Starting phenix.real_space_refine on Tue Nov 19 22:33:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdz_4836/11_2024/6rdz_4836.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdz_4836/11_2024/6rdz_4836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdz_4836/11_2024/6rdz_4836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdz_4836/11_2024/6rdz_4836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdz_4836/11_2024/6rdz_4836.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdz_4836/11_2024/6rdz_4836.cif" } resolution = 3.5 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= 0.000 sd= 1.038 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34282 2.51 5 N 9107 2.21 5 O 10163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 434 residue(s): 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 53720 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 29.63, per 1000 atoms: 0.55 Number of scatterers: 53720 At special positions: 0 Unit cell: (216.918, 127.413, 263.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10163 8.00 N 9107 7.00 C 34282 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 - 3.00 Amino acid : True - 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: 13.40 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13076 Finding SS restraints... Secondary structure from input PDB file: 310 helices and 37 sheets defined 58.2% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.81 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.838A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 30 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 57 through 61 Processing helix chain '1' and resid 45 through 72 Processing helix chain '1' and resid 77 through 81 removed outlier: 3.512A pdb=" N LYS 1 80 " --> pdb=" O PRO 1 77 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN 1 81 " --> pdb=" O LEU 1 78 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 77 through 81' Processing helix chain '1' and resid 96 through 100 removed outlier: 3.732A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 96 through 100' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.640A pdb=" N GLU 1 136 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.576A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 203 removed outlier: 3.775A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 224 removed outlier: 3.637A pdb=" N SER 1 214 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 271 removed outlier: 3.630A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 273 through 277 Processing helix chain '1' and resid 278 through 286 removed outlier: 3.613A pdb=" N PHE 1 282 " --> pdb=" O LEU 1 279 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP 1 283 " --> pdb=" O ASN 1 280 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA 1 284 " --> pdb=" O GLU 1 281 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 1 286 " --> pdb=" O ASP 1 283 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 removed outlier: 3.705A pdb=" N GLY 1 292 " --> pdb=" O LYS 1 289 " (cutoff:3.500A) Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 316 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.520A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 335 removed outlier: 4.262A pdb=" N GLU 1 334 " --> pdb=" O LYS 1 330 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 removed outlier: 3.753A pdb=" N LEU 1 351 " --> pdb=" O LYS 1 347 " (cutoff:3.500A) Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 4.048A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 Processing helix chain '1' and resid 392 through 421 removed outlier: 3.577A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.783A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 447 through 459 removed outlier: 3.733A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 Processing helix chain '1' and resid 479 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.772A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.722A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 577 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '2' and resid 7 through 19 removed outlier: 3.593A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 removed outlier: 3.507A pdb=" N VAL 2 29 " --> pdb=" O SER 2 25 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 58 removed outlier: 3.987A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA 2 58 " --> pdb=" O LYS 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 4.030A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 3.547A pdb=" N TYR 2 121 " --> pdb=" O ASN 2 117 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 155 through 168 removed outlier: 4.136A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 197 removed outlier: 3.944A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 200 No H-bonds generated for 'chain '2' and resid 198 through 200' Processing helix chain '2' and resid 206 through 221 removed outlier: 3.859A pdb=" N ALA 2 210 " --> pdb=" O SER 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 235 Processing helix chain '2' and resid 240 through 254 removed outlier: 3.824A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 267 Processing helix chain '2' and resid 269 through 276 Processing helix chain '2' and resid 281 through 295 removed outlier: 3.530A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 4.106A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS 2 321 " --> pdb=" O ALA 2 317 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 341 removed outlier: 3.584A pdb=" N LEU 2 329 " --> pdb=" O ALA 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 354 Processing helix chain '2' and resid 396 through 408 removed outlier: 3.670A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 420 through 424 removed outlier: 3.568A pdb=" N ALA 2 423 " --> pdb=" O GLU 2 420 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU 2 424 " --> pdb=" O PHE 2 421 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 420 through 424' Processing helix chain '2' and resid 426 through 442 removed outlier: 3.707A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 91 through 99 removed outlier: 3.616A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL 3 98 " --> pdb=" O ASN 3 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 Processing helix chain '3' and resid 117 through 129 removed outlier: 4.362A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS 3 129 " --> pdb=" O ALA 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 removed outlier: 3.601A pdb=" N LEU 3 135 " --> pdb=" O VAL 3 132 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 168 removed outlier: 3.593A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 172 removed outlier: 3.544A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 169 through 172' Processing helix chain '3' and resid 173 through 187 removed outlier: 3.910A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 Processing helix chain '3' and resid 211 through 214 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.698A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 245 through 251 removed outlier: 3.742A pdb=" N LYS 3 251 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 272 removed outlier: 3.992A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 287 removed outlier: 4.174A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 Processing helix chain '4' and resid 9 through 15 removed outlier: 3.821A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE 4 14 " --> pdb=" O GLU 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.841A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 3.719A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.754A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 Processing helix chain '4' and resid 131 through 150 removed outlier: 3.945A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 176 removed outlier: 3.983A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 188 removed outlier: 3.578A pdb=" N ILE 4 183 " --> pdb=" O PRO 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 234 removed outlier: 4.387A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.751A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.548A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 59 removed outlier: 3.706A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.747A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 removed outlier: 3.501A pdb=" N LEU 5 68 " --> pdb=" O VAL 5 65 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 81 removed outlier: 3.525A pdb=" N PHE 5 81 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 106 removed outlier: 4.188A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 51 through 57 Processing helix chain '6' and resid 72 through 95 removed outlier: 3.518A pdb=" N SER 6 94 " --> pdb=" O ALA 6 90 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS 6 95 " --> pdb=" O ASP 6 91 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 118 removed outlier: 3.985A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '6' and resid 133 through 138 removed outlier: 4.114A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 67 removed outlier: 3.539A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 63 through 67' Processing helix chain '7' and resid 68 through 72 removed outlier: 3.667A pdb=" N GLY 7 71 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER 7 72 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 68 through 72' Processing helix chain '7' and resid 83 through 105 removed outlier: 3.695A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 114 removed outlier: 3.592A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 removed outlier: 3.558A pdb=" N TYR 7 120 " --> pdb=" O LYS 7 116 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 145 removed outlier: 3.674A pdb=" N THR 7 145 " --> pdb=" O TYR 7 141 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 154 Processing helix chain '7' and resid 157 through 165 Processing helix chain '7' and resid 174 through 187 Processing helix chain '8' and resid 26 through 31 removed outlier: 3.532A pdb=" N THR 8 30 " --> pdb=" O HIS 8 26 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 26 through 31' Processing helix chain '8' and resid 31 through 39 removed outlier: 3.549A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 78 removed outlier: 3.754A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 17 Processing helix chain '9' and resid 32 through 55 removed outlier: 3.708A pdb=" N TYR 9 36 " --> pdb=" O SER 9 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL 9 37 " --> pdb=" O LYS 9 33 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 4.424A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.513A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.799A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.995A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.917A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.330A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.694A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.038A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.041A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.917A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.732A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 3.697A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 3.835A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 98 through 127 removed outlier: 4.286A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.998A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 