Starting phenix.real_space_refine on Tue Mar 19 15:22:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl4_33272/03_2024/7xl4_33272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl4_33272/03_2024/7xl4_33272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl4_33272/03_2024/7xl4_33272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl4_33272/03_2024/7xl4_33272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl4_33272/03_2024/7xl4_33272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl4_33272/03_2024/7xl4_33272.pdb" } resolution = 3.86 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 82 5.16 5 C 15397 2.51 5 N 4497 2.21 5 O 4581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C ARG 533": "NH1" <-> "NH2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C ASP 680": "OD1" <-> "OD2" Residue "C ARG 740": "NH1" <-> "NH2" Residue "C ARG 846": "NH1" <-> "NH2" Residue "C GLU 872": "OE1" <-> "OE2" Residue "C GLU 881": "OE1" <-> "OE2" Residue "C ASP 959": "OD1" <-> "OD2" Residue "C ARG 1051": "NH1" <-> "NH2" Residue "C ARG 1076": "NH1" <-> "NH2" Residue "C ASP 1105": "OD1" <-> "OD2" Residue "C ARG 1147": "NH1" <-> "NH2" Residue "C GLU 1150": "OE1" <-> "OE2" Residue "C ARG 1159": "NH1" <-> "NH2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C GLU 1221": "OE1" <-> "OE2" Residue "C ARG 1226": "NH1" <-> "NH2" Residue "C ARG 1231": "NH1" <-> "NH2" Residue "C GLU 1289": "OE1" <-> "OE2" Residue "C ARG 1329": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D ARG 652": "NH1" <-> "NH2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D ARG 764": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ASP 802": "OD1" <-> "OD2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 846": "NH1" <-> "NH2" Residue "D ARG 908": "NH1" <-> "NH2" Residue "D ARG 978": "NH1" <-> "NH2" Residue "D ARG 1330": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1373": "NH1" <-> "NH2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G ASP 65": "OD1" <-> "OD2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "F ASP 228": "OD1" <-> "OD2" Residue "F ASP 258": "OD1" <-> "OD2" Residue "F ARG 306": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24560 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1700 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 218} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 9297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1324, 9297 Classifications: {'peptide': 1324} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 53, 'TRANS': 1270} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1073 Unresolved non-hydrogen angles: 1385 Unresolved non-hydrogen dihedrals: 842 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 31, 'PHE:plan': 12, 'GLU:plan': 45, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 633 Chain: "D" Number of atoms: 9403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 9403 Classifications: {'peptide': 1339} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 60, 'TRANS': 1278} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1022 Unresolved non-hydrogen angles: 1309 Unresolved non-hydrogen dihedrals: 805 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 43, 'PHE:plan': 10, 'GLU:plan': 48, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 630 Chain: "E" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 500 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 194 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1895 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 11, 'TRANS': 266} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 11, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 213 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13014 SG CYS D 72 114.989 48.653 64.498 1.00 53.33 S ATOM 13114 SG CYS D 85 117.378 48.252 67.785 1.00 53.73 S ATOM 19078 SG CYS D 898 79.659 69.095 122.992 1.00 17.60 S Time building chain proxies: 13.36, per 1000 atoms: 0.54 Number of scatterers: 24560 At special positions: 0 Unit cell: (141.9, 155.1, 155.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 82 16.00 Mg 1 11.99 O 4581 8.00 N 4497 7.00 C 15397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.98 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6428 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 46 sheets defined 37.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.580A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 211 through 232 removed outlier: 3.828A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 49 removed outlier: 3.702A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.613A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.866A pdb=" N ILE B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.561A pdb=" N VAL B 231 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.674A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.656A pdb=" N LEU C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.586A pdb=" N ALA C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 228 removed outlier: 4.000A pdb=" N PHE C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.855A pdb=" N GLU C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 284' Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.893A pdb=" N ILE C 298 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY C 299 " --> pdb=" O TYR C 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 299' Processing helix chain 'C' and resid 323 through 333 removed outlier: 3.589A pdb=" N ALA C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.777A pdb=" N THR C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 376 removed outlier: 3.782A pdb=" N ALA C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET C 375 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.659A pdb=" N GLU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 removed outlier: 3.766A pdb=" N ARG C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 414 " --> pdb=" O PHE C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.651A pdb=" N LEU C 437 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 454 No H-bonds generated for 'chain 'C' and resid 452 through 454' Processing helix chain 'C' and resid 460 through 475 removed outlier: 3.626A pdb=" N ASN C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 468 " --> pdb=" O MET C 464 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY C 472 " --> pdb=" O GLN C 468 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.818A