Starting phenix.real_space_refine on Sat Dec 9 09:52:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji8_9833/12_2023/6ji8_9833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji8_9833/12_2023/6ji8_9833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji8_9833/12_2023/6ji8_9833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji8_9833/12_2023/6ji8_9833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji8_9833/12_2023/6ji8_9833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji8_9833/12_2023/6ji8_9833.pdb" } resolution = 3.6 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= 0.007 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 692 5.16 5 C 73184 2.51 5 N 19700 2.21 5 O 21480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 478": "NH1" <-> "NH2" Residue "A TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1944": "NH1" <-> "NH2" Residue "A ARG 2519": "NH1" <-> "NH2" Residue "A ARG 3596": "NH1" <-> "NH2" Residue "A ARG 3616": "NH1" <-> "NH2" Residue "A PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3940": "NH1" <-> "NH2" Residue "A ARG 4148": "NH1" <-> "NH2" Residue "A ARG 4158": "NH1" <-> "NH2" Residue "A ARG 4498": "NH1" <-> "NH2" Residue "A ARG 4504": "NH1" <-> "NH2" Residue "A ARG 4609": "NH1" <-> "NH2" Residue "A TYR 4617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4755": "NH1" <-> "NH2" Residue "A ARG 4791": "NH1" <-> "NH2" Residue "A ARG 4823": "NH1" <-> "NH2" Residue "A PHE 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1944": "NH1" <-> "NH2" Residue "D ARG 2419": "NH1" <-> "NH2" Residue "D ARG 2519": "NH1" <-> "NH2" Residue "D ARG 3596": "NH1" <-> "NH2" Residue "D ARG 3616": "NH1" <-> "NH2" Residue "D PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3940": "NH1" <-> "NH2" Residue "D ARG 4148": "NH1" <-> "NH2" Residue "D ARG 4158": "NH1" <-> "NH2" Residue "D ARG 4498": "NH1" <-> "NH2" Residue "D ARG 4504": "NH1" <-> "NH2" Residue "D ARG 4609": "NH1" <-> "NH2" Residue "D TYR 4617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4755": "NH1" <-> "NH2" Residue "D ARG 4791": "NH1" <-> "NH2" Residue "D ARG 4823": "NH1" <-> "NH2" Residue "D PHE 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "G PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G ARG 257": "NH1" <-> "NH2" Residue "G ARG 414": "NH1" <-> "NH2" Residue "G ARG 478": "NH1" <-> "NH2" Residue "G TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 1944": "NH1" <-> "NH2" Residue "G ARG 2519": "NH1" <-> "NH2" Residue "G ARG 3596": "NH1" <-> "NH2" Residue "G ARG 3616": "NH1" <-> "NH2" Residue "G PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3940": "NH1" <-> "NH2" Residue "G ARG 4148": "NH1" <-> "NH2" Residue "G ARG 4158": "NH1" <-> "NH2" Residue "G ARG 4498": "NH1" <-> "NH2" Residue "G ARG 4504": "NH1" <-> "NH2" Residue "G ARG 4609": "NH1" <-> "NH2" Residue "G TYR 4617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 4755": "NH1" <-> "NH2" Residue "G ARG 4791": "NH1" <-> "NH2" Residue "G ARG 4823": "NH1" <-> "NH2" Residue "G PHE 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 4919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 13": "NH1" <-> "NH2" Residue "J PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 190": "NH1" <-> "NH2" Residue "J ARG 257": "NH1" <-> "NH2" Residue "J ARG 414": "NH1" <-> "NH2" Residue "J ARG 478": "NH1" <-> "NH2" Residue "J TYR 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 1944": "NH1" <-> "NH2" Residue "J ARG 2419": "NH1" <-> "NH2" Residue "J ARG 2519": "NH1" <-> "NH2" Residue "J ARG 3596": "NH1" <-> "NH2" Residue "J ARG 3616": "NH1" <-> "NH2" Residue "J PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 3940": "NH1" <-> "NH2" Residue "J ARG 4148": "NH1" <-> "NH2" Residue "J ARG 4158": "NH1" <-> "NH2" Residue "J ARG 4498": "NH1" <-> "NH2" Residue "J ARG 4504": "NH1" <-> "NH2" Residue "J ARG 4609": "NH1" <-> "NH2" Residue "J TYR 4617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 4755": "NH1" <-> "NH2" Residue "J ARG 4791": "NH1" <-> "NH2" Residue "J ARG 4823": "NH1" <-> "NH2" Residue "J PHE 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 4919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 13": "NH1" <-> "NH2" Time to flip residues: 0.31s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 115060 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 26851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3511, 26851 Classifications: {'peptide': 3511} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 342} Link IDs: {'PTRANS': 122, 'TRANS': 3388} Chain breaks: 60 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1397 Unresolved non-hydrogen angles: 1779 Unresolved non-hydrogen dihedrals: 1161 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 34, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 763 Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1094 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 26851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3511, 26851 Classifications: {'peptide': 3511} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 342} Link IDs: {'PTRANS': 122, 'TRANS': 3388} Chain breaks: 60 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1397 Unresolved non-hydrogen angles: 1779 Unresolved non-hydrogen dihedrals: 1161 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 34, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 763 Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1094 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 26851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3511, 26851 Classifications: {'peptide': 3511} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 342} Link IDs: {'PTRANS': 122, 'TRANS': 3388} Chain breaks: 60 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1397 Unresolved non-hydrogen angles: 1779 Unresolved non-hydrogen dihedrals: 1161 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 34, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 763 Chain: "H" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "I" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1094 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 26851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3511, 26851 Classifications: {'peptide': 3511} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 342} Link IDs: {'PTRANS': 122, 'TRANS': 3388} Chain breaks: 60 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1397 Unresolved non-hydrogen angles: 1779 Unresolved non-hydrogen dihedrals: 1161 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 20, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 34, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 763 Chain: "K" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "L" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1094 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26210 SG CYS A4889 177.992 203.266 88.306 1.00 28.06 S ATOM 26235 SG CYS A4892 179.529 203.266 91.517 1.00 26.71 S ATOM 54974 SG CYS D4889 203.272 202.017 88.317 1.00 28.06 S ATOM 54999 SG CYS D4892 203.272 200.480 91.528 1.00 26.71 S ATOM 83738 SG CYS G4889 202.023 176.728 88.323 1.00 28.06 S ATOM 83763 SG CYS G4892 200.486 176.728 91.534 1.00 26.71 S ATOM A09NA SG CYS J4889 176.724 177.990 88.328 1.00 28.06 S ATOM A09NZ SG CYS J4892 176.724 179.527 91.539 1.00 26.71 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N HIS B 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS B 87 " occ=0.99 residue: pdb=" N HIS E 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS E 87 " occ=0.99 residue: pdb=" N HIS H 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS H 87 " occ=0.99 residue: pdb=" N HIS K 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS K 87 " occ=0.99 Time building chain proxies: 41.32, per 1000 atoms: 0.36 Number of scatterers: 115060 At special positions: 0 Unit cell: (381.33, 381.33, 214.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 692 16.00 O 21480 8.00 N 19700 7.00 C 73184 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: 30.18 Conformation dependent library (CDL) restraints added in 14.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4914 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4892 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4889 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4914 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4892 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4889 " pdb=" ZN G6000 " pdb="ZN ZN G6000 " - pdb=" NE2 HIS G4914 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4892 " pdb="ZN ZN G6000 " - pdb=" SG CYS G4889 " pdb=" ZN J6000 " pdb="ZN ZN J6000 " - pdb=" NE2 HIS J4914 " pdb="ZN ZN J6000 " - pdb=" SG CYS J4892 " pdb="ZN ZN J6000 " - pdb=" SG CYS J4889 " 29008 Ramachandran restraints generated. 14504 Oldfield, 0 Emsley, 14504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28184 Finding SS restraints... Secondary structure from input PDB file: 591 helices and 120 sheets defined 52.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.37 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.814A pdb=" N CYS A 65 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.799A pdb=" N SER A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 428 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 471 through 492 Processing helix chain 'A' and resid 493 through 506 removed outlier: 3.924A pdb=" N LEU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 540 Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.513A pdb=" N CYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.878A pdb=" N LEU A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 581 removed outlier: 4.157A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 821 through 826 removed outlier: 3.548A pdb=" N ALA A 825 " --> pdb=" O CYS A 822 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 826 " --> pdb=" O TYR A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 900 removed outlier: 4.277A pdb=" N ILE A 881 " --> pdb=" O HIS A 877 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 897 " --> pdb=" O TRP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 944 removed outlier: 3.615A pdb=" N MET A 935 " --> pdb=" O TYR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1043 through 1060 Processing helix chain 'A' and resid 1091 through 1095 Processing helix chain 'A' and resid 1140 through 1142 No H-bonds generated for 'chain 'A' and resid 1140 through 1142' Processing helix chain 'A' and resid 1220 through 1224 removed outlier: 3.722A pdb=" N LEU A1224 " --> pdb=" O VAL A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1575 Processing helix chain 'A' and resid 1642 through 1646 removed outlier: 3.807A pdb=" N THR A1645 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A1646 " --> pdb=" O GLU A1643 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1642 through 1646' Processing helix chain 'A' and resid 1647 through 1665 removed outlier: 3.670A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 4.348A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1682 through 1691 removed outlier: 3.984A pdb=" N GLU A1690 " --> pdb=" O LEU A1686 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A1691 " --> pdb=" O TYR A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1711 Processing helix chain 'A' and resid 1711 through 1722 removed outlier: 3.558A pdb=" N MET A1721 " --> pdb=" O ALA A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1735 Processing helix chain 'A' and resid 1783 through 1803 removed outlier: 3.619A pdb=" N LEU A1787 " --> pdb=" O PRO A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1830 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1835 through 1847 removed outlier: 4.249A pdb=" N HIS A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1950 removed outlier: 3.613A pdb=" N LYS A1904 " --> pdb=" O PRO A1900 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A1932 " --> pdb=" O ALA A1928 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A1935 " --> pdb=" O ASP A1931 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A1936 " --> pdb=" O ASP A1932 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1996 removed outlier: 3.596A pdb=" N GLU A1991 " --> pdb=" O CYS A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2011 Processing helix chain 'A' and resid 2026 through 2037 removed outlier: 3.740A pdb=" N LEU A2030 " --> pdb=" O ILE A2026 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU A2035 " --> pdb=" O LEU A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2074 removed outlier: 4.447A pdb=" N VAL A2068 " --> pdb=" O SER A2064 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A2074 " --> pdb=" O TRP A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2094 removed outlier: 4.007A pdb=" N VAL A2082 " --> pdb=" O ASP A2078 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A2087 " --> pdb=" O ARG A2083 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A2088 " --> pdb=" O ALA A2084 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A2093 " --> pdb=" O LEU A2089 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2103 Processing helix chain 'A' and resid 2104 through 2106 No H-bonds generated for 'chain 'A' and resid 2104 through 2106' Processing helix chain 'A' and resid 2113 through 2130 Processing helix chain 'A' and resid 2131 through 2133 No H-bonds generated for 'chain 'A' and resid 2131 through 2133' Processing helix chain 'A' and resid 2139 through 2151 Processing helix chain 'A' and resid 2154 through 2159 Processing helix chain 'A' and resid 2159 