight: 8.9990 chunk 473 optimal weight: 3.9990 chunk 358 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 113 ASN A 261 GLN B 304 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN E 424 HIS E 466 GLN ** g 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 GLN h 345 HIS ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 494 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 430 ASN ** z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 356 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 62697 Z= 0.156 Angle : 0.577 8.364 84560 Z= 0.293 Chirality : 0.043 0.205 10175 Planarity : 0.003 0.115 10863 Dihedral : 3.879 30.233 8578 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 0.01 % Allowed : 1.21 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.09), residues: 8076 helix: 0.59 (0.08), residues: 3814 sheet: -0.33 (0.20), residues: 650 loop : -0.59 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 560 HIS 0.010 0.001 HIS E 424 PHE 0.034 0.001 PHE A 176 TYR 0.033 0.001 TYR h 427 ARG 0.010 0.000 ARG d 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1543 time to evaluate : 7.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1543 average time/residue: 0.5638 time to fit residues: 1503.5219 Evaluate side-chains 1215 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1215 time to evaluate : 5.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 8.9990 chunk 309 optimal weight: 1.9990 chunk 463 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 150 optimal weight: 0.0970 chunk 493 optimal weight: 0.0670 chunk 528 optimal weight: 9.9990 chunk 383 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 609 optimal weight: 7.9990 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 GLN ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 430 ASN a 481 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 261 GLN ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 HIS E 432 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 515 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.7959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 62697 Z= 0.210 Angle : 0.631 10.553 84560 Z= 0.324 Chirality : 0.044 0.292 10175 Planarity : 0.004 0.079 10863 Dihedral : 4.132 30.306 8578 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 0.01 % Allowed : 0.92 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.09), residues: 8076 helix: 0.52 (0.08), residues: 3828 sheet: -0.34 (0.20), residues: 648 loop : -0.70 (0.10), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 560 HIS 0.010 0.001 HIS E 424 PHE 0.036 0.002 PHE Z 132 TYR 0.039 0.001 TYR H 226 ARG 0.011 0.001 ARG d 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1503 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1502 time to evaluate : 5.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1502 average time/residue: 0.5818 time to fit residues: 1515.7200 Evaluate side-chains 1190 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1189 time to evaluate : 5.488 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5267 time to fit residues: 8.5264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.1980 chunk 743 optimal weight: 0.9990 chunk 678 optimal weight: 5.9990 chunk 723 optimal weight: 7.9990 chunk 435 optimal weight: 0.0980 chunk 314 optimal weight: 0.9980 chunk 567 optimal weight: 0.2980 chunk 221 optimal weight: 5.9990 chunk 653 optimal weight: 6.9990 chunk 683 optimal weight: 7.9990 chunk 720 optimal weight: 8.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 452 GLN ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 165 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN ** g 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN ** z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.8036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 62697 Z= 0.163 Angle : 0.608 10.471 84560 Z= 0.306 Chirality : 0.044 0.291 10175 Planarity : 0.003 0.055 10863 Dihedral : 4.007 30.517 8578 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.09), residues: 8076 helix: 0.58 (0.08), residues: 3835 sheet: -0.32 (0.20), residues: 619 loop : -0.63 (0.10), residues: 3622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 560 HIS 0.008 0.001 HIS E 424 PHE 0.031 0.001 PHE Z 132 TYR 0.034 0.001 TYR h 427 ARG 0.011 0.000 ARG d 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1512 time to evaluate : 5.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1513 average time/residue: 0.5767 time to fit residues: 1520.8127 Evaluate side-chains 1210 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1210 time to evaluate : 5.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 10.0000 chunk 764 optimal weight: 2.9990 chunk 466 optimal weight: 0.5980 chunk 362 optimal weight: 5.9990 chunk 531 optimal weight: 1.9990 chunk 801 optimal weight: 4.9990 chunk 738 optimal weight: 0.0070 chunk 638 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 493 optimal weight: 0.9980 chunk 391 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 380 HIS ** a 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN b 142 ASN B 192 HIS ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN g 567 GLN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS G 535 HIS ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 92 GLN q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 451 GLN ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.8162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 62697 Z= 0.161 Angle : 0.605 13.490 84560 Z= 0.305 Chirality : 0.044 0.278 10175 Planarity : 0.003 0.052 10863 Dihedral : 3.928 28.744 8578 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 0.01 % Allowed : 0.32 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 8076 helix: 0.61 (0.08), residues: 3828 sheet: -0.34 (0.21), residues: 597 loop : -0.59 (0.10), residues: 3651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 560 HIS 0.010 0.001 HIS D 473 PHE 0.035 0.001 PHE E 179 TYR 0.020 0.001 TYR H 226 ARG 0.007 0.000 ARG Z 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16152 Ramachandran restraints generated. 8076 Oldfield, 0 Emsley, 8076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1507 time to evaluate : 5.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1507 average time/residue: 0.5652 time to fit residues: 1475.4826 Evaluate side-chains 1200 residues out of total 6852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1200 time to evaluate : 5.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 4.9990 chunk 680 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 588 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 639 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 656 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN A 261 GLN B 192 HIS ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 ASN e 537 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 503 GLN g 535 HIS ** g 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 HIS ** h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 482 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.149822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.124921 restraints weight = 216529.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.127692 restraints weight = 149144.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.129158 restraints weight = 106328.534| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.8336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 62697 Z= 0.168 Angle : 0.612 12.628 84560 Z= 0.309 Chirality : 0.044 0.273 10175 Planarity : 0.003 0.101 10863 Dihedral : 3.926 22.244 8578 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 8076 helix: 0.62 (0.09), residues: 3835 sheet: -0.36 (0.21), residues: 617 loop : -0.60 (0.10), residues: 3624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 560 HIS 0.008 0.001 HIS E 353 PHE 0.040 0.001 PHE A 129 TYR 0.037 0.001 TYR z 425 ARG 0.012 0.000 ARG d 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21759.90 seconds wall clock time: 378 minutes 44.31 seconds (22724.31 seconds total)