pdb=" N ALA C 479 " --> pdb=" O ARG C 475 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 485 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.526A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 removed outlier: 3.532A pdb=" N TYR C 560 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 617 removed outlier: 3.685A pdb=" N GLU C 616 " --> pdb=" O ALA C 613 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 617 " --> pdb=" O ILE C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 613 through 617' Processing helix chain 'C' and resid 661 through 665 removed outlier: 3.953A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.890A pdb=" N LEU C 672 " --> pdb=" O VAL C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 691 removed outlier: 3.521A pdb=" N MET C 686 " --> pdb=" O ASN C 682 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 688 " --> pdb=" O ALA C 684 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C 689 " --> pdb=" O LEU C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 715 removed outlier: 3.698A pdb=" N ALA C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 830 removed outlier: 3.689A pdb=" N GLU C 830 " --> pdb=" O ARG C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 911 removed outlier: 3.823A pdb=" N LEU C 907 " --> pdb=" O GLU C 903 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 909 " --> pdb=" O LYS C 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 981 removed outlier: 3.666A pdb=" N LEU C 951 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 952 " --> pdb=" O SER C 948 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 953 " --> pdb=" O ARG C 949 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 965 " --> pdb=" O ILE C 961 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 971 " --> pdb=" O GLU C 967 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 979 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.695A pdb=" N ASN C1025 " --> pdb=" O ASP C1021 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C1040 " --> pdb=" O SER C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 3.934A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1150 Processing helix chain 'C' and resid 1154 through 1167 removed outlier: 3.704A pdb=" N LEU C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C1160 " --> pdb=" O ALA C1156 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C1161 " --> pdb=" O GLU C1157 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C1165 " --> pdb=" O PHE C1161 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C1167 " --> pdb=" O HIS C1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1189 removed outlier: 3.890A pdb=" N LEU C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1217 removed outlier: 4.007A pdb=" N MET C1213 " --> pdb=" O GLU C1209 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C1214 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS C1215 " --> pdb=" O LYS C1211 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C1216 " --> pdb=" O ALA C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1253 through 1257 removed outlier: 3.605A pdb=" N ASP C1256 " --> pdb=" O LEU C1253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C1257 " --> pdb=" O VAL C1254 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1253 through 1257' Processing helix chain 'C' and resid 1286 through 1296 removed outlier: 3.548A pdb=" N VAL C1290 " --> pdb=" O GLY C1286 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C1292 " --> pdb=" O MET C1288 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR C1296 " --> pdb=" O ALA C1292 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1308 removed outlier: 3.551A pdb=" N LEU C1306 " --> pdb=" O LEU C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1313 through 1326 removed outlier: 4.022A pdb=" N THR C1317 " --> pdb=" O VAL C1313 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C1321 " --> pdb=" O THR C1317 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C1322 " --> pdb=" O LYS C1318 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1347 removed outlier: 3.584A pdb=" N ASN C1339 " --> pdb=" O PRO C1335 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C1340 " --> pdb=" O GLU C1336 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C1341 " --> pdb=" O SER C1337 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.817A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.663A pdb=" N ILE D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.825A pdb=" N PHE D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.998A pdb=" N VAL D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.599A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.639A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.540A pdb=" N MET D 237 " --> pdb=" O PRO D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 283 removed outlier: 3.894A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.772A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.886A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 removed outlier: 3.545A pdb=" N PHE D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 402 removed outlier: 3.524A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.738A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL D 415 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.537A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.591A pdb=" N GLU D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.856A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.641A pdb=" N VAL D 533 " --> pdb=" O ASP D 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG D 535 " --> pdb=" O GLN D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.645A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.923A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D 604 " --> pdb=" O ALA D 600 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN D 606 " --> pdb=" O SER D 602 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 635 removed outlier: 3.761A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 635 " --> pdb=" O TYR D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 removed outlier: 3.562A pdb=" N ILE D 653 " --> pdb=" O GLU D 649 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP D 659 " --> pdb=" O ASN D 655 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 662 " --> pdb=" O THR D 658 