91 removed outlier: 3.850A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.652A pdb=" N ILE F 95 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 96' Processing helix chain 'F' and resid 97 through 126 removed outlier: 3.768A pdb=" N LEU F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 removed outlier: 3.971A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 90 removed outlier: 4.386A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 127 removed outlier: 3.528A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.918A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 90 removed outlier: 4.087A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 95 through 126 removed outlier: 4.026A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE H 126 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 4.348A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.039A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.088A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.112A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 92 removed outlier: 4.053A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 127 removed outlier: 3.787A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 120 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 165 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 201 removed outlier: 3.579A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY M 201 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 230 removed outlier: 4.323A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 259 removed outlier: 4.042A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 265 removed outlier: 3.504A pdb=" N PHE M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 309 removed outlier: 4.029A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 62 Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.563A pdb=" N GLU P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.980A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 127 removed outlier: 3.733A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 134 removed outlier: 4.472A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 149 removed outlier: 4.015A pdb=" N ALA P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS P 148 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'P' and resid 175 through 177 No H-bonds generated for 'chain 'P' and resid 175 through 177' Processing helix chain 'P' and resid 211 through 226 Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 42 removed outlier: 3.622A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 39 removed outlier: 4.444A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 161 through 170 removed outlier: 3.958A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 3.508A pdb=" N LEU R 187 " --> pdb=" O ALA R 183 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 79 removed outlier: 3.836A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 90 Processing helix chain 'S' and resid 117 through 130 removed outlier: 3.507A pdb=" N LEU S 127 " --> pdb=" O THR S 123 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 removed outlier: 3.615A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 removed outlier: 3.561A pdb=" N ALA S 175 " --> pdb=" O THR S 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 222 removed outlier: 3.980A pdb=" N ASP S 222 " --> pdb=" O GLN S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.759A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 75 removed outlier: 3.578A pdb=" N LYS T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 4.042A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.641A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 212 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.525A pdb=" N VAL T 234 " --> pdb=" O GLY T 230 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.175A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR T 316 " --> pdb=" O TYR T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.690A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 400 Processing helix chain 'T' and resid 409 through 414 Processing helix chain 'T' and resid 431 through 435 removed outlier: 4.107A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 460 removed outlier: 3.561A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU T 446 " --> pdb=" O VAL T 442 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.790A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.572A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 528 removed outlier: 4.519A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 540 removed outlier: 4.175A pdb=" N PHE T 533 " --> pdb=" O ASN T 529 " (cutoff:3.500A) Processing helix chain 'T' and resid 545 through 556 removed outlier: 4.120A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 49 removed outlier: 3.538A pdb=" N LEU U 48 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 72 removed outlier: 4.428A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.905A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.937A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 284 removed outlier: 3.724A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.870A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 341 Processing helix chain 'U' and resid 346 through 350 removed outlier: 3.579A pdb=" N PHE U 350 " --> pdb=" O ARG U 347 " (cutoff:3.500A) Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.680A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 removed outlier: 3.542A pdb=" N GLY U 373 " --> pdb=" O LYS U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 409 through 415 removed outlier: 3.591A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 458 removed outlier: 4.287A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 467 through 484 removed outlier: 3.853A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 496 Processing helix chain 'U' and resid 497 through 506 Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.914A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.514A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.926A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.956A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.583A pdb=" N THR V 159 " --> pdb=" O GLY V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 211 Processing helix chain 'V' and resid 230 through 246 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 284 removed outlier: 3.847A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.617A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.681A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.617A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.614A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 439 through 457 removed outlier: 3.861A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 484 removed outlier: 3.574A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.805A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS V 506 " --> pdb=" O TYR V 502 " (cutoff:3.500A) Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.989A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 540 removed outlier: 3.783A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 548 removed outlier: 4.087A pdb=" N ALA V 548 " --> pdb=" O PRO V 544 " (cutoff:3.500A) Processing helix chain 'V' and resid 548 through 553 removed outlier: 3.764A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.142A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 260 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.756A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 300 Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 341 through 345 removed outlier: 3.606A pdb=" N ASP X 344 " --> pdb=" O VAL X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 393 through 420 removed outlier: 3.620A pdb=" N LEU X 413 " --> pdb=" O ASP X 409 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU X 420 " --> pdb=" O ILE X 416 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.696A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 475 Processing helix chain 'X' and resid 482 through 486 Processing helix chain 'X' and resid 491 through 503 removed outlier: 4.033A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 532 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 190 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 4.232A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.569A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 299 removed outlier: 3.815A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 342 through 345 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.668A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 371 removed outlier: 3.613A pdb=" N ALA Y 369 " --> pdb=" O SER Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 393 through 412 removed outlier: 3.929A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 421 Processing helix chain 'Y' and resid 422 through 425 removed outlier: 3.709A pdb=" N LEU Y 425 " --> pdb=" O MET Y 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 422 through 425' Processing helix chain 'Y' and resid 426 through 443 removed outlier: 3.534A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU Y 443 " --> pdb=" O ILE Y 439 " (cutoff:3.500A) Processing helix chain 'Y' and resid 450 through 455 Processing helix chain 'Y' and resid 462 through 476 Processing helix chain 'Y' and resid 482 through 486 removed outlier: 3.607A pdb=" N ALA Y 485 " --> pdb=" O PRO Y 482 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 505 removed outlier: 3.786A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 511 through 515 removed outlier: 4.664A pdb=" N ASN Y 514 " --> pdb=" O GLU Y 511 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS Y 515 " --> pdb=" O ALA Y 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 511 through 515' Processing helix chain 'Y' and resid 526 through 532 Processing helix chain 'Y' and resid 541 through 543 No H-bonds generated for 'chain 'Y' and resid 541 through 543' Processing helix chain 'Y' and resid 544 through 550 removed outlier: 3.783A pdb=" N ASP Y 548 " --> pdb=" O GLY Y 544 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 170 Processing helix chain 'Z' and resid 188 through 201 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.730A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.633A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.793A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA Z 299 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 342 through 345 Processing helix chain 'Z' and resid 348 through 354 removed outlier: 4.201A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.589A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 418 removed outlier: 4.654A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.581A pdb=" N VAL Z 433 " --> pdb=" O ASP Z 429 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.687A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 506 removed outlier: 3.672A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 534 removed outlier: 4.012A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE Z 534 " --> pdb=" O LEU Z 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '2' and resid 369 through 372 removed outlier: 3.553A pdb=" N ALA 2 375 " --> pdb=" O LYS 2 372 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LYS 2 376 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 Processing sheet with id=AA4, first strand: chain '7' and resid 36 through 39 removed outlier: 3.681A pdb=" N ALA 7 55 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '7' and resid 36 through 39 Processing sheet with id=AA6, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.407A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 61 through 65 removed outlier: 3.599A pdb=" N GLN Q 49 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN S 159 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA S 163 " --> pdb=" O SER S 141 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS S 99 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN S 191 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL S 101 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU S 193 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL S 103 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASN S 195 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL S 105 " --> pdb=" O ASN S 195 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N PHE S 197 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'R' and resid 80 through 82 removed outlier: 7.801A pdb=" N ILE R 144 " --> pdb=" O PRO R 71 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN R 73 " --> pdb=" O ILE R 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 99 through 100 removed outlier: 4.175A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.572A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AB3, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.572A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 116 through 122 current: chain 'Y' and resid 61 through 65 removed outlier: 4.454A pdb=" N SER Y 61 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AB4, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AB5, first strand: chain 'T' and resid 163 through 164 removed outlier: 6.600A pdb=" N GLY T 320 " --> pdb=" O THR T 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 201 through 202 removed outlier: 4.237A pdb=" N ILE T 215 " --> pdb=" O LEU T 202 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 382 through 384 removed outlier: 7.095A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 116 through 122 removed outlier: 3.909A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL U 87 " --> pdb=" O TYR U 98 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N TYR U 98 " --> pdb=" O VAL U 87 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AC1, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.692A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR U 256 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE U 323 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL U 258 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP U 325 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL U 260 " --> pdb=" O ASP U 325 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR U 378 " --> pdb=" O GLY U 320 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 201 through 202 removed outlier: 4.440A pdb=" N ILE U 215 " --> pdb=" O LEU U 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 223 through 225 Processing sheet with id=AC4, first strand: chain 'V' and resid 84 through 91 removed outlier: 6.588A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL V 90 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE V 94 " --> pdb=" O VAL V 90 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR V 147 " --> pdb=" O LEU V 108 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AC6, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.484A pdb=" N THR V 164 " --> pdb=" O SER V 289 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR V 256 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE V 323 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL V 258 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP V 325 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL V 260 " --> pdb=" O ASP V 325 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 201 through 202 removed outlier: 4.451A pdb=" N ILE V 215 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'V' and resid 382 through 384 removed outlier: 7.935A pdb=" N ILE V 383 " --> pdb=" O GLU V 221 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE V 223 " --> pdb=" O ILE V 383 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.552A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.081A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN X 250 " --> pdb=" O MET X 122 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL X 280 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL X 336 " --> pdb=" O VAL X 280 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU X 282 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA X 338 " --> pdb=" O LEU X 282 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL X 284 " --> pdb=" O ALA X 338 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AD3, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id=AD4, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.212A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE Y 207 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS Y 178 " --> pdb=" O ALA Y 360 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR Y 362 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY Y 180 " --> pdb=" O THR Y 362 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.326A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.536A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR Z 84 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N HIS Z 79 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG Z 86 " --> pdb=" O ALA Z 77 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.593A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.358A pdb=" N MET Z 122 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL Z 280 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU Z 282 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA Z 338 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL Z 284 " --> pdb=" O ALA Z 338 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR Z 340 " --> pdb=" O VAL Z 284 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE Z 179 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL Z 339 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU Z 181 " --> pdb=" O VAL Z 339 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY Z 180 " --> pdb=" O THR Z 362 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 159 through 160 removed outlier: 3.956A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 559 through 561 2837 hydrogen bonds defined for protein. 8259 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: 28.88 Time building geometry restraints manager: 15.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16757 1.34 - 1.46: 9103 1.46 - 1.57: 28523 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54658 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.26e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.28e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.59e+01 ... (remaining 54653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 73650 4.08 - 8.17: 424 8.17 - 12.25: 41 12.25 - 16.33: 2 16.33 - 20.41: 4 Bond angle restraints: 74121 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 119.46 20.41 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 120.66 19.21 1.00e+00 1.00e+00 3.69e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 121.48 18.39 1.00e+00 1.00e+00 3.38e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 120.06 16.77 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.73e+02 ... (remaining 74116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 32303 35.22 - 70.44: 638 70.44 - 105.67: 62 105.67 - 140.89: 1 140.89 - 176.11: 1 Dihedral angle restraints: 33005 sinusoidal: 12661 harmonic: 20344 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -127.72 -52.28 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -130.85 -49.15 0 5.00e+00 4.00e-02 9.66e+01 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual 180.00 -144.44 -35.56 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 33002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 7212 0.076 - 0.152: 1342 0.152 - 0.227: 108 0.227 - 0.303: 20 0.303 - 0.379: 1 Chirality restraints: 8683 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB VAL V 209 " pdb=" CA VAL V 209 " pdb=" CG1 VAL V 209 " pdb=" CG2 VAL V 209 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE B 95 " pdb=" CA ILE B 95 " pdb=" CG1 ILE B 95 " pdb=" CG2 ILE B 95 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 8680 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.032 2.00e-02 2.50e+03 6.22e-02 3.87e+01 pdb=" C ALA Z 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.12e-02 3.74e+01 pdb=" C ALA Y 503 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA T 296 " -0.053 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO T 297 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO T 297 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO T 297 " -0.045 5.00e-02 4.00e+02 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 265 2.46 - 3.07: 32662 3.07 - 3.68: 84083 3.68 - 4.29: 125691 4.29 - 4.90: 208574 Nonbonded interactions: 451275 Sorted by model distance: nonbonded pdb=" SG CYS P 154 " pdb=" CA MET P 186 " model vdw 1.846 3.830 nonbonded pdb=" CZ PHE G 107 " pdb=" OE1 GLU G 111 " model vdw 1.921 3.340 nonbonded pdb=" CG2 THR P 171 " pdb=" CE MET P 186 " model vdw 1.952 3.880 nonbonded pdb=" O ALA X 499 " pdb=" CB ALA X 503 " model vdw 2.002 2.768 nonbonded pdb=" O LEU 3 195 " pdb=" OH TYR 3 226 " model vdw 2.227 3.040 ... (remaining 451270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 562 or resid 1001 through 1002)) selection = chain 'V' } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } 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: 10.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.800 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 129.720 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.490 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: 0.030 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.009 0.108 54658 Z= 0.567 Angle : 0.958 20.413 74121 Z= 0.544 Chirality : 0.058 0.379 8683 Planarity : 0.008 0.079 9504 Dihedral : 15.000 176.109 19929 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.43 % Favored : 94.38 % Rotamer: Outliers : 0.43 % Allowed : 9.49 % Favored : 90.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.22 (0.08), residues: 7034 helix: -2.99 (0.06), residues: 3796 sheet: -1.95 (0.20), residues: 584 loop : -2.39 (0.10), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP Y 141 HIS 0.015 0.002 HIS S 250 PHE 0.028 0.003 PHE S 249 TYR 0.026 0.003 TYR V 393 ARG 0.009 0.001 ARG U 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 5633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 904 time to evaluate : 5.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8104 (mptt) REVERT: 1 55 GLN cc_start: 0.8196 (mm110) cc_final: 0.7583 (tt0) REVERT: 1 328 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8557 (mmt90) REVERT: 1 347 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7792 (tppt) REVERT: 1 456 LYS cc_start: 0.7528 (mmtm) cc_final: 0.7207 (ttmt) REVERT: 1 548 MET cc_start: 0.9121 (mtm) cc_final: 0.8503 (mtp) REVERT: 2 122 ASN cc_start: 0.8536 (t0) cc_final: 0.8276 (t0) REVERT: 2 246 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7272 (mm-30) REVERT: 2 322 ARG cc_start: 0.7829 (ttm170) cc_final: 0.7474 (mtm-85) REVERT: 4 91 ASN cc_start: 0.8637 (m-40) cc_final: 0.8214 (m-40) REVERT: 4 129 TYR cc_start: 0.8908 (m-80) cc_final: 0.8643 (m-80) REVERT: 4 242 ARG cc_start: 0.8438 (mtt90) cc_final: 0.8211 (mtt180) REVERT: 4 254 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8566 (tppt) REVERT: 4 271 ASP cc_start: 0.7540 (m-30) cc_final: 0.7340 (m-30) REVERT: 5 54 LYS cc_start: 0.8289 (tttt) cc_final: 0.7913 (tttm) REVERT: 5 115 ILE cc_start: 0.8636 (tp) cc_final: 0.8404 (tp) REVERT: 5 119 LYS cc_start: 0.8474 (mmtp) cc_final: 0.7998 (mtpt) REVERT: 6 93 GLN cc_start: 0.8104 (mt0) cc_final: 0.7823 (mt0) REVERT: 9 9 LYS cc_start: 0.7745 (ttpt) cc_final: 0.7247 (mtpp) REVERT: 9 13 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7496 (pttp) REVERT: 9 16 TYR cc_start: 0.8036 (m-80) cc_final: 0.7686 (m-80) REVERT: D 61 MET cc_start: 0.7246 (mmt) cc_final: 0.6959 (mmt) REVERT: D 115 LEU cc_start: 0.7425 (tp) cc_final: 0.7187 (pp) REVERT: F 92 ASN cc_start: 0.7186 (m-40) cc_final: 0.6778 (m110) REVERT: H 81 MET cc_start: 0.6541 (ttp) cc_final: 0.6185 (ttp) REVERT: P 72 ASP cc_start: 0.6342 (t70) cc_final: 0.6131 (t0) REVERT: P 81 PHE cc_start: 0.8527 (m-10) cc_final: 0.8290 (m-10) REVERT: P 163 ASP cc_start: 0.7559 (m-30) cc_final: 0.7347 (m-30) REVERT: P 169 GLU cc_start: 0.7918 (tp30) cc_final: 0.7717 (tp30) REVERT: P 182 PHE cc_start: 0.8725 (m-80) cc_final: 0.8459 (m-80) REVERT: P 209 MET cc_start: 0.7203 (mmm) cc_final: 0.6688 (tpt) REVERT: R 120 SER cc_start: 0.7074 (m) cc_final: 0.6136 (t) REVERT: S 119 ILE cc_start: 0.7222 (pt) cc_final: 0.7000 (pt) REVERT: S 177 LEU cc_start: 0.7841 (mt) cc_final: 0.7629 (mt) REVERT: S 180 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6450 (mt-10) REVERT: S 295 LYS cc_start: 0.8467 (mttm) cc_final: 0.8219 (mtpp) REVERT: T 282 MET cc_start: 0.8695 (tpp) cc_final: 0.8194 (tpt) REVERT: T 309 MET cc_start: 0.8733 (mtt) cc_final: 0.8518 (mtt) REVERT: T 325 ASP cc_start: 0.8367 (t70) cc_final: 0.7892 (t0) REVERT: V 112 ASP cc_start: 0.8333 (p0) cc_final: 0.8101 (p0) REVERT: V 311 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7046 (mt-10) REVERT: V 325 ASP cc_start: 0.7932 (t0) cc_final: 0.7667 (t0) REVERT: V 506 LYS cc_start: 0.7047 (mmtm) cc_final: 0.6342 (mmmt) REVERT: X 195 GLU cc_start: 0.8021 (tp30) cc_final: 0.7725 (tp30) REVERT: X 410 TYR cc_start: 0.8222 (t80) cc_final: 0.7872 (t80) REVERT: X 488 MET cc_start: 0.7712 (mmt) cc_final: 0.7295 (mmm) REVERT: Y 195 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6443 (tm-30) REVERT: Y 439 ILE cc_start: 0.8851 (pt) cc_final: 0.8504 (mt) REVERT: Z 90 MET cc_start: 0.8481 (mmt) cc_final: 0.8275 (mmt) REVERT: Z 195 GLU cc_start: 0.7308 (tp30) cc_final: 0.7103 (tp30) REVERT: Z 385 ARG cc_start: 0.7137 (mmt180) cc_final: 0.6600 (mpt-90) REVERT: Z 448 GLN cc_start: 0.6155 (tm-30) cc_final: 0.5520 (mt0) REVERT: Z 488 MET cc_start: 0.7940 (mmt) cc_final: 0.7707 (mmt) outliers start: 24 outliers final: 12 residues processed: 923 average time/residue: 0.7431 time to fit residues: 1133.8373 Evaluate side-chains 629 residues out of total 5633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 617 time to evaluate : 5.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 283 ASP Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain Z residue 314 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 588 optimal weight: 0.9990 chunk 528 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 356 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 546 optimal weight: 0.0770 chunk 211 optimal weight: 0.8980 chunk 332 optimal weight: 0.2980 chunk 406 optimal weight: 0.7980 chunk 632 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 65 GLN 1 81 ASN 1 316 ASN 1 394 GLN 1 582 GLN 1 606 ASN 2 44 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 243 GLN 2 289 HIS 2 380 GLN 2 427 GLN 3 206 ASN 3 229 ASN 4 38 GLN 4 135 ASN 4 240 GLN 6 74 GLN 7 60 GLN 7 98 ASN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 50 ASN 9 56 ASN B 94 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN I 94 ASN M 108 ASN M 121 ASN M 163 ASN P 76 GLN P 223 ASN Q 29 ASN Q 46 HIS Q 49 GLN R 66 HIS R 104 HIS R 137 HIS R 178 GLN S 118 ASN S 186 ASN S 267 HIS T 64 GLN T 104 GLN T 134 ASN T 241 HIS T 358 HIS T 386 GLN T 452 GLN U 104 GLN U 140 GLN U 196 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 264 GLN U 319 HIS U 441 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 242 GLN V 244 ASN V 264 GLN V 278 GLN V 386 GLN V 486 GLN V 497 GLN X 144 HIS X 174 GLN X 199 ASN X 322 GLN X 337 GLN Y 199 ASN Y 241 ASN Y 278 GLN Y 292 GLN Y 412 ASN Z 174 GLN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 54658 Z= 0.171 Angle : 0.584 9.418 74121 Z= 0.306 Chirality : 0.042 0.211 8683 Planarity : 0.005 0.062 9504 Dihedral : 6.681 171.084 7681 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.57 % Favored : 96.29 % Rotamer: Outliers : 1.40 % Allowed : 13.29 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.34 (0.09), residues: 7034 helix: -1.21 (0.08), residues: 3856 sheet: -1.65 (0.20), residues: 636 loop : -1.83 (0.11), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 9 93 HIS 0.007 0.001 HIS U 61 PHE 0.026 0.001 PHE H 116 TYR 0.024 0.001 TYR 4 211 ARG 0.016 0.000 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 5633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 719 time to evaluate : 5.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8061 (mptt) REVERT: 1 24 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8383 (pp) REVERT: 1 328 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8642 (mmt90) REVERT: 1 347 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7577 (tppt) REVERT: 1 456 LYS cc_start: 0.7372 (mmtm) cc_final: 0.7107 (ttmt) REVERT: 1 548 MET cc_start: 0.9002 (mtm) cc_final: 0.8344 (mtp) REVERT: 2 122 ASN cc_start: 0.8284 (t0) cc_final: 0.8079 (t0) REVERT: 2 246 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7242 (mm-30) REVERT: 3 256 GLN cc_start: 0.7863 (mt0) cc_final: 0.7568 (mt0) REVERT: 4 91 ASN cc_start: 0.8658 (m-40) cc_final: 0.8227 (m-40) REVERT: 4 242 ARG cc_start: 0.8464 (mtt90) cc_final: 0.8202 (mtt180) REVERT: 4 271 ASP cc_start: 0.7489 (m-30) cc_final: 0.7285 (m-30) REVERT: 5 54 LYS cc_start: 0.8244 (tttt) cc_final: 0.7868 (tttm) REVERT: 5 63 ASP cc_start: 0.8471 (p0) cc_final: 0.8222 (p0) REVERT: 5 119 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7526 (mtmt) REVERT: 7 78 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7532 (mt-10) REVERT: 9 9 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7217 (mtpp) REVERT: 9 13 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7474 (pttp) REVERT: 9 82 ASP cc_start: 0.7763 (t0) cc_final: 0.7500 (t0) REVERT: D 115 LEU cc_start: 0.7332 (tp) cc_final: 0.7076 (pp) REVERT: F 92 ASN cc_start: 0.7121 (m-40) cc_final: 0.6874 (m-40) REVERT: F 124 ILE cc_start: 0.7045 (tt) cc_final: 0.6791 (tt) REVERT: H 81 MET cc_start: 0.6304 (ttp) cc_final: 0.5987 (ttp) REVERT: H 116 PHE cc_start: 0.7223 (m-80) cc_final: 0.6365 (t80) REVERT: I 81 MET cc_start: 0.6715 (ttp) cc_final: 0.5985 (tmm) REVERT: M 203 LYS cc_start: 0.6873 (ptpt) cc_final: 0.6583 (pttp) REVERT: P 72 ASP cc_start: 0.6430 (t70) cc_final: 0.6205 (t0) REVERT: P 169 GLU cc_start: 0.7943 (tp30) cc_final: 0.7674 (tp30) REVERT: P 182 PHE cc_start: 0.8770 (m-80) cc_final: 0.8532 (m-80) REVERT: P 209 MET cc_start: 0.7367 (mmm) cc_final: 0.6879 (tpt) REVERT: T 227 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7480 (ttp-110) REVERT: T 282 MET cc_start: 0.8504 (tpp) cc_final: 0.7764 (tpt) REVERT: U 220 ARG cc_start: 0.8553 (mpp80) cc_final: 0.8285 (mtm110) REVERT: V 112 ASP cc_start: 0.8165 (p0) cc_final: 0.7548 (p0) REVERT: V 282 MET cc_start: 0.8779 (tpt) cc_final: 0.8313 (tpt) REVERT: V 445 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6604 (t) REVERT: V 506 LYS cc_start: 0.6896 (mmtm) cc_final: 0.6460 (mmmt) REVERT: X 488 MET cc_start: 0.7796 (mmt) cc_final: 0.7334 (ttp) REVERT: Y 195 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6466 (tm-30) REVERT: Y 199 ASN cc_start: 0.8328 (m-40) cc_final: 0.7627 (m110) REVERT: Y 422 MET cc_start: 0.7598 (mpp) cc_final: 0.7344 (mpp) REVERT: Y 439 ILE cc_start: 0.8798 (pt) cc_final: 0.8567 (mt) REVERT: Z 448 GLN cc_start: 0.6118 (tm-30) cc_final: 0.5505 (mt0) REVERT: Z 488 MET cc_start: 0.7913 (mmt) cc_final: 0.7664 (mmt) outliers start: 79 outliers final: 48 residues processed: 772 average time/residue: 0.6547 time to fit residues: 843.1449 Evaluate side-chains 636 residues out of total 5633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 586 time to evaluate : 5.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 52 ILE Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 391 ASP Chi-restraints excluded: chain 1 residue 414 GLU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 427 GLN Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 3 residue 175 GLU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 5 residue 20 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 77 ILE Chi-restraints excluded: chain 8 residue 17 THR Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 68 MET Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain Q residue 42 ARG Chi-restraints excluded: chain R residue 54 TYR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 510 ASP Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 226 ASP Chi-restraints excluded: chain U residue 236 ILE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 551 LYS Chi-restraints excluded: chain V residue 405 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 417 ILE Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain Z residue 160 LEU Chi-restraints excluded: chain Z residue 314 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.8306 > 50: distance: 40 - 45: 32.439 distance: 45 - 46: 38.810 distance: 46 - 47: 67.740 distance: 46 - 49: 60.574 distance: 47 - 48: 35.559 distance: 47 - 53: 56.693 distance: 49 - 50: 46.037 distance: 50 - 51: 25.061 distance: 50 - 52: 27.346 distance: 53 - 54: 56.666 distance: 55 - 56: 56.666 distance: 57 - 58: 56.600 distance: 59 - 60: 5.519 distance: 60 - 61: 7.090 distance: 60 - 63: 41.864 distance: 61 - 62: 40.903 distance: 61 - 65: 56.041 distance: 63 - 64: 41.761 distance: 66 - 67: 40.491 distance: 66 - 69: 40.482 distance: 67 - 68: 39.762 distance: 67 - 74: 56.833 distance: 69 - 70: 25.877 distance: 70 - 71: 22.981 distance: 71 - 72: 17.188 distance: 72 - 73: 39.963 distance: 74 - 75: 56.281 distance: 75 - 76: 9.465 distance: 76 - 77: 44.524 distance: 76 - 78: 39.916 distance: 79 - 80: 68.923 distance: 79 - 82: 57.207 distance: 80 - 87: 47.331 distance: 81 - 111: 3.216 distance: 82 - 83: 40.392 distance: 83 - 84: 33.471 distance: 84 - 85: 9.312 distance: 84 - 86: 34.506 distance: 87 - 88: 15.090 distance: 88 - 89: 18.963 distance: 89 - 90: 44.499 distance: 89 - 99: 44.827 distance: 90 - 119: 34.271 distance: 91 - 92: 35.601 distance: 92 - 93: 11.732 distance: 92 - 94: 4.929 distance: 93 - 95: 24.221 distance: 94 - 96: 34.332 distance: 95 - 97: 38.558 distance: 96 - 97: 40.042 distance: 97 - 98: 11.924 distance: 100 - 101: 27.174 distance: 100 - 103: 34.544 distance: 101 - 102: 48.806 distance: 101 - 106: 47.957 distance: 102 - 128: 35.258 distance: 103 - 104: 38.995 distance: 103 - 105: 40.339 distance: 106 - 107: 41.227 distance: 107 - 108: 56.608 distance: 107 - 110: 41.337 distance: 108 - 109: 43.510 distance: 108 - 111: 40.339 distance: 112 - 113: 41.427 distance: 112 - 115: 41.509 distance: 113 - 114: 56.755 distance: 113 - 119: 34.335 distance: 114 - 140: 31.229 distance: 115 - 116: 40.261 distance: 116 - 117: 40.360 distance: 116 - 118: 48.680