through 2167 removed outlier: 4.006A pdb=" N MET A2163 " --> pdb=" O HIS A2159 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A2164 " --> pdb=" O PRO A2160 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2180 Processing helix chain 'A' and resid 2192 through 2205 removed outlier: 3.828A pdb=" N ARG A2199 " --> pdb=" O ALA A2195 " (cutoff:3.500A) Processing helix chain 'A' and resid 2208 through 2217 removed outlier: 3.581A pdb=" N GLN A2212 " --> pdb=" O SER A2208 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A2213 " --> pdb=" O ARG A2209 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A2214 " --> pdb=" O GLN A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2223 Processing helix chain 'A' and resid 2225 through 2229 removed outlier: 3.573A pdb=" N VAL A2228 " --> pdb=" O ASN A2225 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A2229 " --> pdb=" O SER A2226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2225 through 2229' Processing helix chain 'A' and resid 2239 through 2247 Processing helix chain 'A' and resid 2252 through 2258 removed outlier: 3.807A pdb=" N LEU A2258 " --> pdb=" O LEU A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2259 through 2272 removed outlier: 3.509A pdb=" N LEU A2263 " --> pdb=" O ARG A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2308 removed outlier: 3.882A pdb=" N TYR A2299 " --> pdb=" O GLU A2295 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2328 removed outlier: 4.698A pdb=" N VAL A2320 " --> pdb=" O GLU A2316 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A2328 " --> pdb=" O LEU A2324 " (cutoff:3.500A) Processing helix chain 'A' and resid 2344 through 2349 Processing helix chain 'A' and resid 2350 through 2354 removed outlier: 4.023A pdb=" N LYS A2353 " --> pdb=" O GLU A2350 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A2354 " --> pdb=" O ALA A2351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2350 through 2354' Processing helix chain 'A' and resid 2387 through 2400 Processing helix chain 'A' and resid 2406 through 2411 Processing helix chain 'A' and resid 2415 through 2427 removed outlier: 3.586A pdb=" N LEU A2427 " --> pdb=" O ILE A2423 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2438 Processing helix chain 'A' and resid 2464 through 2474 Processing helix chain 'A' and resid 2482 through 2489 removed outlier: 3.683A pdb=" N LEU A2488 " --> pdb=" O PHE A2484 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A2489 " --> pdb=" O LEU A2485 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2499 Processing helix chain 'A' and resid 2512 through 2517 Processing helix chain 'A' and resid 2519 through 2524 removed outlier: 3.749A pdb=" N THR A2523 " --> pdb=" O ARG A2519 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A2524 " --> pdb=" O TYR A2520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2519 through 2524' Processing helix chain 'A' and resid 2525 through 2529 removed outlier: 3.659A pdb=" N LEU A2529 " --> pdb=" O LEU A2526 " (cutoff:3.500A) Processing helix chain 'A' and resid 2538 through 2552 Processing helix chain 'A' and resid 2559 through 2575 Processing helix chain 'A' and resid 2583 through 2597 removed outlier: 3.767A pdb=" N ARG A2592 " --> pdb=" O HIS A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2598 through 2600 No H-bonds generated for 'chain 'A' and resid 2598 through 2600' Processing helix chain 'A' and resid 2606 through 2622 Processing helix chain 'A' and resid 2635 through 2650 Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2668 - end of helix Processing helix chain 'A' and resid 2715 through 2741 removed outlier: 3.601A pdb=" N GLU A2719 " --> pdb=" O PRO A2715 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE A2721 " --> pdb=" O LYS A2717 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A2723 " --> pdb=" O GLU A2719 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A2724 " --> pdb=" O TYR A2720 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A2727 " --> pdb=" O ASN A2723 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A2740 " --> pdb=" O ASP A2736 " (cutoff:3.500A) Processing helix chain 'A' and resid 2769 through 2786 Proline residue: A2775 - end of helix removed outlier: 3.900A pdb=" N THR A2782 " --> pdb=" O GLU A2778 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP A2786 " --> pdb=" O THR A2782 " (cutoff:3.500A) Processing helix chain 'A' and resid 2835 through 2862 removed outlier: 3.894A pdb=" N GLU A2860 " --> pdb=" O LYS A2856 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A2862 " --> pdb=" O LYS A2858 " (cutoff:3.500A) Processing helix chain 'A' and resid 2874 through 2878 removed outlier: 3.895A pdb=" N LEU A2878 " --> pdb=" O TYR A2875 " (cutoff:3.500A) Processing helix chain 'A' and resid 2880 through 2900 removed outlier: 4.306A pdb=" N ASP A2886 " --> pdb=" O GLU A2882 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A2894 " --> pdb=" O ALA A2890 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A2896 " --> pdb=" O ASP A2892 " (cutoff:3.500A) Processing helix chain 'A' and resid 2983 through 3002 Proline residue: A2990 - end of helix Processing helix chain 'A' and resid 3010 through 3026 Processing helix chain 'A' and resid 3035 through 3050 Processing helix chain 'A' and resid 3062 through 3080 removed outlier: 4.046A pdb=" N LEU A3069 " --> pdb=" O ALA A3065 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU A3070 " --> pdb=" O ALA A3066 " (cutoff:3.500A) Processing helix chain 'A' and resid 3101 through 3116 Processing helix chain 'A' and resid 3125 through 3143 removed outlier: 3.543A pdb=" N THR A3143 " --> pdb=" O TYR A3139 " (cutoff:3.500A) Processing helix chain 'A' and resid 3150 through 3163 Processing helix chain 'A' and resid 3171 through 3179 Processing helix chain 'A' and resid 3594 through 3606 removed outlier: 3.893A pdb=" N ARG A3598 " --> pdb=" O LYS A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3615 through 3630 removed outlier: 3.540A pdb=" N TRP A3629 " --> pdb=" O TYR A3625 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A3630 " --> pdb=" O GLU A3626 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 removed outlier: 4.211A pdb=" N LYS A3640 " --> pdb=" O TYR A3636 " (cutoff:3.500A) Processing helix chain 'A' and resid 3663 through 3677 Processing helix chain 'A' and resid 3686 through 3699 removed outlier: 3.935A pdb=" N ASP A3694 " --> pdb=" O MET A3690 " (cutoff:3.500A) Processing helix chain 'A' and resid 3715 through 3734 removed outlier: 3.903A pdb=" N LEU A3732 " --> pdb=" O GLN A3728 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3748 removed outlier: 3.701A pdb=" N VAL A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A3746 " --> pdb=" O LEU A3742 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A3748 " --> pdb=" O THR A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3753 through 3767 Processing helix chain 'A' and resid 3771 through 3785 removed outlier: 3.870A pdb=" N GLN A3775 " --> pdb=" O ASN A3771 " (cutoff:3.500A) Processing helix chain 'A' and resid 3788 through 3801 removed outlier: 4.109A pdb=" N SER A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3807 through 3820 Processing helix chain 'A' and resid 3833 through 3847 removed outlier: 3.912A pdb=" N THR A3837 " --> pdb=" O ASP A3833 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A3842 " --> pdb=" O CYS A3838 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3859 Processing helix chain 'A' and resid 3870 through 3891 removed outlier: 3.651A pdb=" N SER A3874 " --> pdb=" O ASN A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3900 through 3926 removed outlier: 3.509A pdb=" N GLN A3904 " --> pdb=" O ASP A3900 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A3909 " --> pdb=" O ARG A3905 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A3913 " --> pdb=" O LYS A3909 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A3925 " --> pdb=" O LEU A3921 " (cutoff:3.500A) Processing helix chain 'A' and resid 3929 through 3938 Processing helix chain 'A' and resid 3940 through 3960 removed outlier: 4.197A pdb=" N ALA A3944 " --> pdb=" O ARG A3940 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS A3954 " --> pdb=" O HIS A3950 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3987 Processing helix chain 'A' and resid 3994 through 4007 Processing helix chain 'A' and resid 4007 through 4029 removed outlier: 3.604A pdb=" N VAL A4011 " --> pdb=" O SER A4007 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET A4013 " --> pdb=" O ASN A4009 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A4021 " --> pdb=" O PHE A4017 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A4023 " --> pdb=" O ASP A4019 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU A4024 " --> pdb=" O MET A4020 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS A4025 " --> pdb=" O PHE A4021 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A4029 " --> pdb=" O LYS A4025 " (cutoff:3.500A) Processing helix chain 'A' and resid 4032 through 4037 removed outlier: 4.313A pdb=" N ASP A4037 " --> pdb=" O PHE A4033 " (cutoff:3.500A) Processing helix chain 'A' and resid 4045 through 4054 removed outlier: 3.824A pdb=" N ALA A4052 " --> pdb=" O ASP A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4060 through 4071 removed outlier: 3.713A pdb=" N ALA A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4081 through 4086 Processing helix chain 'A' and resid 4089 through 4110 Processing helix chain 'A' and resid 4113 through 4122 Processing helix chain 'A' and resid 4123 through 4128 removed outlier: 4.144A pdb=" N LEU A4127 " --> pdb=" O ALA A4123 " (cutoff:3.500A) Processing helix chain 'A' and resid 4155 through 4161 removed outlier: 3.913A pdb=" N TRP A4161 " --> pdb=" O SER A4157 " (cutoff:3.500A) Processing helix chain 'A' and resid 4165 through 4181 removed outlier: 4.003A pdb=" N ARG A4171 " --> pdb=" O LYS A4167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A4179 " --> pdb=" O PHE A4175 " (cutoff:3.500A) Processing helix chain 'A' and resid 4185 through 4205 Processing helix chain 'A' and resid 4487 through 4494 removed outlier: 3.604A pdb=" N LYS A4491 " --> pdb=" O ALA A4487 " (cutoff:3.500A) Processing helix chain 'A' and resid 4499 through 4519 removed outlier: 3.647A pdb=" N MET A4503 " --> pdb=" O ASN A4499 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4593 removed outlier: 3.642A pdb=" N LEU A4573 " --> pdb=" O MET A4569 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A4578 " --> pdb=" O ARG A4574 " (cutoff:3.500A) Processing helix chain 'A' and resid 4595 through 4612 removed outlier: 3.647A pdb=" N VAL A4599 " --> pdb=" O LYS A4595 " (cutoff:3.500A) Processing helix chain 'A' and resid 4626 through 4631 Processing helix chain 'A' and resid 4632 through 4637 removed outlier: 3.837A pdb=" N ILE A4636 " --> pdb=" O ASP A4632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN A4637 " --> pdb=" O ARG A4633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4632 through 4637' Processing helix chain 'A' and resid 4649 through 4659 Processing helix chain 'A' and resid 4663 through 4672 removed outlier: 3.599A pdb=" N ILE A4667 " --> pdb=" O GLY A4663 " (cutoff:3.500A) Processing helix chain 'A' and resid 4698 through 4702 removed outlier: 4.024A pdb=" N ILE A4702 " --> pdb=" O LEU A4699 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4716 removed outlier: 3.669A pdb=" N GLN A4707 " --> pdb=" O ASP A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4736 Processing helix chain 'A' and resid 4738 through 4747 removed outlier: 3.729A pdb=" N HIS A4743 " --> pdb=" O PHE A4740 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A4745 " --> pdb=" O ALA A4742 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A4746 " --> pdb=" O HIS A4743 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A4747 " --> pdb=" O LEU A4744 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4759 Processing helix chain 'A' and resid 4764 through 4790 removed outlier: 3.629A pdb=" N LEU A4768 " --> pdb=" O ASN A4764 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A4788 " --> pdb=" O VAL A4784 " (cutoff:3.500A) Processing helix chain 'A' and resid 4810 through 4820 Processing helix chain 'A' and resid 4840 through 4855 Processing helix chain 'A' and resid 4857 through 4887 removed outlier: 4.042A pdb=" N LYS A4882 " --> pdb=" O GLN A4878 " (cutoff:3.500A) Processing helix chain 'A' and resid 4905 through 4912 Processing helix chain 'A' and resid 4916 through 4929 Processing helix chain 'A' and resid 4935 through 4948 Processing helix chain 'A' and resid 4958 through 4963 removed outlier: 3.647A pdb=" N TYR A4963 " --> pdb=" O PHE A4959 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'C' and resid 6 through 21 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 66 through 92 removed outlier: 3.906A pdb=" N THR C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE C 90 " --> pdb=" O ILE C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.584A pdb=" N THR C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 removed outlier: 4.027A pdb=" N VAL C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.813A pdb=" N CYS D 65 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 74 through 82 Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.799A pdb=" N SER D 413 " --> pdb=" O GLN D 409 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG D 428 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 Processing helix chain 'D' and resid 471 through 492 Processing helix chain 'D' and resid 493 through 506 removed outlier: 3.924A pdb=" N LEU D 497 " --> pdb=" O GLY D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 540 Processing helix chain 'D' and resid 544 through 552 removed outlier: 3.513A pdb=" N CYS D 548 " --> pdb=" O ASN D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 562 removed outlier: 3.878A pdb=" N LEU D 558 " --> pdb=" O SER D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 581 removed outlier: 4.157A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 Processing helix chain 'D' and resid 608 through 619 Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 821 through 826 removed outlier: 3.548A pdb=" N ALA D 825 " --> pdb=" O CYS D 822 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 826 " --> pdb=" O TYR D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 900 removed outlier: 4.277A pdb=" N ILE D 881 " --> pdb=" O HIS D 877 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 897 " --> pdb=" O TRP D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 944 removed outlier: 3.615A pdb=" N MET D 935 " --> pdb=" O TYR D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1011 Processing helix chain 'D' and resid 1043 through 1060 Processing helix chain 'D' and resid 1091 through 1095 Processing helix chain 'D' and resid 1140 through 1142 No H-bonds generated for 'chain 'D' and resid 1140 through 1142' Processing helix chain 'D' and resid 1220 through 1224 removed outlier: 3.722A pdb=" N LEU D1224 " --> pdb=" O VAL D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1571 through 1575 Processing helix chain 'D' and resid 1642 through 1646 removed outlier: 3.807A pdb=" N THR D1645 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D1646 " --> pdb=" O GLU D1643 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1642 through 1646' Processing helix chain 'D' and resid 1647 through 1665 removed outlier: 3.670A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 4.348A pdb=" N ALA D1675 " --> pdb=" O ARG D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1682 through 1691 removed outlier: 3.984A pdb=" N GLU D1690 " --> pdb=" O LEU D1686 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN D1691 " --> pdb=" O TYR D1687 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1711 Processing helix chain 'D' and resid 1711 through 1722 removed outlier: 3.557A pdb=" N MET D1721 " --> pdb=" O ALA D1717 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1735 Processing helix chain 'D' and resid 1783 through 1803 removed outlier: 3.618A pdb=" N LEU D1787 " --> pdb=" O PRO D1783 " (cutoff:3.500A) Processing helix chain 'D' and resid 1814 through 1830 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1835 through 1847 removed outlier: 4.250A pdb=" N HIS D1841 " --> pdb=" O GLU D1837 " (cutoff:3.500A) Processing helix chain 'D' and resid 1900 through 1950 removed outlier: 3.613A pdb=" N LYS D1904 " --> pdb=" O PRO D1900 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP D1932 " --> pdb=" O ALA D1928 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA D1935 " --> pdb=" O ASP D1931 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS D1936 " --> pdb=" O ASP D1932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 1996 removed outlier: 3.595A pdb=" N GLU D1991 " --> pdb=" O CYS D1987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1999 through 2011 Processing helix chain 'D' and resid 2026 through 2037 removed outlier: 3.739A pdb=" N LEU D2030 " --> pdb=" O ILE D2026 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU D2035 " --> pdb=" O LEU D2031 " (cutoff:3.500A) Processing helix chain 'D' and resid 2059 through 2074 removed outlier: 4.447A pdb=" N VAL D2068 " --> pdb=" O SER D2064 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D2074 " --> pdb=" O TRP D2070 " (cutoff:3.500A) Processing helix chain 'D' and resid 2078 through 2094 removed outlier: 4.007A pdb=" N VAL D2082 " --> pdb=" O ASP D2078 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D2087 " --> pdb=" O ARG D2083 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D2088 " --> pdb=" O ALA D2084 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR D2093 " --> pdb=" O LEU D2089 " (cutoff:3.500A) Processing helix chain 'D' and resid 2094 through 2103 Processing helix chain 'D' and resid 2104 through 2106 No H-bonds generated for 'chain 'D' and resid 2104 through 2106' Processing helix chain 'D' and resid 2113 through 2130 Processing helix chain 'D' and resid 2131 through 2133 No H-bonds generated for 'chain 'D' and resid 2131 through 2133' Processing helix chain 'D' and resid 2139 through 2151 Processing helix chain 'D' and resid 2154 through 2159 Processing helix chain 'D' and resid 2159 through 2167 removed outlier: 4.006A pdb=" N MET D2163 " --> pdb=" O HIS D2159 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG D2164 " --> pdb=" O PRO D2160 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2180 Processing helix chain 'D' and resid 2192 through 2205 removed outlier: 3.828A pdb=" N ARG D2199 " --> pdb=" O ALA D2195 " (cutoff:3.500A) Processing helix chain 'D' and resid 2208 through 2217 removed outlier: 3.582A pdb=" N GLN D2212 " --> pdb=" O SER D2208 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D2213 " --> pdb=" O ARG D2209 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D2214 " --> pdb=" O GLN D2210 " (cutoff:3.500A) Processing helix chain 'D' and resid 2218 through 2223 Processing helix chain 'D' and resid 2225 through 2229 removed outlier: 3.573A pdb=" N VAL D2228 " --> pdb=" O ASN D2225 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D2229 " --> pdb=" O SER D2226 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2225 through 2229' Processing helix chain 'D' and resid 2239 through 2247 Processing helix chain 'D' and resid 2252 through 2258 removed outlier: 3.806A pdb=" N LEU D2258 " --> pdb=" O LEU D2254 " (cutoff:3.500A) Processing helix chain 'D' and resid 2259 through 2272 removed outlier: 3.509A pdb=" N LEU D2263 " --> pdb=" O ARG D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2295 through 2308 removed outlier: 3.882A pdb=" N TYR D2299 " --> pdb=" O GLU D2295 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) Processing helix chain 'D' and resid 2314 through 2328 removed outlier: 4.699A pdb=" N VAL D2320 " --> pdb=" O GLU D2316 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG D2328 " --> pdb=" O LEU D2324 " (cutoff:3.500A) Processing helix chain 'D' and resid 2344 through 2349 Processing helix chain 'D' and resid 2350 through 2354 removed outlier: 4.023A pdb=" N LYS D2353 " --> pdb=" O GLU D2350 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D2354 " --> pdb=" O ALA D2351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2350 through 2354' Processing helix chain 'D' and resid 2387 through 2400 Processing helix chain 'D' and resid 2406 through 2411 Processing helix chain 'D' and resid 2415 through 2427 removed outlier: 3.586A pdb=" N LEU D2427 " --> pdb=" O ILE D2423 " (cutoff:3.500A) Processing helix chain 'D' and resid 2432 through 2438 Processing helix chain 'D' and resid 2464 through 2474 Processing helix chain 'D' and resid 2482 through 2489 removed outlier: 3.683A pdb=" N LEU D2488 " --> pdb=" O PHE D2484 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D2489 " --> pdb=" O LEU D2485 " (cutoff:3.500A) Processing helix chain 'D' and resid 2493 through 2499 Processing helix chain 'D' and resid 2512 through 2517 Processing helix chain 'D' and resid 2519 through 2524 removed outlier: 3.749A pdb=" N THR D2523 " --> pdb=" O ARG D2519 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D2524 " --> pdb=" O TYR D2520 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2519 through 2524' Processing helix chain 'D' and resid 2525 through 2529 removed outlier: 3.659A pdb=" N LEU D2529 " --> pdb=" O LEU D2526 " (cutoff:3.500A) Processing helix chain 'D' and resid 2538 through 2552 Processing helix chain 'D' and resid 2559 through 2575 Processing helix chain 'D' and resid 2583 through 2597 removed outlier: 3.767A pdb=" N ARG D2592 " --> pdb=" O HIS D2588 " (cutoff:3.500A) Processing helix chain 'D' and resid 2598 through 2600 No H-bonds generated for 'chain 'D' and resid 2598 through 2600' Processing helix chain 'D' and resid 2606 through 2622 Processing helix chain 'D' and resid 2635 through 2650 Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2668 - end of helix Processing helix chain 'D' and resid 2715 through 2741 removed outlier: 3.601A pdb=" N GLU D2719 " --> pdb=" O PRO D2715 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE D2721 " --> pdb=" O LYS D2717 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN D2723 " --> pdb=" O GLU D2719 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS D2724 " --> pdb=" O TYR D2720 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D2727 " --> pdb=" O ASN D2723 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D2740 " --> pdb=" O ASP D2736 " (cutoff:3.500A) Processing helix chain 'D' and resid 2769 through 2786 Proline residue: D2775 - end of helix removed outlier: 3.900A pdb=" N THR D2782 " --> pdb=" O GLU D2778 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP D2786 " --> pdb=" O THR D2782 " (cutoff:3.500A) Processing helix chain 'D' and resid 2835 through 2862 removed outlier: 3.894A pdb=" N GLU D2860 " --> pdb=" O LYS D2856 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU D2862 " --> pdb=" O LYS D2858 " (cutoff:3.500A) Processing helix chain 'D' and resid 2874 through 2878 removed outlier: 3.896A pdb=" N LEU D2878 " --> pdb=" O TYR D2875 " (cutoff:3.500A) Processing helix chain 'D' and resid 2880 through 2900 removed outlier: 4.306A pdb=" N ASP D2886 " --> pdb=" O GLU D2882 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D2894 " --> pdb=" O ALA D2890 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D2896 " --> pdb=" O ASP D2892 " (cutoff:3.500A) Processing helix chain 'D' and resid 2983 through 3002 Proline residue: D2990 - end of helix Processing helix chain 'D' and resid 3010 through 3026 Processing helix chain 'D' and resid 3035 through 3050 Processing helix chain 'D' and resid 3062 through 3080 removed outlier: 4.046A pdb=" N LEU D3069 " --> pdb=" O ALA D3065 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU D3070 " --> pdb=" O ALA D3066 " (cutoff:3.500A) Processing helix chain 'D' and resid 3101 through 3116 Processing helix chain 'D' and resid 3125 through 3143 removed outlier: 3.544A pdb=" N THR D3143 " --> pdb=" O TYR D3139 " (cutoff:3.500A) Processing helix chain 'D' and resid 3150 through 3163 Processing helix chain 'D' and resid 3171 through 3179 Processing helix chain 'D' and resid 3594 through 3606 removed outlier: 3.892A pdb=" N ARG D3598 " --> pdb=" O LYS D3594 " (cutoff:3.500A) Processing helix chain 'D' and resid 3615 through 3630 removed outlier: 3.541A pdb=" N TRP D3629 " --> pdb=" O TYR D3625 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D3630 " --> pdb=" O GLU D3626 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 removed outlier: 4.211A pdb=" N LYS D3640 " --> pdb=" O TYR D3636 " (cutoff:3.500A) Processing helix chain 'D' and resid 3663 through 3677 Processing helix chain 'D' and resid 3686 through 3699 removed outlier: 3.935A pdb=" N ASP D3694 " --> pdb=" O MET D3690 " (cutoff:3.500A) Processing helix chain 'D' and resid 3715 through 3734 removed outlier: 3.903A pdb=" N LEU D3732 " --> pdb=" O GLN D3728 " (cutoff:3.500A) Processing helix chain 'D' and resid 3736 through 3748 removed outlier: 3.701A pdb=" N VAL D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER D3746 " --> pdb=" O LEU D3742 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D3748 " --> pdb=" O THR D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3753 through 3767 Processing helix chain 'D' and resid 3771 through 3785 removed outlier: 3.870A pdb=" N GLN D3775 " --> pdb=" O ASN D3771 " (cutoff:3.500A) Processing helix chain 'D' and resid 3788 through 3801 removed outlier: 4.108A pdb=" N SER D3800 " --> pdb=" O GLY D3796 " (cutoff:3.500A) Processing helix chain 'D' and resid 3807 through 3820 Processing helix chain 'D' and resid 3833 through 3847 removed outlier: 3.913A pdb=" N THR D3837 " --> pdb=" O ASP D3833 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG D3842 " --> pdb=" O CYS D3838 " (cutoff:3.500A) Processing helix chain 'D' and resid 3852 through 3859 Processing helix chain 'D' and resid 3870 through 3891 removed outlier: 3.651A pdb=" N SER D3874 " --> pdb=" O ASN D3870 " (cutoff:3.500A) Processing helix chain 'D' and resid 3900 through 3926 removed outlier: 3.509A pdb=" N GLN D3904 " --> pdb=" O ASP D3900 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS D3909 " --> pdb=" O ARG D3905 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D3913 " --> pdb=" O LYS D3909 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D3925 " --> pdb=" O LEU D3921 " (cutoff:3.500A) Processing helix chain 'D' and resid 3929 through 3938 Processing helix chain 'D' and resid 3940 through 3960 removed outlier: 4.197A pdb=" N ALA D3944 " --> pdb=" O ARG D3940 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS D3954 " --> pdb=" O HIS D3950 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER D3960 " --> pdb=" O GLN D3956 " (cutoff:3.500A) Processing helix chain 'D' and resid 3965 through 3987 Processing helix chain 'D' and resid 3994 through 4007 Processing helix chain 'D' and resid 4007 through 4029 removed outlier: 3.604A pdb=" N VAL D4011 " --> pdb=" O SER D4007 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET D4013 " --> pdb=" O ASN D4009 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE D4021 " --> pdb=" O PHE D4017 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D4023 " --> pdb=" O ASP D4019 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU D4024 " --> pdb=" O MET D4020 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS D4025 " --> pdb=" O PHE D4021 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER D4029 " --> pdb=" O LYS D4025 " (cutoff:3.500A) Processing helix chain 'D' and resid 4032 through 4037 removed outlier: 4.313A pdb=" N ASP D4037 " --> pdb=" O PHE D4033 " (cutoff:3.500A) Processing helix chain 'D' and resid 4045 through 4054 removed outlier: 3.824A pdb=" N ALA D4052 " --> pdb=" O ASP D4048 " (cutoff:3.500A) Processing helix chain 'D' and resid 4060 through 4071 removed outlier: 3.713A pdb=" N ALA D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4081 through 4086 Processing helix chain 'D' and resid 4089 through 4110 Processing helix chain 'D' and resid 4113 through 4122 Processing helix chain 'D' and resid 4123 through 4128 removed outlier: 4.145A pdb=" N LEU D4127 " --> pdb=" O ALA D4123 " (cutoff:3.500A) Processing helix chain 'D' and resid 4155 through 4161 removed outlier: 3.914A pdb=" N TRP D4161 " --> pdb=" O SER D4157 " (cutoff:3.500A) Processing helix chain 'D' and resid 4165 through 4181 removed outlier: 4.003A pdb=" N ARG D4171 " --> pdb=" O LYS D4167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D4179 " --> pdb=" O PHE D4175 " (cutoff:3.500A) Processing helix chain 'D' and resid 4185 through 4205 Processing helix chain 'D' and resid 4487 through 4494 removed outlier: 3.604A pdb=" N LYS D4491 " --> pdb=" O ALA D4487 " (cutoff:3.500A) Processing helix chain 'D' and resid 4499 through 4519 removed outlier: 3.647A pdb=" N MET D4503 " --> pdb=" O ASN D4499 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4593 removed outlier: 3.641A pdb=" N LEU D4573 " --> pdb=" O MET D4569 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE D4578 " --> pdb=" O ARG D4574 " (cutoff:3.500A) Processing helix chain 'D' and resid 4595 through 4612 removed outlier: 3.647A pdb=" N VAL D4599 " --> pdb=" O LYS D4595 " (cutoff:3.500A) Processing helix chain 'D' and resid 4626 through 4631 Processing helix chain 'D' and resid 4632 through 4637 removed outlier: 3.837A pdb=" N ILE D4636 " --> pdb=" O ASP D4632 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN D4637 " --> pdb=" O ARG D4633 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4632 through 4637' Processing helix chain 'D' and resid 4649 through 4659 Processing helix chain 'D' and resid 4663 through 4672 removed outlier: 3.599A pdb=" N ILE D4667 " --> pdb=" O GLY D4663 " (cutoff:3.500A) Processing helix chain 'D' and resid 4698 through 4702 removed outlier: 4.024A pdb=" N ILE D4702 " --> pdb=" O LEU D4699 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4716 removed outlier: 3.668A pdb=" N GLN D4707 " --> pdb=" O ASP D4703 " (cutoff:3.500A) Processing helix chain 'D' and resid 4717 through 4736 Processing helix chain 'D' and resid 4738 through 4747 removed outlier: 3.729A pdb=" N HIS D4743 " --> pdb=" O PHE D4740 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D4745 " --> pdb=" O ALA D4742 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D4746 " --> pdb=" O HIS D4743 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D4747 " --> pdb=" O LEU D4744 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4759 Processing helix chain 'D' and resid 4764 through 4790 removed outlier: 3.629A pdb=" N LEU D4768 " --> pdb=" O ASN D4764 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D4788 " --> pdb=" O VAL D4784 " (cutoff:3.500A) Processing helix chain 'D' and resid 4810 through 4820 Processing helix chain 'D' and resid 4840 through 4855 Processing helix chain 'D' and resid 4857 through 4887 removed outlier: 4.041A pdb=" N LYS D4882 " --> pdb=" O GLN D4878 " (cutoff:3.500A) Processing helix chain 'D' and resid 4905 through 4912 Processing helix chain 'D' and resid 4916 through 4929 Processing helix chain 'D' and resid 4935 through 4948 Processing helix chain 'D' and resid 4958 through 4963 removed outlier: 3.646A pdb=" N TYR D4963 " --> pdb=" O PHE D4959 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 32 through 40 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 66 through 92 removed outlier: 3.906A pdb=" N THR F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 removed outlier: 3.584A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 128 removed outlier: 4.028A pdb=" N VAL F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.813A pdb=" N CYS G 65 " --> pdb=" O LEU G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 323 through 328 Processing helix chain 'G' and resid 409 through 439 removed outlier: 3.799A pdb=" N SER G 413 " --> pdb=" O GLN G 409 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG G 428 " --> pdb=" O PHE G 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS G 438 " --> pdb=" O ASP G 434 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS G 439 " --> pdb=" O ALA G 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 463 Processing helix chain 'G' and resid 471 through 492 Processing helix chain 'G' and resid 493 through 506 removed outlier: 3.924A pdb=" N LEU G 497 " --> pdb=" O GLY G 493 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 540 Processing helix chain 'G' and resid 544 through 552 removed outlier: 3.513A pdb=" N CYS G 548 " --> pdb=" O ASN G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 554 through 562 removed outlier: 3.879A pdb=" N LEU G 558 " --> pdb=" O SER G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 567 through 581 removed outlier: 4.157A pdb=" N GLU G 581 " --> pdb=" O CYS G 577 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 604 Processing helix chain 'G' and resid 608 through 619 Processing helix chain 'G' and resid 625 through 636 Processing helix chain 'G' and resid 821 through 826 removed outlier: 3.548A pdb=" N ALA G 825 " --> pdb=" O CYS G 822 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 826 " --> pdb=" O TYR G 823 " (cutoff:3.500A) Processing helix chain 'G' and resid 875 through 900 removed outlier: 4.276A pdb=" N ILE G 881 " --> pdb=" O HIS G 877 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS G 897 " --> pdb=" O TRP G 893 " (cutoff:3.500A) Processing helix chain 'G' and resid 929 through 944 removed outlier: 3.615A pdb=" N MET G 935 " --> pdb=" O TYR G 931 " (cutoff:3.500A) Processing helix chain 'G' and resid 989 through 1011 Processing helix chain 'G' and resid 1043 through 1060 Processing helix chain 'G' and resid 1091 through 1095 Processing helix chain 'G' and resid 1140 through 1142 No H-bonds generated for 'chain 'G' and resid 1140 through 1142' Processing helix chain 'G' and resid 1220 through 1224 removed outlier: 3.722A pdb=" N LEU G1224 " --> pdb=" O VAL G1221 " (cutoff:3.500A) Processing helix chain 'G' and resid 1571 through 1575 Processing helix chain 'G' and resid 1642 through 1646 removed outlier: 3.806A pdb=" N THR G1645 " --> pdb=" O LEU G1642 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU G1646 " --> pdb=" O GLU G1643 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1642 through 1646' Processing helix chain 'G' and resid 1647 through 1665 removed outlier: 3.670A pdb=" N CYS G1665 " --> pdb=" O TYR G1661 " (cutoff:3.500A) Processing helix chain 'G' and resid 1669 through 1680 removed outlier: 4.348A pdb=" N ALA G1675 " --> pdb=" O ARG G1671 " (cutoff:3.500A) Processing helix chain 'G' and resid 1682 through 1691 removed outlier: 3.984A pdb=" N GLU G1690 " --> pdb=" O LEU G1686 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN G1691 " --> pdb=" O TYR G1687 " (cutoff:3.500A) Processing helix chain 'G' and resid 1695 through 1711 Processing helix chain 'G' and resid 1711 through 1722 removed outlier: 3.557A pdb=" N MET G1721 " --> pdb=" O ALA G1717 " (cutoff:3.500A) Processing helix chain 'G' and resid 1730 through 1735 Processing helix chain 'G' and resid 1783 through 1803 removed outlier: 3.619A pdb=" N LEU G1787 " --> pdb=" O PRO G1783 " (cutoff:3.500A) Processing helix chain 'G' and resid 1814 through 1830 Proline residue: G1820 - end of helix Processing helix chain 'G' and resid 1835 through 1847 removed outlier: 4.249A pdb=" N HIS G1841 " --> pdb=" O GLU G1837 " (cutoff:3.500A) Processing helix chain 'G' and resid 1900 through 1950 removed outlier: 3.613A pdb=" N LYS G1904 " --> pdb=" O PRO G1900 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP G1932 " --> pdb=" O ALA G1928 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA G1935 " --> pdb=" O ASP G1931 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS G1936 " --> pdb=" O ASP G1932 " (cutoff:3.500A) Processing helix chain 'G' and resid 1987 through 1996 removed outlier: 3.596A pdb=" N GLU G1991 " --> pdb=" O CYS G1987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1999 through 2011 Processing helix chain 'G' and resid 2026 through 2037 removed outlier: 3.740A pdb=" N LEU G2030 " --> pdb=" O ILE G2026 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU G2035 " --> pdb=" O LEU G2031 " (cutoff:3.500A) Processing helix chain 'G' and resid 2059 through 2074 removed outlier: 4.447A pdb=" N VAL G2068 " --> pdb=" O SER G2064 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER G2074 " --> pdb=" O TRP G2070 " (cutoff:3.500A) Processing helix chain 'G' and resid 2078 through 2094 removed outlier: 4.007A pdb=" N VAL G2082 " --> pdb=" O ASP G2078 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL G2087 " --> pdb=" O ARG G2083 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU G2088 " --> pdb=" O ALA G2084 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR G2093 " --> pdb=" O LEU G2089 " (cutoff:3.500A) Processing helix chain 'G' and resid 2094 through 2103 Processing helix chain 'G' and resid 2104 through 2106 No H-bonds generated for 'chain 'G' and resid 2104 through 2106' Processing helix chain 'G' and resid 2113 through 2130 Processing helix chain 'G' and resid 2131 through 2133 No H-bonds generated for 'chain 'G' and resid 2131 through 2133' Processing helix chain 'G' and resid 2139 through 2151 Processing helix chain 'G' and resid 2154 through 2159 Processing helix chain 'G' and resid 2159 through 2167 removed outlier: 4.006A pdb=" N MET G2163 " --> pdb=" O HIS G2159 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG G2164 " --> pdb=" O PRO G2160 " (cutoff:3.500A) Processing helix chain 'G' and resid 2167 through 2180 Processing helix chain 'G' and resid 2192 through 2205 removed outlier: 3.828A pdb=" N ARG G2199 " --> pdb=" O ALA G2195 " (cutoff:3.500A) Processing helix chain 'G' and resid 2208 through 2217 removed outlier: 3.581A pdb=" N GLN G2212 " --> pdb=" O SER G2208 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS G2213 " --> pdb=" O ARG G2209 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA G2214 " --> pdb=" O GLN G2210 " (cutoff:3.500A) Processing helix chain 'G' and resid 2218 through 2223 Processing helix chain 'G' and resid 2225 through 2229 removed outlier: 3.573A pdb=" N VAL G2228 " --> pdb=" O ASN G2225 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G2229 " --> pdb=" O SER G2226 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2225 through 2229' Processing helix chain 'G' and resid 2239 through 2247 Processing helix chain 'G' and resid 2252 through 2258 removed outlier: 3.807A pdb=" N LEU G2258 " --> pdb=" O LEU G2254 " (cutoff:3.500A) Processing helix chain 'G' and resid 2259 through 2272 removed outlier: 3.509A pdb=" N LEU G2263 " --> pdb=" O ARG G2259 " (cutoff:3.500A) Processing helix chain 'G' and resid 2295 through 2308 removed outlier: 3.882A pdb=" N TYR G2299 " --> pdb=" O GLU G2295 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE G2308 " --> pdb=" O ARG G2304 " (cutoff:3.500A) Processing helix chain 'G' and resid 2314 through 2328 removed outlier: 4.698A pdb=" N VAL G2320 " --> pdb=" O GLU G2316 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG G2328 " --> pdb=" O LEU G2324 " (cutoff:3.500A) Processing helix chain 'G' and resid 2344 through 2349 Processing helix chain 'G' and resid 2350 through 2354 removed outlier: 4.023A pdb=" N LYS G2353 " --> pdb=" O GLU G2350 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE G2354 " --> pdb=" O ALA G2351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2350 through 2354' Processing helix chain 'G' and resid 2387 through 2400 Processing helix chain 'G' and resid 2406 through 2411 Processing helix chain 'G' and resid 2415 through 2427 removed outlier: 3.586A pdb=" N LEU G2427 " --> pdb=" O ILE G2423 " (cutoff:3.500A) Processing helix chain 'G' and resid 2432 through 2438 Processing helix chain 'G' and resid 2464 through 2474 Processing helix chain 'G' and resid 2482 through 2489 removed outlier: 3.682A pdb=" N LEU G2488 " --> pdb=" O PHE G2484 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G2489 " --> pdb=" O LEU G2485 " (cutoff:3.500A) Processing helix chain 'G' and resid 2493 through 2499 Processing helix chain 'G' and resid 2512 through 2517 Processing helix chain 'G' and resid 2519 through 2524 removed outlier: 3.749A pdb=" N THR G2523 " --> pdb=" O ARG G2519 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G2524 " --> pdb=" O TYR G2520 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2519 through 2524' Processing helix chain 'G' and resid 2525 through 2529 removed outlier: 3.658A pdb=" N LEU G2529 " --> pdb=" O LEU G2526 " (cutoff:3.500A) Processing helix chain 'G' and resid 2538 through 2552 Processing helix chain 'G' and resid 2559 through 2575 Processing helix chain 'G' and resid 2583 through 2597 removed outlier: 3.766A pdb=" N ARG G2592 " --> pdb=" O HIS G2588 " (cutoff:3.500A) Processing helix chain 'G' and resid 2598 through 2600 No H-bonds generated for 'chain 'G' and resid 2598 through 2600' Processing helix chain 'G' and resid 2606 through 2622 Processing helix chain 'G' and resid 2635 through 2650 Processing helix chain 'G' and resid 2659 through 2677 Proline residue: G2668 - end of helix Processing helix chain 'G' and resid 2715 through 2741 removed outlier: 3.602A pdb=" N GLU G2719 " --> pdb=" O PRO G2715 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE G2721 " --> pdb=" O LYS G2717 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN G2723 " --> pdb=" O GLU G2719 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS G2724 " --> pdb=" O TYR G2720 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU G2727 " --> pdb=" O ASN G2723 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN G2740 " --> pdb=" O ASP G2736 " (cutoff:3.500A) Processing helix chain 'G' and resid 2769 through 2786 Proline residue: G2775 - end of helix removed outlier: 3.901A pdb=" N THR G2782 " --> pdb=" O GLU G2778 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP G2786 " --> pdb=" O THR G2782 " (cutoff:3.500A) Processing helix chain 'G' and resid 2835 through 2862 removed outlier: 3.894A pdb=" N GLU G2860 " --> pdb=" O LYS G2856 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU G2862 " --> pdb=" O LYS G2858 " (cutoff:3.500A) Processing helix chain 'G' and resid 2874 through 2878 removed outlier: 3.895A pdb=" N LEU G2878 " --> pdb=" O TYR G2875 " (cutoff:3.500A) Processing helix chain 'G' and resid 2880 through 2900 removed outlier: 4.306A pdb=" N ASP G2886 " --> pdb=" O GLU G2882 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE G2893 " --> pdb=" O LYS G2889 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU G2894 " --> pdb=" O ALA G2890 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE G2896 " --> pdb=" O ASP G2892 " (cutoff:3.500A) Processing helix chain 'G' and resid 2983 through 3002 Proline residue: G2990 - end of helix Processing helix chain 'G' and resid 3010 through 3026 Processing helix chain 'G' and resid 3035 through 3050 Processing helix chain 'G' and resid 3062 through 3080 removed outlier: 4.046A pdb=" N LEU G3069 " --> pdb=" O ALA G3065 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU G3070 " --> pdb=" O ALA G3066 " (cutoff:3.500A) Processing helix chain 'G' and resid 3101 through 3116 Processing helix chain 'G' and resid 3125 through 3143 removed outlier: 3.543A pdb=" N THR G3143 " --> pdb=" O TYR G3139 " (cutoff:3.500A) Processing helix chain 'G' and resid 3150 through 3163 Processing helix chain 'G' and resid 3171 through 3179 Processing helix chain 'G' and resid 3594 through 3606 removed outlier: 3.892A pdb=" N ARG G3598 " --> pdb=" O LYS G3594 " (cutoff:3.500A) Processing helix chain 'G' and resid 3615 through 3630 removed outlier: 3.540A pdb=" N TRP G3629 " --> pdb=" O TYR G3625 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE G3630 " --> pdb=" O GLU G3626 " (cutoff:3.500A) Processing helix chain 'G' and resid 3636 through 3646 removed outlier: 4.211A pdb=" N LYS G3640 " --> pdb=" O TYR G3636 " (cutoff:3.500A) Processing helix chain 'G' and resid 3663 through 3677 Processing helix chain 'G' and resid 3686 through 3699 removed outlier: 3.934A pdb=" N ASP G3694 " --> pdb=" O MET G3690 " (cutoff:3.500A) Processing helix chain 'G' and resid 3715 through 3734 removed outlier: 3.903A pdb=" N LEU G3732 " --> pdb=" O GLN G3728 " (cutoff:3.500A) Processing helix chain 'G' and resid 3736 through 3748 removed outlier: 3.701A pdb=" N VAL G3741 " --> pdb=" O ALA G3737 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER G3746 " --> pdb=" O LEU G3742 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G3748 " --> pdb=" O THR G3744 " (cutoff:3.500A) Processing helix chain 'G' and resid 3753 through 3767 Processing helix chain 'G' and resid 3771 through 3785 removed outlier: 3.870A pdb=" N GLN G3775 " --> pdb=" O ASN G3771 " (cutoff:3.500A) Processing helix chain 'G' and resid 3788 through 3801 removed outlier: 4.109A pdb=" N SER G3800 " --> pdb=" O GLY G3796 " (cutoff:3.500A) Processing helix chain 'G' and resid 3807 through 3820 Processing helix chain 'G' and resid 3833 through 3847 removed outlier: 3.912A pdb=" N THR G3837 " --> pdb=" O ASP G3833 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG G3842 " --> pdb=" O CYS G3838 " (cutoff:3.500A) Processing helix chain 'G' and resid 3852 through 3859 Processing helix chain 'G' and resid 3870 through 3891 removed outlier: 3.651A pdb=" N SER G3874 " --> pdb=" O ASN G3870 " (cutoff:3.500A) Processing helix chain 'G' and resid 3900 through 3926 removed outlier: 3.509A pdb=" N GLN G3904 " --> pdb=" O ASP G3900 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS G3909 " --> pdb=" O ARG G3905 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL G3913 " --> pdb=" O LYS G3909 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE G3925 " --> pdb=" O LEU G3921 " (cutoff:3.500A) Processing helix chain 'G' and resid 3929 through 3938 Processing helix chain 'G' and resid 3940 through 3960 removed outlier: 4.197A pdb=" N ALA G3944 " --> pdb=" O ARG G3940 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS G3954 " --> pdb=" O HIS G3950 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G3960 " --> pdb=" O GLN G3956 " (cutoff:3.500A) Processing helix chain 'G' and resid 3965 through 3987 Processing helix chain 'G' and resid 3994 through 4007 Processing helix chain 'G' and resid 4007 through 4029 removed outlier: 3.604A pdb=" N VAL G4011 " --> pdb=" O SER G4007 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET G4013 " --> pdb=" O ASN G4009 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE G4021 " --> pdb=" O PHE G4017 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS G4023 " --> pdb=" O ASP G4019 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU G4024 " --> pdb=" O MET G4020 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS G4025 " --> pdb=" O PHE G4021 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER G4029 " --> pdb=" O LYS G4025 " (cutoff:3.500A) Processing helix chain 'G' and resid 4032 through 4037 removed outlier: 4.313A pdb=" N ASP G4037 " --> pdb=" O PHE G4033 " (cutoff:3.500A) Processing helix chain 'G' and resid 4045 through 4054 removed outlier: 3.824A pdb=" N ALA G4052 " --> pdb=" O ASP G4048 " (cutoff:3.500A) Processing helix chain 'G' and resid 4060 through 4071 removed outlier: 3.713A pdb=" N ALA G4071 " --> pdb=" O LEU G4067 " (cutoff:3.500A) Processing helix chain 'G' and resid 4081 through 4110 removed outlier: 4.514A pdb=" N ARG G4087 " --> pdb=" O GLU G4083 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE G4088 " --> pdb=" O PHE G4084 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU G4090 " --> pdb=" O LYS G4086 " (cutoff:3.500A) Proline residue: G4091 - end of helix Processing helix chain 'G' and resid 4113 through 4122 Processing helix chain 'G' and resid 4123 through 4128 removed outlier: 4.144A pdb=" N LEU G4127 " --> pdb=" O ALA G4123 " (cutoff:3.500A) Processing helix chain 'G' and resid 4155 through 4161 removed outlier: 3.913A pdb=" N TRP G4161 " --> pdb=" O SER G4157 " (cutoff:3.500A) Processing helix chain 'G' and resid 4165 through 4181 removed outlier: 4.003A pdb=" N ARG G4171 " --> pdb=" O LYS G4167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN G4179 " --> pdb=" O PHE G4175 " (cutoff:3.500A) Processing helix chain 'G' and resid 4185 through 4205 Processing helix chain 'G' and resid 4487 through 4494 removed outlier: 3.604A pdb=" N LYS G4491 " --> pdb=" O ALA G4487 " (cutoff:3.500A) Processing helix chain 'G' and resid 4499 through 4519 removed outlier: 3.647A pdb=" N MET G4503 " --> pdb=" O ASN G4499 " (cutoff:3.500A) Processing helix chain 'G' and resid 4568 through 4593 removed outlier: 3.642A pdb=" N LEU G4573 " --> pdb=" O MET G4569 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE G4578 " --> pdb=" O ARG G4574 " (cutoff:3.500A) Processing helix chain 'G' and resid 4595 through 4612 removed outlier: 3.648A pdb=" N VAL G4599 " --> pdb=" O LYS G4595 " (cutoff:3.500A) Processing helix chain 'G' and resid 4626 through 4631 Processing helix chain 'G' and resid 4632 through 4637 removed outlier: 3.837A pdb=" N ILE G4636 " --> pdb=" O ASP G4632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN G4637 " --> pdb=" O ARG G4633 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4632 through 4637' Processing helix chain 'G' and resid 4649 through 4659 Processing helix chain 'G' and resid 4663 through 4672 removed outlier: 3.599A pdb=" N ILE G4667 " --> pdb=" O GLY G4663 " (cutoff:3.500A) Processing helix chain 'G' and resid 4698 through 4702 removed outlier: 4.024A pdb=" N ILE G4702 " --> pdb=" O LEU G4699 " (cutoff:3.500A) Processing helix chain 'G' and resid 4703 through 4716 removed outlier: 3.669A pdb=" N GLN G4707 " --> pdb=" O ASP G4703 " (cutoff:3.500A) Processing helix chain 'G' and resid 4717 through 4736 Processing helix chain 'G' and resid 4738 through 4747 removed outlier: 3.729A pdb=" N HIS G4743 " --> pdb=" O PHE G4740 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G4745 " --> pdb=" O ALA G4742 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP G4746 " --> pdb=" O HIS G4743 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE G4747 " --> pdb=" O LEU G4744 " (cutoff:3.500A) Processing helix chain 'G' and resid 4752 through 4759 Processing helix chain 'G' and resid 4764 through 4790 removed outlier: 3.629A pdb=" N LEU G4768 " --> pdb=" O ASN G4764 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN G4788 " --> pdb=" O VAL G4784 " (cutoff:3.500A) Processing helix chain 'G' and resid 4810 through 4820 Processing helix chain 'G' and resid 4840 through 4855 Processing helix chain 'G' and resid 4857 through 4887 removed outlier: 4.042A pdb=" N LYS G4882 " --> pdb=" O GLN G4878 " (cutoff:3.500A) Processing helix chain 'G' and resid 4905 through 4912 Processing helix chain 'G' and resid 4916 through 4929 Processing helix chain 'G' and resid 4935 through 4948 Processing helix chain 'G' and resid 4958 through 4963 removed outlier: 3.646A pdb=" N TYR G4963 " --> pdb=" O PHE G4959 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 64 Processing helix chain 'I' and resid 6 through 21 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 66 through 92 removed outlier: 3.906A pdb=" N THR I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE I 90 " --> pdb=" O ILE I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 111 removed outlier: 3.585A pdb=" N THR I 111 " --> pdb=" O ARG I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 128 removed outlier: 4.027A pdb=" N VAL I 122 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU I 128 " --> pdb=" O GLU I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 147 Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.813A pdb=" N CYS J 65 " --> pdb=" O LEU J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 74 through 82 Processing helix chain 'J' and resid 323 through 328 Processing helix chain 'J' and resid 409 through 439 removed outlier: 3.799A pdb=" N SER J 413 " --> pdb=" O GLN J 409 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG J 428 " --> pdb=" O PHE J 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS J 438 " --> pdb=" O ASP J 434 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS J 439 " --> pdb=" O ALA J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 463 Processing helix chain 'J' and resid 471 through 492 Processing helix chain 'J' and resid 493 through 506 removed outlier: 3.924A pdb=" N LEU J 497 " --> pdb=" O GLY J 493 " (cutoff:3.500A) Processing helix chain 'J' and resid 525 through 540 Processing helix chain 'J' and resid 544 through 552 removed outlier: 3.513A pdb=" N CYS J 548 " --> pdb=" O ASN J 544 " (cutoff:3.500A) Processing helix chain 'J' and resid 554 through 562 removed outlier: 3.879A pdb=" N LEU J 558 " --> pdb=" O SER J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 567 through 581 removed outlier: 4.157A pdb=" N GLU J 581 " --> pdb=" O CYS J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 604 Processing helix chain 'J' and resid 608 through 619 Processing helix chain 'J' and resid 625 through 636 Processing helix chain 'J' and resid 821 through 826 removed outlier: 3.548A pdb=" N ALA J 825 " --> pdb=" O CYS J 822 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL J 826 " --> pdb=" O TYR J 823 " (cutoff:3.500A) Processing helix chain 'J' and resid 875 through 900 removed outlier: 4.276A pdb=" N ILE J 881 " --> pdb=" O HIS J 877 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS J 897 " --> pdb=" O TRP J 893 " (cutoff:3.500A) Processing helix chain 'J' and resid 929 through 944 removed outlier: 3.615A pdb=" N MET J 935 " --> pdb=" O TYR J 931 " (cutoff:3.500A) Processing helix chain 'J' and resid 989 through 1011 Processing helix chain 'J' and resid 1043 through 1060 Processing helix chain 'J' and resid 1091 through 1095 Processing helix chain 'J' and resid 1140 through 1142 No H-bonds generated for 'chain 'J' and resid 1140 through 1142' Processing helix chain 'J' and resid 1220 through 1224 removed outlier: 3.722A pdb=" N LEU J1224 " --> pdb=" O VAL J1221 " (cutoff:3.500A) Processing helix chain 'J' and resid 1571 through 1575 Processing helix chain 'J' and resid 1642 through 1646 removed outlier: 3.807A pdb=" N THR J1645 " --> pdb=" O LEU J1642 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU J1646 " --> pdb=" O GLU J1643 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1642 through 1646' Processing helix chain 'J' and resid 1647 through 1665 removed outlier: 3.670A pdb=" N CYS J1665 " --> pdb=" O TYR J1661 " (cutoff:3.500A) Processing helix chain 'J' and resid 1669 through 1680 removed outlier: 4.348A pdb=" N ALA J1675 " --> pdb=" O ARG J1671 " (cutoff:3.500A) Processing helix chain 'J' and resid 1682 through 1691 removed outlier: 3.983A pdb=" N GLU J1690 " --> pdb=" O LEU J1686 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN J1691 " --> pdb=" O TYR J1687 " (cutoff:3.500A) Processing helix chain 'J' and resid 1695 through 1711 Processing helix chain 'J' and resid 1711 through 1722 removed outlier: 3.558A pdb=" N MET J1721 " --> pdb=" O ALA J1717 " (cutoff:3.500A) Processing helix chain 'J' and resid 1730 through 1735 Processing helix chain 'J' and resid 1783 through 1803 removed outlier: 3.619A pdb=" N LEU J1787 " --> pdb=" O PRO J1783 " (cutoff:3.500A) Processing helix chain 'J' and resid 1814 through 1830 Proline residue: J1820 - end of helix Processing helix chain 'J' and resid 1835 through 1847 removed outlier: 4.249A pdb=" N HIS J1841 " --> pdb=" O GLU J1837 " (cutoff:3.500A) Processing helix chain 'J' and resid 1900 through 1950 removed outlier: 3.613A pdb=" N LYS J1904 " --> pdb=" O PRO J1900 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP J1932 " --> pdb=" O ALA J1928 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA J1935 " --> pdb=" O ASP J1931 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS J1936 " --> pdb=" O ASP J1932 " (cutoff:3.500A) Processing helix chain 'J' and resid 1987 through 1996 removed outlier: 3.596A pdb=" N GLU J1991 " --> pdb=" O CYS J1987 " (cutoff:3.500A) Processing helix chain 'J' and resid 1999 through 2011 Processing helix chain 'J' and resid 2026 through 2037 removed outlier: 3.740A pdb=" N LEU J2030 " --> pdb=" O ILE J2026 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU J2035 " --> pdb=" O LEU J2031 " (cutoff:3.500A) Processing helix chain 'J' and resid 2059 through 2074 removed outlier: 4.447A pdb=" N VAL J2068 " --> pdb=" O SER J2064 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER J2074 " --> pdb=" O TRP J2070 " (cutoff:3.500A) Processing helix chain 'J' and resid 2078 through 2094 removed outlier: 4.007A pdb=" N VAL J2082 " --> pdb=" O ASP J2078 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL J2087 " --> pdb=" O ARG J2083 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU J2088 " --> pdb=" O ALA J2084 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR J2093 " --> pdb=" O LEU J2089 " (cutoff:3.500A) Processing helix chain 'J' and resid 2094 through 2103 Processing helix chain 'J' and resid 2104 through 2106 No H-bonds generated for 'chain 'J' and resid 2104 through 2106' Processing helix chain 'J' and resid 2113 through 2130 Processing helix chain 'J' and resid 2131 through 2133 No H-bonds generated for 'chain 'J' and resid 2131 through 2133' Processing helix chain 'J' and resid 2139 through 2151 Processing helix chain 'J' and resid 2154 through 2159 Processing helix chain 'J' and resid 2159 through 2167 removed outlier: 4.006A pdb=" N MET J2163 " --> pdb=" O HIS J2159 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG J2164 " --> pdb=" O PRO J2160 " (cutoff:3.500A) Processing helix chain 'J' and resid 2167 through 2180 Processing helix chain 'J' and resid 2192 through 2205 removed outlier: 3.828A pdb=" N ARG J2199 " --> pdb=" O ALA J2195 " (cutoff:3.500A) Processing helix chain 'J' and resid 2208 through 2217 removed outlier: 3.582A pdb=" N GLN J2212 " --> pdb=" O SER J2208 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS J2213 " --> pdb=" O ARG J2209 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA J2214 " --> pdb=" O GLN J2210 " (cutoff:3.500A) Processing helix chain 'J' and resid 2218 through 2223 Processing helix chain 'J' and resid 2225 through 2229 removed outlier: 3.573A pdb=" N VAL J2228 " --> pdb=" O ASN J2225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY J2229 " --> pdb=" O SER J2226 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2225 through 2229' Processing helix chain 'J' and resid 2239 through 2247 Processing helix chain 'J' and resid 2252 through 2258 removed outlier: 3.806A pdb=" N LEU J2258 " --> pdb=" O LEU J2254 " (cutoff:3.500A) Processing helix chain 'J' and resid 2259 through 2272 removed outlier: 3.509A pdb=" N LEU J2263 " --> pdb=" O ARG J2259 " (cutoff:3.500A) Processing helix chain 'J' and resid 2295 through 2308 removed outlier: 3.882A pdb=" N TYR J2299 " --> pdb=" O GLU J2295 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE J2308 " --> pdb=" O ARG J2304 " (cutoff:3.500A) Processing helix chain 'J' and resid 2314 through 2328 removed outlier: 4.698A pdb=" N VAL J2320 " --> pdb=" O GLU J2316 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG J2328 " --> pdb=" O LEU J2324 " (cutoff:3.500A) Processing helix chain 'J' and resid 2344 through 2349 Processing helix chain 'J' and resid 2350 through 2354 removed outlier: 4.023A pdb=" N LYS J2353 " --> pdb=" O GLU J2350 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE J2354 " --> pdb=" O ALA J2351 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2350 through 2354' Processing helix chain 'J' and resid 2387 through 2400 Processing helix chain 'J' and resid 2406 through 2411 Processing helix chain 'J' and resid 2415 through 2427 removed outlier: 3.586A pdb=" N LEU J2427 " --> pdb=" O ILE J2423 " (cutoff:3.500A) Processing helix chain 'J' and resid 2432 through 2438 Processing helix chain 'J' and resid 2464 through 2474 Processing helix chain 'J' and resid 2482 through 2489 removed outlier: 3.683A pdb=" N LEU J2488 " --> pdb=" O PHE J2484 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU J2489 " --> pdb=" O LEU J2485 " (cutoff:3.500A) Processing helix chain 'J' and resid 2493 through 2499 Processing helix chain 'J' and resid 2512 through 2517 Processing helix chain 'J' and resid 2519 through 2524 removed outlier: 3.749A pdb=" N THR J2523 " --> pdb=" O ARG J2519 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA J2524 " --> pdb=" O TYR J2520 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2519 through 2524' Processing helix chain 'J' and resid 2525 through 2529 removed outlier: 3.659A pdb=" N LEU J2529 " --> pdb=" O LEU J2526 " (cutoff:3.500A) Processing helix chain 'J' and resid 2538 through 2552 Processing helix chain 'J' and resid 2559 through 2575 Processing helix chain 'J' and resid 2583 through 2597 removed outlier: 3.766A pdb=" N ARG J2592 " --> pdb=" O HIS J2588 " (cutoff:3.500A) Processing helix chain 'J' and resid 2598 through 2600 No H-bonds generated for 'chain 'J' and resid 2598 through 2600' Processing helix chain 'J' and resid 2606 through 2622 Processing helix chain 'J' and resid 2635 through 2650 Processing helix chain 'J' and resid 2659 through 2677 Proline residue: J2668 - end of helix Processing helix chain 'J' and resid 2715 through 2741 removed outlier: 3.601A pdb=" N GLU J2719 " --> pdb=" O PRO J2715 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE J2721 " --> pdb=" O LYS J2717 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN J2723 " --> pdb=" O GLU J2719 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS J2724 " --> pdb=" O TYR J2720 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU J2727 " --> pdb=" O ASN J2723 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN J2740 " --> pdb=" O ASP J2736 " (cutoff:3.500A) Processing helix chain 'J' and resid 2769 through 2786 Proline residue: J2775 - end of helix removed outlier: 3.899A pdb=" N THR J2782 " --> pdb=" O GLU J2778 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP J2786 " --> pdb=" O THR J2782 " (cutoff:3.500A) Processing helix chain 'J' and resid 2835 through 2862 removed outlier: 3.895A pdb=" N GLU J2860 " --> pdb=" O LYS J2856 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU J2862 " --> pdb=" O LYS J2858 " (cutoff:3.500A) Processing helix chain 'J' and resid 2874 through 2878 removed outlier: 3.895A pdb=" N LEU J2878 " --> pdb=" O TYR J2875 " (cutoff:3.500A) Processing helix chain 'J' and resid 2880 through 2900 removed outlier: 4.306A pdb=" N ASP J2886 " --> pdb=" O GLU J2882 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE J2893 " --> pdb=" O LYS J2889 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU J2894 " --> pdb=" O ALA J2890 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE J2896 " --> pdb=" O ASP J2892 " (cutoff:3.500A) Processing helix chain 'J' and resid 2983 through 3002 Proline residue: J2990 - end of helix Processing helix chain 'J' and resid 3010 through 3026 Processing helix chain 'J' and resid 3035 through 3050 Processing helix chain 'J' and resid 3062 through 3080 removed outlier: 4.046A pdb=" N LEU J3069 " --> pdb=" O ALA J3065 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU J3070 " --> pdb=" O ALA J3066 " (cutoff:3.500A) Processing helix chain 'J' and resid 3101 through 3116 Processing helix chain 'J' and resid 3125 through 3143 removed outlier: 3.544A pdb=" N THR J3143 " --> pdb=" O TYR J3139 " (cutoff:3.500A) Processing helix chain 'J' and resid 3150 through 3163 Processing helix chain 'J' and resid 3171 through 3179 Processing helix chain 'J' and resid 3594 through 3606 removed outlier: 3.894A pdb=" N ARG J3598 " --> pdb=" O LYS J3594 " (cutoff:3.500A) Processing helix chain 'J' and resid 3615 through 3630 removed outlier: 3.540A pdb=" N TRP J3629 " --> pdb=" O TYR J3625 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE J3630 " --> pdb=" O GLU J3626 " (cutoff:3.500A) Processing helix chain 'J' and resid 3636 through 3646 removed outlier: 4.211A pdb=" N LYS J3640 " --> pdb=" O TYR J3636 " (cutoff:3.500A) Processing helix chain 'J' and resid 3663 through 3677 Processing helix chain 'J' and resid 3686 through 3699 removed outlier: 3.935A pdb=" N ASP J3694 " --> pdb=" O MET J3690 " (cutoff:3.500A) Processing helix chain 'J' and resid 3715 through 3734 removed outlier: 3.903A pdb=" N LEU J3732 " --> pdb=" O GLN J3728 " (cutoff:3.500A) Processing helix chain 'J' and resid 3736 through 3748 removed outlier: 3.701A pdb=" N VAL J3741 " --> pdb=" O ALA J3737 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER J3746 " --> pdb=" O LEU J3742 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER J3748 " --> pdb=" O THR J3744 " (cutoff:3.500A) Processing helix chain 'J' and resid 3753 through 3767 Processing helix chain 'J' and resid 3771 through 3785 removed outlier: 3.870A pdb=" N GLN J3775 " --> pdb=" O ASN J3771 " (cutoff:3.500A) Processing helix chain 'J' and resid 3788 through 3801 removed outlier: 4.109A pdb=" N SER J3800 " --> pdb=" O GLY J3796 " (cutoff:3.500A) Processing helix chain 'J' and resid 3807 through 3820 Processing helix chain 'J' and resid 3833 through 3847 removed outlier: 3.913A pdb=" N THR J3837 " --> pdb=" O ASP J3833 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG J3842 " --> pdb=" O CYS J3838 " (cutoff:3.500A) Processing helix chain 'J' and resid 3852 through 3859 Processing helix chain 'J' and resid 3870 through 3891 removed outlier: 3.651A pdb=" N SER J3874 " --> pdb=" O ASN J3870 " (cutoff:3.500A) Processing helix chain 'J' and resid 3900 through 3926 removed outlier: 3.509A pdb=" N GLN J3904 " --> pdb=" O ASP J3900 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS J3909 " --> pdb=" O ARG J3905 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL J3913 " --> pdb=" O LYS J3909 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE J3925 " --> pdb=" O LEU J3921 " (cutoff:3.500A) Processing helix chain 'J' and resid 3929 through 3938 Processing helix chain 'J' and resid 3940 through 3960 removed outlier: 4.197A pdb=" N ALA J3944 " --> pdb=" O ARG J3940 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS J3954 " --> pdb=" O HIS J3950 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER J3960 " --> pdb=" O GLN J3956 " (cutoff:3.500A) Processing helix chain 'J' and resid 3965 through 3987 Processing helix chain 'J' and resid 3994 through 4007 Processing helix chain 'J' and resid 4007 through 4029 removed outlier: 3.603A pdb=" N VAL J4011 " --> pdb=" O SER J4007 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET J4013 " --> pdb=" O ASN J4009 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE J4021 " --> pdb=" O PHE J4017 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS J4023 " --> pdb=" O ASP J4019 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU J4024 " --> pdb=" O MET J4020 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS J4025 " --> pdb=" O PHE J4021 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER J4029 " --> pdb=" O LYS J4025 " (cutoff:3.500A) Processing helix chain 'J' and resid 4032 through 4037 removed outlier: 4.314A pdb=" N ASP J4037 " --> pdb=" O PHE J4033 " (cutoff:3.500A) Processing helix chain 'J' and resid 4045 through 4054 removed outlier: 3.824A pdb=" N ALA J4052 " --> pdb=" O ASP J4048 " (cutoff:3.500A) Processing helix chain 'J' and resid 4060 through 4071 removed outlier: 3.713A pdb=" N ALA J4071 " --> pdb=" O LEU J4067 " (cutoff:3.500A) Processing helix chain 'J' and resid 4081 through 4086 Processing helix chain 'J' and resid 4089 through 4110 Processing helix chain 'J' and resid 4113 through 4122 Processing helix chain 'J' and resid 4123 through 4128 removed outlier: 4.144A pdb=" N LEU J4127 " --> pdb=" O ALA J4123 " (cutoff:3.500A) Processing helix chain 'J' and resid 4155 through 4161 removed outlier: 3.913A pdb=" N TRP J4161 " --> pdb=" O SER J4157 " (cutoff:3.500A) Processing helix chain 'J' and resid 4165 through 4181 removed outlier: 4.003A pdb=" N ARG J4171 " --> pdb=" O LYS J4167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN J4179 " --> pdb=" O PHE J4175 " (cutoff:3.500A) Processing helix chain 'J' and resid 4185 through 4205 Processing helix chain 'J' and resid 4487 through 4494 removed outlier: 3.604A pdb=" N LYS J4491 " --> pdb=" O ALA J4487 " (cutoff:3.500A) Processing helix chain 'J' and resid 4499 through 4519 removed outlier: 3.648A pdb=" N MET J4503 " --> pdb=" O ASN J4499 " (cutoff:3.500A) Processing helix chain 'J' and resid 4568 through 4593 removed outlier: 3.641A pdb=" N LEU J4573 " --> pdb=" O MET J4569 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE J4578 " --> pdb=" O ARG J4574 " (cutoff:3.500A) Processing helix chain 'J' and resid 4595 through 4612 removed outlier: 3.647A pdb=" N VAL J4599 " --> pdb=" O LYS J4595 " (cutoff:3.500A) Processing helix chain 'J' and resid 4626 through 4631 Processing helix chain 'J' and resid 4632 through 4637 removed outlier: 3.837A pdb=" N ILE J4636 " --> pdb=" O ASP J4632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN J4637 " --> pdb=" O ARG J4633 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4632 through 4637' Processing helix chain 'J' and resid 4649 through 4659 Processing helix chain 'J' and resid 4663 through 4672 removed outlier: 3.599A pdb=" N ILE J4667 " --> pdb=" O GLY J4663 " (cutoff:3.500A) Processing helix chain 'J' and resid 4698 through 4702 removed outlier: 4.024A pdb=" N ILE J4702 " --> pdb=" O LEU J4699 " (cutoff:3.500A) Processing helix chain 'J' and resid 4703 through 4716 removed outlier: 3.670A pdb=" N GLN J4707 " --> pdb=" O ASP J4703 " (cutoff:3.500A) Processing helix chain 'J' and resid 4717 through 4736 Processing helix chain 'J' and resid 4738 through 4747 removed outlier: 3.730A pdb=" N HIS J4743 " --> pdb=" O PHE J4740 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J4745 " --> pdb=" O ALA J4742 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP J4746 " --> pdb=" O HIS J4743 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE J4747 " --> pdb=" O LEU J4744 " (cutoff:3.500A) Processing helix chain 'J' and resid 4752 through 4759 Processing helix chain 'J' and resid 4764 through 4790 removed outlier: 3.629A pdb=" N LEU J4768 " --> pdb=" O ASN J4764 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN J4788 " --> pdb=" O VAL J4784 " (cutoff:3.500A) Processing helix chain 'J' and resid 4810 through 4820 Processing helix chain 'J' and resid 4840 through 4855 Processing helix chain 'J' and resid 4857 through 4887 removed outlier: 4.042A pdb=" N LYS J4882 " --> pdb=" O GLN J4878 " (cutoff:3.500A) Processing helix chain 'J' and resid 4905 through 4912 Processing helix chain 'J' and resid 4916 through 4929 Processing helix chain 'J' and resid 4935 through 4948 Processing helix chain 'J' and resid 4958 through 4963 removed outlier: 3.646A pdb=" N TYR J4963 " --> pdb=" O PHE J4959 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 64 Processing helix chain 'L' and resid 6 through 21 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 32 through 40 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 66 through 92 removed outlier: 3.906A pdb=" N THR L 80 " --> pdb=" O LYS L 76 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 111 removed outlier: 3.584A pdb=" N THR L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 128 removed outlier: 4.027A pdb=" N VAL L 122 " --> pdb=" O THR L 118 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.598A pdb=" N LEU A 69 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG A 122 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN A 71 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 removed outlier: 4.437A pdb=" N GLU A 40 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LEU A 46 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.020A pdb=" N VAL A 147 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 203 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 246 removed outlier: 3.570A pdb=" N THR A 246 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS A 261 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.513A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'A' and resid 329 through 332 Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 374 Processing sheet with id=AB1, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 654 Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 654 removed outlier: 3.691A pdb=" N PHE A 789 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 773 through 774 removed outlier: 4.082A pdb=" N GLU A 676 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 803 " --> pdb=" O GLU A 676 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A1619 " --> pdb=" O VAL A 800 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB6, first strand: chain 'A' and resid 1086 through 1089 removed outlier: 4.047A pdb=" N ARG A1086 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A1207 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A1136 " --> pdb=" O TRP A1145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1100 through 1103 removed outlier: 3.699A pdb=" N PHE A1103 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1160 through 1161 Processing sheet with id=AB9, first strand: chain 'A' and resid 1172 through 1173 Processing sheet with id=AC1, first strand: chain 'A' and resid 1176 through 1177 Processing sheet with id=AC2, first strand: chain 'A' and resid 1250 through 1252 Processing sheet with id=AC3, first strand: chain 'A' and resid 1257 through 1259 removed outlier: 4.258A pdb=" N LEU A1595 " --> pdb=" O PHE A1301 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE A1301 " --> pdb=" O LEU A1595 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A1545 " --> pdb=" O MET A1300 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1521 through 1522 Processing sheet with id=AC5, first strand: chain 'A' and resid 1727 through 1728 removed outlier: 6.545A pdb=" N VAL A1727 " --> pdb=" O ILE A2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 2743 through 2744 removed outlier: 6.129A pdb=" N ILE A2743 " --> pdb=" O GLN A2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 4134 through 4139 removed outlier: 3.566A pdb=" N GLY A4135 " --> pdb=" O PHE A4151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 3 through 8 removed outlier: 6.007A pdb=" N ILE B 4 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR B 75 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 6 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 73 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 97 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 3 through 8 removed outlier: 6.007A pdb=" N ILE B 4 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR B 75 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 6 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 73 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.529A pdb=" N PHE B 48 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AD4, first strand: chain 'D' and resid 19 through 20 removed outlier: 5.598A pdb=" N LEU D 69 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG D 122 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN D 71 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 35 through 41 removed outlier: 4.437A pdb=" N GLU D 40 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LEU D 46 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 129 through 132 removed outlier: 4.020A pdb=" N VAL D 147 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL D 203 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 275 through 276 Processing sheet with id=AD8, first strand: chain 'D' and resid 244 through 246 removed outlier: 3.570A pdb=" N THR D 246 " --> pdb=" O HIS D 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS D 261 " --> pdb=" O THR D 246 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 298 through 299 removed outlier: 3.513A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AE2, first strand: chain 'D' and resid 329 through 332 Processing sheet with id=AE3, first strand: chain 'D' and resid 371 through 374 Processing sheet with id=AE4, first strand: chain 'D' and resid 646 through 647 Processing sheet with id=AE5, first strand: chain 'D' and resid 653 through 654 Processing sheet with id=AE6, first strand: chain 'D' and resid 653 through 654 removed outlier: 3.690A pdb=" N PHE D 789 " --> pdb=" O ALA D 698 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 773 through 774 removed outlier: 4.083A pdb=" N GLU D 676 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 803 " --> pdb=" O GLU D 676 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL D1619 " --> pdb=" O VAL D 800 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 779 through 780 Processing sheet with id=AE9, first strand: chain 'D' and resid 1086 through 1089 removed outlier: 4.047A pdb=" N ARG D1086 " --> pdb=" O LEU D1207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D1207 " --> pdb=" O ARG D1086 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D1136 " --> pdb=" O TRP D1145 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1100 through 1103 removed outlier: 3.699A pdb=" N PHE D1103 " --> pdb=" O CYS D1164 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1160 through 1161 Processing sheet with id=AF3, first strand: chain 'D' and resid 1172 through 1173 Processing sheet with id=AF4, first strand: chain 'D' and resid 1176 through 1177 Processing sheet with id=AF5, first strand: chain 'D' and resid 1250 through 1252 Processing sheet with id=AF6, first strand: chain 'D' and resid 1257 through 1259 removed outlier: 4.258A pdb=" N LEU D1595 " --> pdb=" O PHE D1301 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE D1301 " --> pdb=" O LEU D1595 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D1545 " --> pdb=" O MET D1300 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1521 through 1522 Processing sheet with id=AF8, first strand: chain 'D' and resid 1727 through 1728 removed outlier: 6.545A pdb=" N VAL D1727 " --> pdb=" O ILE D2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 2743 through 2744 removed outlier: 6.128A pdb=" N ILE D2743 " --> pdb=" O GLN D2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'D' and resid 4134 through 4139 removed outlier: 3.566A pdb=" N GLY D4135 " --> pdb=" O PHE D4151 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.007A pdb=" N ILE E 4 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR E 75 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR E 6 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS E 73 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 97 " --> pdb=" O CYS E 76 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.007A pdb=" N ILE E 4 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR E 75 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR E 6 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS E 73 " --> pdb=" O THR E 6 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 21 through 24 removed outlier: 3.529A pdb=" N PHE E 48 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AG6, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AG7, first strand: chain 'G' and resid 19 through 20 removed outlier: 5.598A pdb=" N LEU G 69 " --> pdb=" O ARG G 122 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG G 122 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN G 71 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 35 through 41 removed outlier: 4.437A pdb=" N GLU G 40 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LEU G 46 " --> pdb=" O GLU G 40 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 129 through 132 removed outlier: 4.020A pdb=" N VAL G 147 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL G 203 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 275 through 276 Processing sheet with id=AH2, first strand: chain 'G' and resid 244 through 246 removed outlier: 3.570A pdb=" N THR G 246 " --> pdb=" O HIS G 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS G 261 " --> pdb=" O THR G 246 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 298 through 299 removed outlier: 3.513A pdb=" N LYS G 304 " --> pdb=" O HIS G 299 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 308 through 309 Processing sheet with id=AH5, first strand: chain 'G' and resid 329 through 332 Processing sheet with id=AH6, first strand: chain 'G' and resid 371 through 374 Processing sheet with id=AH7, first strand: chain 'G' and resid 646 through 647 Processing sheet with id=AH8, first strand: chain 'G' and resid 653 through 654 Processing sheet with id=AH9, first strand: chain 'G' and resid 653 through 654 removed outlier: 3.691A pdb=" N PHE G 789 " --> pdb=" O ALA G 698 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 773 through 774 removed outlier: 4.082A pdb=" N GLU G 676 " --> pdb=" O LEU G 803 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 803 " --> pdb=" O GLU G 676 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS G 799 " --> pdb=" O ASP G 680 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G1619 " --> pdb=" O VAL G 800 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 779 through 780 Processing sheet with id=AI3, first strand: chain 'G' and resid 1086 through 1089 removed outlier: 4.047A pdb=" N ARG G1086 " --> pdb=" O LEU G1207 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G1207 " --> pdb=" O ARG G1086 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G1136 " --> pdb=" O TRP G1145 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 1100 through 1103 removed outlier: 3.699A pdb=" N PHE G1103 " --> pdb=" O CYS G1164 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 1160 through 1161 Processing sheet with id=AI6, first strand: chain 'G' and resid 1172 through 1173 Processing sheet with id=AI7, first strand: chain 'G' and resid 1176 through 1177 Processing sheet with id=AI8, first strand: chain 'G' and resid 1250 through 1252 Processing sheet with id=AI9, first strand: chain 'G' and resid 1257 through 1259 removed outlier: 4.258A pdb=" N LEU G1595 " --> pdb=" O PHE G1301 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE G1301 " --> pdb=" O LEU G1595 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA G1545 " --> pdb=" O MET G1300 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 1521 through 1522 Processing sheet with id=AJ2, first strand: chain 'G' and resid 1727 through 1728 removed outlier: 6.545A pdb=" N VAL G1727 " --> pdb=" O ILE G2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'G' and resid 2743 through 2744 removed outlier: 6.129A pdb=" N ILE G2743 " --> pdb=" O GLN G2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'G' and resid 4134 through 4139 removed outlier: 3.566A pdb=" N GLY G4135 " --> pdb=" O PHE G4151 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.007A pdb=" N ILE H 4 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR H 75 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR H 6 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS H 73 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU H 97 " --> pdb=" O CYS H 76 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.007A pdb=" N ILE H 4 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR H 75 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR H 6 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS H 73 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'H' and resid 21 through 24 removed outlier: 3.530A pdb=" N PHE H 48 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'I' and resid 27 through 28 Processing sheet with id=AJ9, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AK1, first strand: chain 'J' and resid 19 through 20 removed outlier: 5.598A pdb=" N LEU J 69 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG J 122 " --> pdb=" O LEU J 69 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN J 71 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'J' and resid 35 through 41 removed outlier: 4.438A pdb=" N GLU J 40 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LEU J 46 " --> pdb=" O GLU J 40 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J' and resid 129 through 132 removed outlier: 4.020A pdb=" N VAL J 147 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL J 203 " --> pdb=" O VAL J 147 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 275 through 276 Processing sheet with id=AK5, first strand: chain 'J' and resid 244 through 246 removed outlier: 3.570A pdb=" N THR J 246 " --> pdb=" O HIS J 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS J 261 " --> pdb=" O THR J 246 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 298 through 299 removed outlier: 3.513A pdb=" N LYS J 304 " --> pdb=" O HIS J 299 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'J' and resid 308 through 309 Processing sheet with id=AK8, first strand: chain 'J' and resid 329 through 332 Processing sheet with id=AK9, first strand: chain 'J' and resid 371 through 374 Processing sheet with id=AL1, first strand: chain 'J' and resid 646 through 647 Processing sheet with id=AL2, first strand: chain 'J' and resid 653 through 654 Processing sheet with id=AL3, first strand: chain 'J' and resid 653 through 654 removed outlier: 3.690A pdb=" N PHE J 789 " --> pdb=" O ALA J 698 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'J' and resid 773 through 774 removed outlier: 4.083A pdb=" N GLU J 676 " --> pdb=" O LEU J 803 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU J 803 " --> pdb=" O GLU J 676 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS J 799 " --> pdb=" O ASP J 680 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL J1619 " --> pdb=" O VAL J 800 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 779 through 780 Processing sheet with id=AL6, first strand: chain 'J' and resid 1086 through 1089 removed outlier: 4.047A pdb=" N ARG J1086 " --> pdb=" O LEU J1207 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU J1207 " --> pdb=" O ARG J1086 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J1136 " --> pdb=" O TRP J1145 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'J' and resid 1100 through 1103 removed outlier: 3.699A pdb=" N PHE J1103 " --> pdb=" O CYS J1164 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'J' and resid 1160 through 1161 Processing sheet with id=AL9, first strand: chain 'J' and resid 1172 through 1173 Processing sheet with id=AM1, first strand: chain 'J' and resid 1176 through 1177 Processing sheet with id=AM2, first strand: chain 'J' and resid 1250 through 1252 Processing sheet with id=AM3, first strand: chain 'J' and resid 1257 through 1259 removed outlier: 4.258A pdb=" N LEU J1595 " --> pdb=" O PHE J1301 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE J1301 " --> pdb=" O LEU J1595 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA J1545 " --> pdb=" O MET J1300 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'J' and resid 1521 through 1522 Processing sheet with id=AM5, first strand: chain 'J' and resid 1727 through 1728 removed outlier: 6.545A pdb=" N VAL J1727 " --> pdb=" O ILE J2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM5 Processing sheet with id=AM6, first strand: chain 'J' and resid 2743 through 2744 removed outlier: 6.129A pdb=" N ILE J2743 " --> pdb=" O GLN J2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM6 Processing sheet with id=AM7, first strand: chain 'J' and resid 4134 through 4139 removed outlier: 3.566A pdb=" N GLY J4135 " --> pdb=" O PHE J4151 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.007A pdb=" N ILE K 4 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR K 75 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR K 6 " --> pdb=" O LYS K 73 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS K 73 " --> pdb=" O THR K 6 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU K 97 " --> pdb=" O CYS K 76 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.007A pdb=" N ILE K 4 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR K 75 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR K 6 " --> pdb=" O LYS K 73 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS K 73 " --> pdb=" O THR K 6 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'K' and resid 21 through 24 removed outlier: 3.528A pdb=" N PHE K 48 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'L' and resid 27 through 28 Processing sheet with id=AN3, first strand: chain 'L' and resid 100 through 102 5632 hydrogen bonds defined for protein. 16260 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: 75.71 Time building geometry restraints manager: 33.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 34424 1.33 - 1.46: 21825 1.46 - 1.58: 59807 1.58 - 1.70: 0 1.70 - 1.82: 1116 Bond restraints: 117172 Sorted by residual: bond pdb=" C ASN G1577 " pdb=" N PRO G1578 " ideal model delta sigma weight residual 1.335 1.386 -0.051 8.70e-03 1.32e+04 3.38e+01 bond pdb=" C ASN A1577 " pdb=" N PRO A1578 " ideal model delta sigma weight residual 1.335 1.386 -0.051 8.70e-03 1.32e+04 3.38e+01 bond pdb=" C ASN D1577 " pdb=" N PRO D1578 " ideal model delta sigma weight residual 1.335 1.386 -0.051 8.70e-03 1.32e+04 3.38e+01 bond pdb=" C ASN J1577 " pdb=" N PRO J1578 " ideal model delta sigma weight residual 1.335 1.385 -0.050 8.70e-03 1.32e+04 3.33e+01 bond pdb=" CG1 ILE G4146 " pdb=" CD1 ILE G4146 " ideal model delta sigma weight residual 1.513 1.380 0.133 3.90e-02 6.57e+02 1.17e+01 ... (remaining 117167 not shown) Histogram of bond angle deviations from ideal: 95.10 - 102.92: 810 102.92 - 110.73: 37219 110.73 - 118.55: 53982 118.55 - 126.36: 64722 126.36 - 134.18: 1631 Bond angle restraints: 158364 Sorted by residual: angle pdb=" CA GLU D4090 " pdb=" C GLU D4090 " pdb=" N PRO D4091 " ideal model delta sigma weight residual 120.52 114.90 5.62 8.30e-01 1.45e+00 4.58e+01 angle pdb=" CA GLU A4090 " pdb=" C GLU A4090 " pdb=" N PRO A4091 " ideal model delta sigma weight residual 120.52 114.98 5.54 8.30e-01 1.45e+00 4.45e+01 angle pdb=" CA GLU J4090 " pdb=" C GLU J4090 " pdb=" N PRO J4091 " ideal model delta sigma weight residual 120.52 115.07 5.45 8.30e-01 1.45e+00 4.31e+01 angle pdb=" CA GLU G4090 " pdb=" C GLU G4090 " pdb=" N PRO G4091 " ideal model delta sigma weight residual 120.52 115.23 5.29 8.30e-01 1.45e+00 4.07e+01 angle pdb=" N THR J 687 " pdb=" CA THR J 687 " pdb=" C THR J 687 " ideal model delta sigma weight residual 110.80 98.63 12.17 2.13e+00 2.20e-01 3.27e+01 ... (remaining 158359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 65007 16.72 - 33.45: 4013 33.45 - 50.17: 834 50.17 - 66.89: 66 66.89 - 83.62: 84 Dihedral angle restraints: 70004 sinusoidal: 26580 harmonic: 43424 Sorted by residual: dihedral pdb=" CA GLU J1847 " pdb=" C GLU J1847 " pdb=" N PRO J1848 " pdb=" CA PRO J1848 " ideal model delta harmonic sigma weight residual -180.00 -111.47 -68.53 0 5.00e+00 4.00e-02 1.88e+02 dihedral pdb=" CA GLU G1847 " pdb=" C GLU G1847 " pdb=" N PRO G1848 " pdb=" CA PRO G1848 " ideal model delta harmonic sigma weight residual -180.00 -111.48 -68.52 0 5.00e+00 4.00e-02 1.88e+02 dihedral pdb=" CA GLU A1847 " pdb=" C GLU A1847 " pdb=" N PRO A1848 " pdb=" CA PRO A1848 " ideal model delta harmonic sigma weight residual -180.00 -111.48 -68.52 0 5.00e+00 4.00e-02 1.88e+02 ... (remaining 70001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 14737 0.081 - 0.163: 2853 0.163 - 0.244: 222 0.244 - 0.325: 28 0.325 - 0.407: 8 Chirality restraints: 17848 Sorted by residual: chirality pdb=" CA ASN D4915 " pdb=" N ASN D4915 " pdb=" C ASN D4915 " pdb=" CB ASN D4915 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA ASN G4915 " pdb=" N ASN G4915 " pdb=" C ASN G4915 " pdb=" CB ASN G4915 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA ASN A4915 " pdb=" N ASN A4915 " pdb=" C ASN A4915 " pdb=" CB ASN A4915 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 17845 not shown) Planarity restraints: 20416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A4163 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.36e+01 pdb=" N PRO A4164 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO A4164 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A4164 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J4163 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.36e+01 pdb=" N PRO J4164 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO J4164 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO J4164 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D4163 " 0.080 5.00e-02 4.00e+02 1.22e-01 2.36e+01 pdb=" N PRO D4164 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO D4164 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO D4164 " 0.067 5.00e-02 4.00e+02 ... (remaining 20413 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 11678 2.74 - 3.28: 110488 3.28 - 3.82: 185968 3.82 - 4.36: 214000 4.36 - 4.90: 362267 Nonbonded interactions: 884401 Sorted by model distance: nonbonded pdb=" CG2 THR A4753 " pdb=" CD1 LEU J4770 " model vdw 2.196 3.880 nonbonded pdb=" N CYS J4892 " pdb="ZN ZN J6000 " model vdw 2.203 2.310 nonbonded pdb=" N CYS D4892 " pdb="ZN ZN D6000 " model vdw 2.203 2.310 nonbonded pdb=" N CYS G4892 " pdb="ZN ZN G6000 " model vdw 2.203 2.310 nonbonded pdb=" N CYS A4892 " pdb="ZN ZN A6000 " model vdw 2.203 2.310 ... (remaining 884396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.99 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 17.500 Check model and map are aligned: 1.210 Set scattering table: 0.760 Process input model: 263.670 Find NCS groups from input model: 5.230 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 293.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.010 0.133 117172 Z= 0.648 Angle : 1.256 15.532 158364 Z= 0.683 Chirality : 0.062 0.407 17848 Planarity : 0.008 0.122 20416 Dihedral : 11.977 83.616 41820 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.48 % Favored : 89.02 % Rotamer: Outliers : 1.03 % Allowed : 4.67 % Favored : 94.30 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.65 % Twisted General : 0.73 % 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: -4.77 (0.05), residues: 14504 helix: -2.64 (0.04), residues: 7560 sheet: -2.96 (0.14), residues: 1156 loop : -3.82 (0.07), residues: 5788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP D1250 HIS 0.021 0.003 HIS J 630 PHE 0.052 0.004 PHE D4586 TYR 0.043 0.004 TYR D1703 ARG 0.025 0.001 ARG G4948 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29008 Ramachandran restraints generated. 14504 Oldfield, 0 Emsley, 14504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29008 Ramachandran restraints generated. 14504 Oldfield, 0 Emsley, 14504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2676 residues out of total 13192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 2548 time to evaluate : 9.155 Fit side-chains revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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