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.947A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP D 686 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER D 687 " --> pdb=" O ILE D 683 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.604A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 738 removed outlier: 3.661A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 733 through 738' Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.675A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.768A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 4.028A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 873 " --> pdb=" O VAL D 869 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 874 " --> pdb=" O ASP D 870 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET D 875 " --> pdb=" O PHE D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.756A pdb=" N CYS D 888 " --> pdb=" O PRO D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.773A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 919 " --> pdb=" O VAL D 915 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 920 " --> pdb=" O GLY D 916 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.729A pdb=" N ASP D1143 " --> pdb=" O PRO D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.841A pdb=" N ILE D1220 " --> pdb=" O ASN D1216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1243 removed outlier: 3.840A pdb=" N ALA D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS D1231 " --> pdb=" O SER D1227 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D1241 " --> pdb=" O ILE D1237 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.113A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN D1259 " --> pdb=" O THR D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 3.686A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D1286 " --> pdb=" O LEU D1282 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D1291 " --> pdb=" O GLU D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1311 through 1315 removed outlier: 3.700A pdb=" N SER D1315 " --> pdb=" O ALA D1312 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.618A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.832A pdb=" N VAL D1351 " --> pdb=" O LEU D1347 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1372 Processing helix chain 'E' and resid 9 through 14 removed outlier: 3.923A pdb=" N VAL E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.861A pdb=" N GLN E 29 " --> pdb=" O LYS E 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.762A pdb=" N ALA E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 52 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.580A pdb=" N VAL E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE E 69 " --> pdb=" O GLN E 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 78 removed outlier: 3.527A pdb=" N PHE G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 75 " --> pdb=" O MET G 71 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 70 removed outlier: 3.588A pdb=" N TYR F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 91 removed outlier: 4.001A pdb=" N VAL F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N HIS F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.995A pdb=" N ARG F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 112 removed outlier: 4.108A pdb=" N VAL F 107 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 138 removed outlier: 3.804A pdb=" N LEU F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 132 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 144 removed outlier: 3.639A pdb=" N GLY F 144 " --> pdb=" O PRO F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 167 removed outlier: 3.947A pdb=" N TRP F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 159 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 195 removed outlier: 3.578A pdb=" N LYS F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU F 179 " --> pdb=" O HIS F 175 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU F 180 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 181 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP F 195 " --> pdb=" O THR F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 207 removed outlier: 3.712A pdb=" N ILE F 203 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA F 204 " --> pdb=" O PRO F 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN F 205 " --> pdb=" O GLU F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.788A pdb=" N ARG F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 242 removed outlier: 3.826A pdb=" N ASP F 241 " --> pdb=" O THR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 272 removed outlier: 3.665A pdb=" N ASP F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 283 removed outlier: 3.537A pdb=" N VAL F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 298 Processing helix chain 'F' and resid 305 through 326 removed outlier: 3.763A pdb=" N ILE F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY F 326 " --> pdb=" O LEU F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.797A pdb=" N ARG A 23 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 206 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS A 25 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 204 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR A 27 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A 202 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU A 29 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 200 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 181 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 3.594A pdb=" N VAL A 98 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 7.169A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 4.177A pdb=" N LEU B 197 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 203 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 183 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 61 removed outlier: 8.242A pdb=" N GLY B 150 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N CYS B 54 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY B 148 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL B 56 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 146 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 141 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 102 " --> pdb=" O MET B 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 143 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 98 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.466A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.280A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 70 through 79 removed outlier: 3.627A pdb=" N VAL C 75 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LYS C 103 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR C 77 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG C 101 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 79 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 98 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLY C 129 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU C 100 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 127 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL C 102 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 123 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.567A pdb=" N PHE C 140 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 148 " --> pdb=" O GLN C 518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 456 through 458 removed outlier: 6.030A pdb=" N SER C 151 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 189 through 193 removed outlier: 3.676A pdb=" N CYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 233 through 235 Processing sheet with id=AB6, first strand: chain 'C' and resid 243 through 244 removed outlier: 3.918A pdb=" N LEU C 243 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 290 " --> pdb=" O LEU C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.817A pdb=" N ALA C 255 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 272 " --> pdb=" O ALA C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AB9, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC1, first strand: chain 'C' and resid 639 through 642 removed outlier: 3.541A pdb=" N VAL C 639 " --> pdb=" O LYS C 650 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 721 through 722 removed outlier: 6.437A pdb=" N VAL C 721 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 755 through 757 removed outlier: 3.890A pdb=" N SER C 731 " --> pdb=" O VAL C 738 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 762 through 763 removed outlier: 3.713A pdb=" N ILE C 770 " --> pdb=" O THR C 762 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC6, first strand: chain 'C' and resid 1224 through 1225 removed outlier: 7.910A pdb=" N ILE C 821 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C1096 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU C 823 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ILE C1113 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG C 806 " --> pdb=" O ILE C1113 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU C1115 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA C 808 " --> pdb=" O LEU C1115 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET C1247 " --> pdb=" O GLN C 803 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET C 805 " --> pdb=" O MET C1245 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 835 through 843 removed outlier: 3.666A pdb=" N THR C 835 " --> pdb=" O ARG C1075 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LYS C1074 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLY C 931 " --> pdb=" O LYS C1074 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 931 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 847 through 848 removed outlier: 4.050A pdb=" N THR C 848 " --> pdb=" O GLY C 851 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 854 through 855 removed outlier: 4.294A pdb=" N GLU C 854 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL C 892 " --> pdb=" O GLU C 854 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 removed outlier: 7.190A pdb=" N LEU C 923 " --> pdb=" O LEU C 888 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.575A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 352 " --> pdb=" O HIS C1259 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C1261 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 350 " --> pdb=" O ARG C1261 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.575A pdb=" N HIS C1259 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 352 " --> pdb=" O HIS C1259 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C1261 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 350 " --> pdb=" O ARG C1261 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 1284 through 1285 Processing sheet with id=AD5, first strand: chain 'C' and resid 1350 through 1354 Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.894A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.266A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.892A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.108A pdb=" N ARG D 551 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 removed outlier: 3.742A pdb=" N THR D 810 " --> pdb=" O ILE D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 821 through 822 removed outlier: 3.653A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.576A pdb=" N VAL D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D1018 " --> pdb=" O VAL D 950 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.981A pdb=" N HIS D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU D 981 " --> pdb=" O HIS D 961 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.687A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1024 through 1025 removed outlier: 3.623A pdb=" N ILE D1124 " --> pdb=" O HIS D1025 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.522A pdb=" N VAL D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.940A pdb=" N ILE D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1188 through 1190 Processing sheet with id=AF1, first strand: chain 'D' and resid 1278 through 1279 786 hydrogen bonds defined for protein. 2220 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: 10.16 Time building geometry restraints manager: 9.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8597 1.34 - 1.46: 4231 1.46 - 1.58: 11897 1.58 - 1.69: 0 1.69 - 1.81: 142 Bond restraints: 24867 Sorted by residual: bond pdb=" C PHE C 61 " pdb=" N PRO C 62 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.28e-01 bond pdb=" CA VAL B 64 " pdb=" CB VAL B 64 " ideal model delta sigma weight residual 1.527 1.536 -0.009 1.31e-02 5.83e+03 4.99e-01 bond pdb=" N ILE C 131 " pdb=" CA ILE C 131 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.89e-01 bond pdb=" C ALA D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.88e-01 bond pdb=" C GLU B 29 " pdb=" N PRO B 30 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.83e-01 ... (remaining 24862 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.13: 631 107.13 - 113.84: 14206 113.84 - 120.55: 9508 120.55 - 127.26: 9218 127.26 - 133.97: 179 Bond angle restraints: 33742 Sorted by residual: angle pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " ideal model delta sigma weight residual 118.44 121.62 -3.18 1.59e+00 3.96e-01 4.00e+00 angle pdb=" N LEU D1138 " pdb=" CA LEU D1138 " pdb=" C LEU D1138 " ideal model delta sigma weight residual 109.81 113.56 -3.75 2.21e+00 2.05e-01 2.88e+00 angle pdb=" CA LEU D 221 " pdb=" CB LEU D 221 " pdb=" CG LEU D 221 " ideal model delta sigma weight residual 116.30 121.95 -5.65 3.50e+00 8.16e-02 2.61e+00 angle pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" O LEU D1138 " ideal model delta sigma weight residual 120.16 117.95 2.21 1.37e+00 5.33e-01 2.60e+00 angle pdb=" NE ARG C 715 " pdb=" CZ ARG C 715 " pdb=" NH1 ARG C 715 " ideal model delta sigma weight residual 121.50 120.01 1.49 1.00e+00 1.00e+00 2.21e+00 ... (remaining 33737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 14555 17.82 - 35.65: 559 35.65 - 53.47: 65 53.47 - 71.30: 6 71.30 - 89.12: 9 Dihedral angle restraints: 15194 sinusoidal: 5243 harmonic: 9951 Sorted by residual: dihedral pdb=" CB GLU D 443 " pdb=" CG GLU D 443 " pdb=" CD GLU D 443 " pdb=" OE1 GLU D 443 " ideal model delta sinusoidal sigma weight residual 0.00 89.12 -89.12 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU C 291 " pdb=" CG GLU C 291 " pdb=" CD GLU C 291 " pdb=" OE1 GLU C 291 " ideal model delta sinusoidal sigma weight residual 0.00 -86.79 86.79 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU F 126 " pdb=" CG GLU F 126 " pdb=" CD GLU F 126 " pdb=" OE1 GLU F 126 " ideal model delta sinusoidal sigma weight residual 0.00 -84.53 84.53 1 3.00e+01 1.11e-03 9.65e+00 ... (remaining 15191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2275 0.026 - 0.053: 1204 0.053 - 0.079: 252 0.079 - 0.106: 217 0.106 - 0.132: 80 Chirality restraints: 4028 Sorted by residual: chirality pdb=" CA VAL D 583 " pdb=" N VAL D 583 " pdb=" C VAL D 583 " pdb=" CB VAL D 583 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE D1190 " pdb=" N ILE D1190 " pdb=" C ILE D1190 " pdb=" CB ILE D1190 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE D1159 " pdb=" N ILE D1159 " pdb=" C ILE D1159 " pdb=" CB ILE D1159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 4025 not shown) Planarity restraints: 4459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 501 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO D 502 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " 0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 30 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO D 851 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.017 5.00e-02 4.00e+02 ... (remaining 4456 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6729 2.80 - 3.32: 20400 3.32 - 3.85: 35952 3.85 - 4.37: 40216 4.37 - 4.90: 71137 Nonbonded interactions: 174434 Sorted by model distance: nonbonded pdb=" O LYS D1251 " pdb=" OG1 THR D1255 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.292 2.170 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.301 2.440 nonbonded pdb=" O SER C 59 " pdb=" OG SER C 59 " model vdw 2.312 2.440 nonbonded pdb=" O SER D 319 " pdb=" OG SER D 319 " model vdw 2.329 2.440 ... (remaining 174429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 13 or (resid 14 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 59 or (resid 60 through \ 62 and (name N or name CA or name C or name O or name CB )) or resid 63 through \ 74 or (resid 75 and (name N or name CA or name C or name O or name CB )) or resi \ d 76 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 89 or (resid 90 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2)) or resid 91 through 94 or (resid 95 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 96 th \ rough 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) \ or resid 106 through 113 or (resid 114 and (name N or name CA or name C or name \ O or name CB )) or resid 115 through 118 or (resid 119 and (name N or name CA o \ r name C or name O or name CB )) or resid 120 through 134 or resid 139 through 1 \ 54 or (resid 155 through 157 and (name N or name CA or name C or name O or name \ CB )) or (resid 169 and (name N or name CA or name C or name O or name CB )) or \ resid 170 through 182 or (resid 183 and (name N or name CA or name C or name O o \ r name CB )) or resid 184 through 189 or (resid 190 and (name N or name CA or na \ me C or name O or name CB )) or resid 191 or (resid 192 and (name N or name CA o \ r name C or name O or name CB )) or resid 193 through 230 or (resid 231 through \ 232 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 8 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 27 and (n \ ame N or name CA or name C or name O or name CB )) or resid 28 through 126 or (r \ esid 127 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 128 through 139 or (resid 140 and (name N or name CA or name C or name O o \ r name CB or name CG )) or resid 141 through 151 or (resid 152 and (name N or na \ me CA or name C or name O or name CB )) or resid 153 through 193 or (resid 194 t \ hrough 196 and (name N or name CA or name C or name O or name CB )) or resid 197 \ through 224 or (resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.030 Extract box with map and model: 4.860 Check model and map are aligned: 0.380 Set scattering table: 0.200 Process input model: 67.800 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.024 24867 Z= 0.087 Angle : 0.361 5.653 33742 Z= 0.215 Chirality : 0.039 0.132 4028 Planarity : 0.002 0.036 4459 Dihedral : 9.417 89.122 8766 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.10), residues: 3455 helix: -4.72 (0.05), residues: 1093 sheet: -1.97 (0.26), residues: 327 loop : -2.58 (0.11), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 115 HIS 0.001 0.000 HIS F 175 PHE 0.004 0.000 PHE D1319 TYR 0.003 0.000 TYR C1296 ARG 0.001 0.000 ARG C1316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6910 Ramachandran restraints generated. 3455 Oldfield, 0 Emsley, 3455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 583 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable