Starting phenix.real_space_refine on Sun Mar 17 12:37:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6g_0686/03_2024/6j6g_0686_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6g_0686/03_2024/6j6g_0686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6g_0686/03_2024/6j6g_0686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6g_0686/03_2024/6j6g_0686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6g_0686/03_2024/6j6g_0686_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6g_0686/03_2024/6j6g_0686_updated.pdb" } resolution = 3.2 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 559 5.49 5 Mg 6 5.21 5 S 241 5.16 5 C 47955 2.51 5 N 13804 2.21 5 O 16471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 737": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ARG 1490": "NH1" <-> "NH2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ARG 1509": "NH1" <-> "NH2" Residue "A ARG 1511": "NH1" <-> "NH2" Residue "A ARG 1750": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C ARG 884": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O ARG 254": "NH1" <-> "NH2" Residue "P ARG 69": "NH1" <-> "NH2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "P ARG 185": "NH1" <-> "NH2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ARG 261": "NH1" <-> "NH2" Residue "S ARG 135": "NH1" <-> "NH2" Residue "T ARG 151": "NH1" <-> "NH2" Residue "Z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 42": "NH1" <-> "NH2" Residue "Z ARG 53": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 108": "NH1" <-> "NH2" Residue "Z ARG 149": "NH1" <-> "NH2" Residue "Z ARG 178": "NH1" <-> "NH2" Residue "Z ARG 191": "NH1" <-> "NH2" Residue "Z ARG 201": "NH1" <-> "NH2" Residue "Z ARG 382": "NH1" <-> "NH2" Residue "Z ARG 439": "NH1" <-> "NH2" Residue "c ARG 85": "NH1" <-> "NH2" Residue "n ARG 60": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "m ARG 88": "NH1" <-> "NH2" Residue "m ARG 117": "NH1" <-> "NH2" Residue "j ARG 23": "NH1" <-> "NH2" Residue "j ARG 30": "NH1" <-> "NH2" Residue "j ARG 64": "NH1" <-> "NH2" Residue "h ARG 26": "NH1" <-> "NH2" Residue "h ARG 82": "NH1" <-> "NH2" Residue "g ARG 8": "NH1" <-> "NH2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g ARG 49": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 87": "NH1" <-> "NH2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g ARG 97": "NH1" <-> "NH2" Residue "k ARG 62": "NH1" <-> "NH2" Residue "k GLU 107": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e ARG 41": "NH1" <-> "NH2" Residue "e ARG 63": "NH1" <-> "NH2" Residue "e GLU 70": "OE1" <-> "OE2" Residue "e ARG 87": "NH1" <-> "NH2" Residue "e GLU 88": "OE1" <-> "OE2" Residue "e ARG 89": "NH1" <-> "NH2" Residue "e ARG 97": "NH1" <-> "NH2" Residue "s ARG 62": "NH1" <-> "NH2" Residue "w ARG 26": "NH1" <-> "NH2" Residue "w ARG 82": "NH1" <-> "NH2" Residue "x ARG 23": "NH1" <-> "NH2" Residue "x ARG 30": "NH1" <-> "NH2" Residue "x ARG 64": "NH1" <-> "NH2" Residue "z ARG 88": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 79042 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 15793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1913, 15793 Classifications: {'peptide': 1913} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 97, 'TRANS': 1811} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 7348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 920, 7348 Classifications: {'peptide': 920} Link IDs: {'PTRANS': 51, 'TRANS': 868} Chain breaks: 2 Chain: "J" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 190 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "O" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2810 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 343} Chain: "P" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1608 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2301 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2089 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1291 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "Z" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3651 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 7, 'TRANS': 439} Chain breaks: 1 Chain: "c" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 2978 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 414} Chain breaks: 8 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 800 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 13, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 367 Chain: "d" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 3881 Classifications: {'peptide': 566} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 11, 'TRANS': 554} Chain breaks: 15 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1000 Unresolved non-hydrogen angles: 1272 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 3, 'TYR:plan': 13, 'ASN:plan1': 6, 'TRP:plan': 6, 'ASP:plan': 19, 'PHE:plan': 13, 'GLU:plan': 35, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 592 Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 822 Classifications: {'peptide': 102} Link IDs: {'TRANS': 101} Chain breaks: 1 Chain: "n" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1894 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 281} Chain breaks: 9 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 338 Chain: "H" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 617 Classifications: {'peptide': 70} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 67} Chain: "B" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1266 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 18, 'rna3p_pyr': 23} Link IDs: {'rna2p': 18, 'rna3p': 41} Chain breaks: 1 Chain: "D" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 3795 Classifications: {'RNA': 179} Modifications used: {'5*END': 1, 'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 70, 'rna3p_pyr': 79} Link IDs: {'rna2p': 30, 'rna3p': 148} Chain breaks: 1 Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2192 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 47, 'rna3p_pyr': 35} Link IDs: {'rna2p': 21, 'rna3p': 81} Chain: "L" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 4382 Classifications: {'RNA': 208} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 19, 'rna3p_pur': 82, 'rna3p_pyr': 99} Link IDs: {'rna2p': 27, 'rna3p': 180} Chain breaks: 10 Chain: "v" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 4625 Classifications: {'peptide': 722} Incomplete info: {'truncation_to_alanine': 368} Link IDs: {'PTRANS': 22, 'TRANS': 699} Chain breaks: 27 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1437 Unresolved non-hydrogen angles: 1831 Unresolved non-hydrogen dihedrals: 1236 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 5, 'TYR:plan': 18, 'ASN:plan1': 15, 'TRP:plan': 11, 'ASP:plan': 24, 'PHE:plan': 22, 'GLU:plan': 39, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 852 Chain: "a" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 416 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 145 Chain: "b" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 841 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 561 Unresolved non-hydrogen angles: 718 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 15, 'TYR:plan': 4, 'ASN:plan1': 14, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 8, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 305 Chain: "t" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 926 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 258 Chain: "u" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 552 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "h" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "g" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 785 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "k" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 809 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 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: "e" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 785 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "s" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 749 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain breaks: 1 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: "l" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "i" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 541 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "w" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "x" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 552 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "y" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 616 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "z" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "r" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 823 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "p" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 843 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "q" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 850 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "o" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 830 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27834 SG CYS Q 13 66.316 141.509 113.878 1.00 54.54 S ATOM 27858 SG CYS Q 16 64.923 145.690 115.291 1.00 53.83 S ATOM 28292 SG CYS Q 71 68.386 143.549 116.041 1.00 39.49 S ATOM 28313 SG CYS Q 74 65.211 142.698 117.260 1.00 38.94 S ATOM 27992 SG CYS Q 34 78.283 146.386 122.952 1.00 31.18 S ATOM 28015 SG CYS Q 37 81.980 146.106 123.170 1.00 31.66 S ATOM 28214 SG CYS Q 61 80.609 145.998 119.794 1.00 33.07 S ATOM 28238 SG CYS Q 64 79.950 143.259 122.044 1.00 34.62 S ATOM 30632 SG CYS R 73 53.645 159.671 133.021 1.00 28.87 S ATOM 30694 SG CYS R 81 52.187 162.937 134.080 1.00 29.83 S ATOM 30734 SG CYS R 87 52.649 162.177 130.392 1.00 33.80 S ATOM 33594 SG CYS T 104 55.332 179.681 114.522 1.00 31.22 S ATOM 33600 SG CYS T 105 59.014 181.177 114.620 1.00 27.39 S ATOM 33625 SG CYS T 108 58.460 177.543 113.792 1.00 29.01 S ATOM 33939 SG CYS T 148 57.161 179.122 117.005 1.00 26.75 S ATOM 33594 SG CYS T 104 55.332 179.681 114.522 1.00 31.22 S ATOM 33728 SG CYS T 122 55.158 176.091 112.884 1.00 32.38 S ATOM 33949 SG CYS T 150 52.089 177.851 114.359 1.00 31.64 S ATOM 33970 SG CYS T 153 53.638 178.805 111.276 1.00 32.22 S ATOM 33625 SG CYS T 108 58.460 177.543 113.792 1.00 29.01 S ATOM 33714 SG CYS T 120 58.010 173.823 113.183 1.00 29.19 S ATOM 33728 SG CYS T 122 55.158 176.091 112.884 1.00 32.38 S ATOM 33916 SG CYS T 145 56.488 175.491 116.275 1.00 28.50 S Time building chain proxies: 31.11, per 1000 atoms: 0.39 Number of scatterers: 79042 At special positions: 0 Unit cell: (246.05, 304.57, 305.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 241 16.00 P 559 15.00 Mg 6 11.99 O 16471 8.00 N 13804 7.00 C 47955 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: 25.91 Conformation dependent library (CDL) restraints added in 9.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 400 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 74 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 71 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 16 " pdb="ZN ZN Q 400 " - pdb=" SG CYS Q 13 " pdb=" ZN Q 401 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 64 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 37 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 34 " pdb="ZN ZN Q 401 " - pdb=" SG CYS Q 61 " pdb=" ZN R 400 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 81 " pdb="ZN ZN R 400 " - pdb=" NE2 HIS R 91 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 73 " pdb="ZN ZN R 400 " - pdb=" SG CYS R 87 " pdb=" ZN T1000 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 148 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 104 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1000 " - pdb=" SG CYS T 105 " pdb=" ZN T1001 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 153 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 150 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1001 " - pdb=" SG CYS T 104 " pdb=" ZN T1002 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 122 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 108 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 120 " pdb="ZN ZN T1002 " - pdb=" SG CYS T 145 " Number of angles added : 33 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 316 helices and 70 sheets defined 44.1% alpha, 10.7% beta 133 base pairs and 306 stacking pairs defined. Time for finding SS restraints: 28.92 Creating SS restraints... Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.560A pdb=" N ILE A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 removed outlier: 4.315A pdb=" N THR A 156 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.742A pdb=" N THR A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 473 through 480 Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 516 through 534 removed outlier: 3.950A pdb=" N SER A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 564 through 585 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 617 through 640 removed outlier: 3.838A pdb=" N THR A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 657 Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 671 through 691 removed outlier: 3.774A pdb=" N ILE A 677 " --> pdb=" O MET A 674 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 680 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 681 " --> pdb=" O ARG A 678 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 683 " --> pdb=" O CYS A 680 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS A 685 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 688 " --> pdb=" O HIS A 685 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 689 " --> pdb=" O ILE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 735 removed outlier: 3.523A pdb=" N VAL A 710 " --> pdb=" O PRO A 706 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 750 through 769 removed outlier: 3.698A pdb=" N ASP A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 794 removed outlier: 3.547A pdb=" N ILE A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 783 " --> pdb=" O ALA A 779 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 786 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 836 Processing helix chain 'A' and resid 842 through 870 removed outlier: 3.730A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 854 " --> pdb=" O GLY A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 893 Processing helix chain 'A' and resid 908 through 922 removed outlier: 4.560A pdb=" N VAL A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 removed outlier: 3.506A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 960 removed outlier: 3.535A pdb=" N LEU A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1006 removed outlier: 4.334A pdb=" N THR A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1034 removed outlier: 3.702A pdb=" N ASN A1033 " --> pdb=" O THR A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1073 removed outlier: 3.588A pdb=" N ARG A1071 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 removed outlier: 3.520A pdb=" N THR A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1135 removed outlier: 4.061A pdb=" N SER A1111 " --> pdb=" O LYS A1108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1113 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A1114 " --> pdb=" O SER A1111 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A1115 " --> pdb=" O PHE A1112 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A1117 " --> pdb=" O PHE A1114 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A1125 " --> pdb=" O ASP A1122 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A1126 " --> pdb=" O LEU A1123 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY A1127 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLN A1128 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU A1129 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A1130 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A1131 " --> pdb=" O GLN A1128 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A1132 " --> pdb=" O GLU A1129 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A1134 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A1135 " --> pdb=" O THR A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1154 Processing helix chain 'A' and resid 1176 through 1189 removed outlier: 3.756A pdb=" N TYR A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1231 Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1328 through 1343 removed outlier: 3.550A pdb=" N SER A1341 " --> pdb=" O THR A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1374 removed outlier: 3.502A pdb=" N VAL A1371 " --> pdb=" O ILE A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1389 Processing helix chain 'A' and resid 1412 through 1415 No H-bonds generated for 'chain 'A' and resid 1412 through 1415' Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1470 removed outlier: 3.652A pdb=" N ARG A1456 " --> pdb=" O LEU A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1483 No H-bonds generated for 'chain 'A' and resid 1481 through 1483' Processing helix chain 'A' and resid 1491 through 1495 Processing helix chain 'A' and resid 1502 through 1504 No H-bonds generated for 'chain 'A' and resid 1502 through 1504' Processing helix chain 'A' and resid 1508 through 1516 removed outlier: 3.754A pdb=" N LYS A1515 " --> pdb=" O ARG A1511 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1533 No H-bonds generated for 'chain 'A' and resid 1530 through 1533' Processing helix chain 'A' and resid 1540 through 1549 removed outlier: 3.975A pdb=" N THR A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A1547 " --> pdb=" O ARG A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1559 removed outlier: 3.604A pdb=" N GLU A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1565 No H-bonds generated for 'chain 'A' and resid 1563 through 1565' Processing helix chain 'A' and resid 1604 through 1609 removed outlier: 3.554A pdb=" N TRP A1609 " --> pdb=" O ARG A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1639 through 1648 removed outlier: 3.929A pdb=" N SER A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1669 Processing helix chain 'A' and resid 1673 through 1676 No H-bonds generated for 'chain 'A' and resid 1673 through 1676' Processing helix chain 'A' and resid 1748 through 1759 removed outlier: 3.565A pdb=" N ARG A1753 " --> pdb=" O SER A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1808 removed outlier: 3.553A pdb=" N GLN A1799 " --> pdb=" O LYS A1795 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A1803 " --> pdb=" O GLN A1799 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A1804 " --> pdb=" O ASN A1800 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A1807 " --> pdb=" O ARG A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1823 Processing helix chain 'A' and resid 1841 through 1843 No H-bonds generated for 'chain 'A' and resid 1841 through 1843' Processing helix chain 'A' and resid 1898 through 1901 removed outlier: 4.286A pdb=" N GLY A1901 " --> pdb=" O VAL A1898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1898 through 1901' Processing helix chain 'A' and resid 1905 through 1923 removed outlier: 3.943A pdb=" N LYS A1910 " --> pdb=" O SER A1906 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP A1911 " --> pdb=" O GLN A1907 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1947 Processing helix chain 'A' and resid 1967 through 1970 No H-bonds generated for 'chain 'A' and resid 1967 through 1970' Processing helix chain 'A' and resid 1972 through 1979 Processing helix chain 'A' and resid 1993 through 1998 removed outlier: 3.616A pdb=" N ASP A1997 " --> pdb=" O ASP A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2017 removed outlier: 3.523A pdb=" N ALA A2014 " --> pdb=" O LEU A2010 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A2016 " --> pdb=" O LEU A2012 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A2017 " --> pdb=" O ARG A2013 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2026 Processing helix chain 'A' and resid 2046 through 2067 removed outlier: 3.614A pdb=" N LYS A2066 " --> pdb=" O GLU A2062 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A2067 " --> pdb=" O TYR A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2083 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 121 through 128 removed outlier: 3.504A pdb=" N ALA C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 Processing helix chain 'C' and resid 166 through 169 No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.615A pdb=" N MET C 222 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP C 223 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 225 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 231 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.575A pdb=" N GLN C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 341 through 344 No H-bonds generated for 'chain 'C' and resid 341 through 344' Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.743A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 403 removed outlier: 3.627A pdb=" N ASN C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 445 through 456 removed outlier: 5.495A pdb=" N ASP C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 512 removed outlier: 4.230A pdb=" N GLU C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 510 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 511 " --> pdb=" O GLU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 585 through 588 removed outlier: 3.642A pdb=" N GLN C 588 " --> pdb=" O ASP C 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 585 through 588' Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix removed outlier: 3.591A pdb=" N LEU C 619 " --> pdb=" O PRO C 616 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 620 " --> pdb=" O LYS C 617 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 622 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 626 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 660 removed outlier: 3.617A pdb=" N ASP C 658 " --> pdb=" O CYS C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 744 through 753 Processing helix chain 'C' and resid 759 through 763 Processing helix chain 'C' and resid 779 through 783 Processing helix chain 'C' and resid 785 through 789 Processing helix chain 'C' and resid 792 through 803 Processing helix chain 'C' and resid 831 through 852 removed outlier: 3.866A pdb=" N SER C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) Proline residue: C 840 - end of helix removed outlier: 3.535A pdb=" N LYS C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 847 " --> pdb=" O LYS C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 882 removed outlier: 3.620A pdb=" N LEU C 873 " --> pdb=" O ALA C 870 " (cutoff:3.500A) Proline residue: C 874 - end of helix removed outlier: 3.691A pdb=" N GLU C 877 " --> pdb=" O PRO C 874 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 882 " --> pdb=" O LEU C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 922 removed outlier: 3.530A pdb=" N ARG C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 974 removed outlier: 3.841A pdb=" N LEU C 962 " --> pdb=" O ILE C 959 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER C 963 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 964 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE C 966 " --> pdb=" O SER C 963 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 967 " --> pdb=" O ARG C 964 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS C 969 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 971 " --> pdb=" O MET C 968 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS C 974 " --> pdb=" O ARG C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1004 removed outlier: 3.535A pdb=" N GLN C1000 " --> pdb=" O GLU C 996 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN C1004 " --> pdb=" O GLN C1000 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 101 Processing helix chain 'O' and resid 111 through 119 removed outlier: 3.673A pdb=" N TYR O 115 " --> pdb=" O ILE O 111 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS O 117 " --> pdb=" O ASN O 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 84 removed outlier: 3.734A pdb=" N ARG P 69 " --> pdb=" O GLU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 163 No H-bonds generated for 'chain 'P' and resid 161 through 163' Processing helix chain 'P' and resid 182 through 185 No H-bonds generated for 'chain 'P' and resid 182 through 185' Processing helix chain 'P' and resid 199 through 244 removed outlier: 3.763A pdb=" N LYS P 226 " --> pdb=" O LYS P 222 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA P 236 " --> pdb=" O GLN P 232 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU P 243 " --> pdb=" O SER P 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 17 No H-bonds generated for 'chain 'Q' and resid 14 through 17' Processing helix chain 'Q' and resid 62 through 67 Processing helix chain 'Q' and resid 84 through 94 removed outlier: 3.612A pdb=" N VAL Q 94 " --> pdb=" O LEU Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 114 removed outlier: 4.041A pdb=" N LEU Q 113 " --> pdb=" O MET Q 109 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER Q 114 " --> pdb=" O LYS Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 129 through 145 removed outlier: 3.707A pdb=" N ASN Q 134 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE Q 135 " --> pdb=" O GLU Q 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN Q 141 " --> pdb=" O ASP Q 137 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE Q 142 " --> pdb=" O LYS Q 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG Q 145 " --> pdb=" O ASN Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 187 removed outlier: 4.071A pdb=" N LEU Q 187 " --> pdb=" O SER Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 216 through 227 removed outlier: 3.540A pdb=" N THR Q 220 " --> pdb=" O GLU Q 216 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 235 No H-bonds generated for 'chain 'Q' and resid 232 through 235' Processing helix chain 'Q' and resid 256 through 264 removed outlier: 3.595A pdb=" N GLU Q 260 " --> pdb=" O GLU Q 257 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Q 263 " --> pdb=" O GLU Q 260 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER Q 264 " --> pdb=" O ARG Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 324 removed outlier: 4.058A pdb=" N LYS Q 311 " --> pdb=" O ALA Q 307 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU Q 312 " --> pdb=" O GLU Q 308 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS Q 318 " --> pdb=" O LEU Q 314 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU Q 319 " --> pdb=" O SER Q 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 58 No H-bonds generated for 'chain 'R' and resid 55 through 58' Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 74 through 77 No H-bonds generated for 'chain 'R' and resid 74 through 77' Processing helix chain 'R' and resid 84 through 86 No H-bonds generated for 'chain 'R' and resid 84 through 86' Processing helix chain 'R' and resid 96 through 104 removed outlier: 5.250A pdb=" N LEU R 104 " --> pdb=" O GLY R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 146 Processing helix chain 'R' and resid 154 through 167 removed outlier: 4.000A pdb=" N ARG R 166 " --> pdb=" O PHE R 162 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU R 167 " --> pdb=" O VAL R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 199 removed outlier: 3.618A pdb=" N GLU R 197 " --> pdb=" O GLU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 214 removed outlier: 4.436A pdb=" N ASP R 213 " --> pdb=" O LYS R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 260 removed outlier: 4.025A pdb=" N ARG R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS R 252 " --> pdb=" O ASN R 248 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN R 255 " --> pdb=" O VAL R 251 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN R 256 " --> pdb=" O HIS R 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 18 Processing helix chain 'S' and resid 28 through 30 No H-bonds generated for 'chain 'S' and resid 28 through 30' Processing helix chain 'S' and resid 164 through 172 removed outlier: 3.550A pdb=" N LYS S 172 " --> pdb=" O GLU S 168 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 33 removed outlier: 4.061A pdb=" N GLU T 17 " --> pdb=" O ASP T 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS T 18 " --> pdb=" O GLY T 15 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS T 20 " --> pdb=" O GLU T 17 " (cutoff:3.500A) Proline residue: T 21 - end of helix removed outlier: 3.717A pdb=" N THR T 24 " --> pdb=" O PRO T 21 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP T 25 " --> pdb=" O THR T 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE T 26 " --> pdb=" O LEU T 23 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE T 28 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN T 29 " --> pdb=" O PHE T 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU T 30 " --> pdb=" O GLU T 27 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA T 33 " --> pdb=" O LEU T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 67 removed outlier: 3.530A pdb=" N ASN T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU T 47 " --> pdb=" O ALA T 43 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE T 52 " --> pdb=" O GLN T 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 83 Processing helix chain 'T' and resid 89 through 95 removed outlier: 3.684A pdb=" N LYS T 94 " --> pdb=" O LEU T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 109 No H-bonds generated for 'chain 'T' and resid 107 through 109' Processing helix chain 'T' and resid 121 through 123 No H-bonds generated for 'chain 'T' and resid 121 through 123' Processing helix chain 'T' and resid 126 through 136 removed outlier: 3.514A pdb=" N LYS T 136 " --> pdb=" O GLU T 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 31 Proline residue: Z 27 - end of helix Processing helix chain 'Z' and resid 37 through 46 Processing helix chain 'Z' and resid 53 through 65 Processing helix chain 'Z' and resid 71 through 86 Proline residue: Z 74 - end of helix removed outlier: 3.753A pdb=" N SER Z 77 " --> pdb=" O PRO Z 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA Z 78 " --> pdb=" O ALA Z 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 108 removed outlier: 3.602A pdb=" N LYS Z 96 " --> pdb=" O GLU Z 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 126 Processing helix chain 'Z' and resid 132 through 144 removed outlier: 3.846A pdb=" N ILE Z 138 " --> pdb=" O VAL Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 165 removed outlier: 3.957A pdb=" N ALA Z 153 " --> pdb=" O ARG Z 149 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE Z 157 " --> pdb=" O ALA Z 153 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP Z 160 " --> pdb=" O LYS Z 156 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS Z 161 " --> pdb=" O ILE Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 183 removed outlier: 3.880A pdb=" N LEU Z 181 " --> pdb=" O LEU Z 177 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN Z 182 " --> pdb=" O ARG Z 178 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR Z 183 " --> pdb=" O TYR Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 203 removed outlier: 3.704A pdb=" N SER Z 193 " --> pdb=" O THR Z 189 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE Z 198 " --> pdb=" O LEU Z 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 237 through 240 Processing helix chain 'Z' and resid 286 through 301 Processing helix chain 'Z' and resid 305 through 314 Processing helix chain 'Z' and resid 322 through 334 removed outlier: 3.824A pdb=" N VAL Z 326 " --> pdb=" O LYS Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 351 Processing helix chain 'Z' and resid 355 through 374 removed outlier: 4.594A pdb=" N ILE Z 373 " --> pdb=" O TYR Z 369 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU Z 374 " --> pdb=" O THR Z 370 " (cutoff:3.500A) Processing helix chain 'Z' and resid 378 through 393 removed outlier: 3.603A pdb=" N ARG Z 382 " --> pdb=" O THR Z 378 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE Z 383 " --> pdb=" O ASP Z 379 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS Z 386 " --> pdb=" O ARG Z 382 " (cutoff:3.500A) Processing helix chain 'Z' and resid 399 through 404 removed outlier: 3.580A pdb=" N ILE Z 404 " --> pdb=" O CYS Z 401 " (cutoff:3.500A) Processing helix chain 'Z' and resid 414 through 431 removed outlier: 3.605A pdb=" N ILE Z 418 " --> pdb=" O PRO Z 414 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU Z 426 " --> pdb=" O PHE Z 422 " (cutoff:3.500A) Processing helix chain 'Z' and resid 433 through 443 removed outlier: 3.517A pdb=" N GLN Z 437 " --> pdb=" O LEU Z 433 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 468 removed outlier: 3.515A pdb=" N ALA Z 467 " --> pdb=" O ASN Z 463 " (cutoff:3.500A) Processing helix chain 'Z' and resid 472 through 484 removed outlier: 3.799A pdb=" N GLU Z 475 " --> pdb=" O LEU Z 472 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP Z 476 " --> pdb=" O LEU Z 473 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG Z 478 " --> pdb=" O GLU Z 475 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER Z 479 " --> pdb=" O ASP Z 476 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR Z 482 " --> pdb=" O SER Z 479 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE Z 483 " --> pdb=" O ARG Z 480 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 28 Processing helix chain 'c' and resid 33 through 36 No H-bonds generated for 'chain 'c' and resid 33 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 67 through 79 removed outlier: 3.666A pdb=" N ARG c 78 " --> pdb=" O LEU c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 91 removed outlier: 3.521A pdb=" N ASP c 89 " --> pdb=" O ARG c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 106 Processing helix chain 'c' and resid 146 through 159 Processing helix chain 'c' and resid 165 through 193 Processing helix chain 'c' and resid 232 through 251 removed outlier: 3.561A pdb=" N ASN c 249 " --> pdb=" O GLU c 245 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG c 250 " --> pdb=" O ARG c 246 " (cutoff:3.500A) Processing helix chain 'c' and resid 338 through 355 Processing helix chain 'c' and resid 359 through 363 removed outlier: 3.635A pdb=" N ARG c 363 " --> pdb=" O LYS c 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 359 through 363' Processing helix chain 'c' and resid 374 through 381 removed outlier: 3.657A pdb=" N GLU c 381 " --> pdb=" O LYS c 377 " (cutoff:3.500A) Processing helix chain 'c' and resid 388 through 400 Processing helix chain 'c' and resid 426 through 437 Proline residue: c 432 - end of helix removed outlier: 3.510A pdb=" N SER c 436 " --> pdb=" O PRO c 432 " (cutoff:3.500A) Processing helix chain 'c' and resid 445 through 468 removed outlier: 3.602A pdb=" N LYS c 465 " --> pdb=" O ASN c 461 " (cutoff:3.500A) Proline residue: c 467 - end of helix Processing helix chain 'c' and resid 483 through 581 removed outlier: 3.652A pdb=" N HIS c 487 " --> pdb=" O SER c 483 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE c 488 " --> pdb=" O ARG c 484 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE c 499 " --> pdb=" O MET c 495 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS c 500 " --> pdb=" O LYS c 496 " (cutoff:3.500A) Proline residue: c 504 - end of helix removed outlier: 3.750A pdb=" N SER c 512 " --> pdb=" O VAL c 508 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER c 515 " --> pdb=" O GLU c 511 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS c 516 " --> pdb=" O SER c 512 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU c 523 " --> pdb=" O SER c 519 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU c 527 " --> pdb=" O LEU c 523 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN c 528 " --> pdb=" O GLN c 524 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS c 529 " --> pdb=" O ARG c 525 " (cutoff:3.500A) Proline residue: c 532 - end of helix removed outlier: 3.729A pdb=" N GLN c 536 " --> pdb=" O PRO c 532 " (cutoff:3.500A) Proline residue: c 550 - end of helix removed outlier: 3.860A pdb=" N ILE c 553 " --> pdb=" O LEU c 549 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN c 556 " --> pdb=" O LEU c 552 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG c 557 " --> pdb=" O ILE c 553 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER c 572 " --> pdb=" O GLN c 568 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG c 577 " --> pdb=" O LEU c 573 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS c 578 " --> pdb=" O GLU c 574 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG c 579 " --> pdb=" O GLY c 575 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU c 580 " --> pdb=" O ARG c 576 " (cutoff:3.500A) Processing helix chain 'c' and resid 583 through 586 No H-bonds generated for 'chain 'c' and resid 583 through 586' Processing helix chain 'd' and resid 40 through 60 Processing helix chain 'd' and resid 65 through 77 Processing helix chain 'd' and resid 81 through 94 removed outlier: 3.897A pdb=" N PHE d 88 " --> pdb=" O ALA d 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL d 94 " --> pdb=" O ARG d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 99 through 111 Processing helix chain 'd' and resid 115 through 128 Processing helix chain 'd' and resid 133 through 145 removed outlier: 3.542A pdb=" N TYR d 139 " --> pdb=" O LEU d 135 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL d 142 " --> pdb=" O LYS d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 161 Processing helix chain 'd' and resid 166 through 179 removed outlier: 3.563A pdb=" N GLU d 176 " --> pdb=" O PHE d 172 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG d 178 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 195 removed outlier: 3.557A pdb=" N GLU d 187 " --> pdb=" O ASN d 183 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET d 194 " --> pdb=" O SER d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 212 removed outlier: 3.598A pdb=" N LYS d 204 " --> pdb=" O GLN d 200 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS d 212 " --> pdb=" O PHE d 208 " (cutoff:3.500A) Processing helix chain 'd' and resid 215 through 231 removed outlier: 3.826A pdb=" N SER d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL d 229 " --> pdb=" O ALA d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 240 through 256 removed outlier: 3.693A pdb=" N LYS d 245 " --> pdb=" O MET d 241 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU d 246 " --> pdb=" O GLU d 242 " (cutoff:3.500A) Processing helix chain 'd' and resid 260 through 273 removed outlier: 4.050A pdb=" N TYR d 267 " --> pdb=" O SER d 263 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN d 268 " --> pdb=" O SER d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 278 through 291 removed outlier: 3.591A pdb=" N ASP d 286 " --> pdb=" O ALA d 282 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE d 287 " --> pdb=" O GLY d 283 " (cutoff:3.500A) Processing helix chain 'd' and resid 294 through 315 removed outlier: 3.995A pdb=" N TYR d 303 " --> pdb=" O GLU d 299 " (cutoff:3.500A) Processing helix chain 'd' and resid 320 through 333 removed outlier: 3.785A pdb=" N LEU d 325 " --> pdb=" O ASP d 321 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP d 328 " --> pdb=" O TRP d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 337 through 349 removed outlier: 3.755A pdb=" N GLU d 343 " --> pdb=" O MET d 339 " (cutoff:3.500A) Processing helix chain 'd' and resid 354 through 369 removed outlier: 4.134A pdb=" N VAL d 358 " --> pdb=" O LEU d 354 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLN d 359 " --> pdb=" O SER d 355 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP d 360 " --> pdb=" O LYS d 356 " (cutoff:3.500A) Processing helix chain 'd' and resid 375 through 385 removed outlier: 5.182A pdb=" N GLU d 385 " --> pdb=" O SER d 381 " (cutoff:3.500A) Processing helix chain 'd' and resid 389 through 397 Proline residue: d 397 - end of helix Processing helix chain 'd' and resid 406 through 417 removed outlier: 3.688A pdb=" N LYS d 412 " --> pdb=" O LEU d 408 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE d 413 " --> pdb=" O MET d 409 " (cutoff:3.500A) Processing helix chain 'd' and resid 425 through 438 removed outlier: 3.549A pdb=" N LEU d 433 " --> pdb=" O LYS d 429 " (cutoff:3.500A) Proline residue: d 435 - end of helix Processing helix chain 'd' and resid 447 through 459 removed outlier: 3.975A pdb=" N GLU d 452 " --> pdb=" O VAL d 448 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE d 453 " --> pdb=" O LYS d 449 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS d 458 " --> pdb=" O ASP d 454 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE d 459 " --> pdb=" O ARG d 455 " (cutoff:3.500A) Processing helix chain 'd' and resid 463 through 474 Proline residue: d 468 - end of helix Processing helix chain 'd' and resid 481 through 493 removed outlier: 3.638A pdb=" N GLY d 485 " --> pdb=" O GLU d 481 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG d 489 " --> pdb=" O GLY d 485 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE d 493 " --> pdb=" O ARG d 489 " (cutoff:3.500A) Processing helix chain 'd' and resid 498 through 511 removed outlier: 4.068A pdb=" N ASP d 503 " --> pdb=" O ASP d 499 " (cutoff:3.500A) Processing helix chain 'd' and resid 515 through 522 Processing helix chain 'd' and resid 532 through 547 removed outlier: 4.006A pdb=" N LEU d 538 " --> pdb=" O TYR d 534 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU d 540 " --> pdb=" O ARG d 536 " (cutoff:3.500A) Proline residue: d 545 - end of helix Processing helix chain 'd' and resid 555 through 570 Proline residue: d 559 - end of helix removed outlier: 3.567A pdb=" N GLN d 562 " --> pdb=" O THR d 558 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU d 570 " --> pdb=" O ASP d 566 " (cutoff:3.500A) Processing helix chain 'd' and resid 576 through 589 removed outlier: 4.029A pdb=" N ASN d 587 " --> pdb=" O ILE d 583 " (cutoff:3.500A) Processing helix chain 'd' and resid 597 through 614 Processing helix chain 'd' and resid 621 through 635 Processing helix chain 'I' and resid 97 through 122 removed outlier: 3.618A pdb=" N LYS I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN I 122 " --> pdb=" O ASN I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 188 removed outlier: 3.776A pdb=" N GLN I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR I 188 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 210 removed outlier: 3.540A pdb=" N SER I 208 " --> pdb=" O ASN I 204 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 61 removed outlier: 3.769A pdb=" N LYS n 61 " --> pdb=" O LYS n 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 65 removed outlier: 3.651A pdb=" N GLU H 49 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU H 57 " --> pdb=" O GLN H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 95 Processing helix chain 'v' and resid 48 through 51 No H-bonds generated for 'chain 'v' and resid 48 through 51' Processing helix chain 'v' and resid 58 through 67 removed outlier: 3.656A pdb=" N GLN v 67 " --> pdb=" O ARG v 63 " (cutoff:3.500A) Processing helix chain 'v' and resid 72 through 83 Processing helix chain 'v' and resid 88 through 100 removed outlier: 3.585A pdb=" N ARG v 92 " --> pdb=" O GLU v 89 " (cutoff:3.500A) Processing helix chain 'v' and resid 106 through 117 Processing helix chain 'v' and resid 122 through 131 Processing helix chain 'v' and resid 137 through 149 removed outlier: 3.738A pdb=" N TRP v 148 " --> pdb=" O HIS v 144 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP v 149 " --> pdb=" O ARG v 145 " (cutoff:3.500A) Processing helix chain 'v' and resid 154 through 163 removed outlier: 3.702A pdb=" N LYS v 158 " --> pdb=" O PHE v 154 " (cutoff:3.500A) Proline residue: v 161 - end of helix Processing helix chain 'v' and resid 168 through 182 Processing helix chain 'v' and resid 186 through 198 Processing helix chain 'v' and resid 202 through 214 removed outlier: 3.671A pdb=" N ILE v 214 " --> pdb=" O TRP v 210 " (cutoff:3.500A) Processing helix chain 'v' and resid 219 through 230 Proline residue: v 223 - end of helix Processing helix chain 'v' and resid 236 through 247 Processing helix chain 'v' and resid 251 through 263 Proline residue: v 262 - end of helix Processing helix chain 'v' and resid 267 through 279 Processing helix chain 'v' and resid 283 through 294 Processing helix chain 'v' and resid 304 through 315 Processing helix chain 'v' and resid 319 through 331 Processing helix chain 'v' and resid 337 through 346 removed outlier: 3.664A pdb=" N ILE v 342 " --> pdb=" O ASP v 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN v 344 " --> pdb=" O ASP v 340 " (cutoff:3.500A) Processing helix chain 'v' and resid 350 through 365 removed outlier: 4.584A pdb=" N ASP v 365 " --> pdb=" O LEU v 361 " (cutoff:3.500A) Processing helix chain 'v' and resid 370 through 381 removed outlier: 3.614A pdb=" N TRP v 374 " --> pdb=" O ASN v 370 " (cutoff:3.500A) Processing helix chain 'v' and resid 386 through 398 removed outlier: 3.551A pdb=" N ASP v 393 " --> pdb=" O ILE v 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN v 397 " --> pdb=" O ASP v 393 " (cutoff:3.500A) Processing helix chain 'v' and resid 405 through 413 Processing helix chain 'v' and resid 420 through 434 removed outlier: 3.828A pdb=" N CYS v 425 " --> pdb=" O ALA v 421 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER v 429 " --> pdb=" O CYS v 425 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU v 430 " --> pdb=" O ASN v 426 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU v 433 " --> pdb=" O SER v 429 " (cutoff:3.500A) Processing helix chain 'v' and resid 445 through 458 removed outlier: 3.521A pdb=" N TRP v 450 " --> pdb=" O PHE v 446 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR v 457 " --> pdb=" O TYR v 453 " (cutoff:3.500A) Processing helix chain 'v' and resid 463 through 474 removed outlier: 3.602A pdb=" N ARG v 467 " --> pdb=" O ILE v 463 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU v 468 " --> pdb=" O SER v 464 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU v 469 " --> pdb=" O THR v 465 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER v 473 " --> pdb=" O LEU v 469 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU v 474 " --> pdb=" O TRP v 470 " (cutoff:3.500A) Processing helix chain 'v' and resid 482 through 498 removed outlier: 3.602A pdb=" N GLU v 486 " --> pdb=" O GLU v 482 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE v 487 " --> pdb=" O ASP v 483 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR v 488 " --> pdb=" O LEU v 484 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU v 495 " --> pdb=" O TRP v 491 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP v 497 " --> pdb=" O ASP v 493 " (cutoff:3.500A) Processing helix chain 'v' and resid 501 through 511 removed outlier: 3.536A pdb=" N LEU v 508 " --> pdb=" O ALA v 504 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP v 510 " --> pdb=" O SER v 506 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA v 511 " --> pdb=" O ILE v 507 " (cutoff:3.500A) Processing helix chain 'v' and resid 518 through 527 Processing helix chain 'v' and resid 538 through 540 No H-bonds generated for 'chain 'v' and resid 538 through 540' Processing helix chain 'v' and resid 542 through 555 Processing helix chain 'v' and resid 565 through 580 removed outlier: 3.533A pdb=" N VAL v 577 " --> pdb=" O ALA v 573 " (cutoff:3.500A) Processing helix chain 'v' and resid 585 through 597 Processing helix chain 'v' and resid 601 through 614 removed outlier: 4.302A pdb=" N GLN v 606 " --> pdb=" O MET v 602 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR v 611 " --> pdb=" O VAL v 607 " (cutoff:3.500A) Proline residue: v 613 - end of helix Processing helix chain 'v' and resid 620 through 633 removed outlier: 3.704A pdb=" N GLU v 626 " --> pdb=" O GLU v 622 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL v 630 " --> pdb=" O GLU v 626 " (cutoff:3.500A) Processing helix chain 'v' and resid 641 through 658 removed outlier: 3.927A pdb=" N LYS v 653 " --> pdb=" O GLU v 649 " (cutoff:3.500A) Processing helix chain 'v' and resid 663 through 676 removed outlier: 3.519A pdb=" N ILE v 667 " --> pdb=" O LYS v 663 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU v 673 " --> pdb=" O TYR v 669 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU v 674 " --> pdb=" O SER v 670 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG v 675 " --> pdb=" O VAL v 671 " (cutoff:3.500A) Processing helix chain 'v' and resid 682 through 690 removed outlier: 3.826A pdb=" N ARG v 688 " --> pdb=" O ILE v 684 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG v 689 " --> pdb=" O GLU v 685 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY v 690 " --> pdb=" O ILE v 686 " (cutoff:3.500A) Processing helix chain 'v' and resid 706 through 714 removed outlier: 4.333A pdb=" N CYS v 712 " --> pdb=" O LEU v 708 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE v 713 " --> pdb=" O TRP v 709 " (cutoff:3.500A) Processing helix chain 'v' and resid 716 through 720 removed outlier: 3.501A pdb=" N LEU v 720 " --> pdb=" O ALA v 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 716 through 720' Processing helix chain 'v' and resid 722 through 733 removed outlier: 4.101A pdb=" N GLU v 727 " --> pdb=" O SER v 723 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU v 728 " --> pdb=" O VAL v 724 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE v 733 " --> pdb=" O TYR v 729 " (cutoff:3.500A) Processing helix chain 'v' and resid 741 through 755 Processing helix chain 'v' and resid 762 through 772 Processing helix chain 'v' and resid 780 through 792 Processing helix chain 'v' and resid 800 through 818 Processing helix chain 'a' and resid 41 through 52 Processing helix chain 'a' and resid 79 through 88 Processing helix chain 'b' and resid 5 through 10 Processing helix chain 'b' and resid 43 through 45 No H-bonds generated for 'chain 'b' and resid 43 through 45' Processing helix chain 'b' and resid 110 through 117 removed outlier: 3.687A pdb=" N LEU b 117 " --> pdb=" O ASP b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 136 No H-bonds generated for 'chain 'b' and resid 133 through 136' Processing helix chain 'b' and resid 140 through 148 Processing helix chain 'b' and resid 161 through 171 Proline residue: b 171 - end of helix Processing helix chain 't' and resid 14 through 31 Processing helix chain 't' and resid 53 through 64 Processing helix chain 't' and resid 73 through 76 No H-bonds generated for 'chain 't' and resid 73 through 76' Processing helix chain 't' and resid 83 through 109 Proline residue: t 96 - end of helix Proline residue: t 105 - end of helix Processing helix chain 't' and resid 111 through 174 removed outlier: 3.734A pdb=" N ILE t 116 " --> pdb=" O LEU t 113 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL t 117 " --> pdb=" O LEU t 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS t 122 " --> pdb=" O SER t 119 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS t 123 " --> pdb=" O TYR t 120 " (cutoff:3.500A) Proline residue: t 133 - end of helix removed outlier: 3.529A pdb=" N SER t 137 " --> pdb=" O GLN t 134 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN t 139 " --> pdb=" O VAL t 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP t 140 " --> pdb=" O SER t 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE t 142 " --> pdb=" O GLN t 139 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP t 145 " --> pdb=" O ILE t 142 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE t 147 " --> pdb=" O ASN t 144 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG t 148 " --> pdb=" O ASP t 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS t 151 " --> pdb=" O ARG t 148 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU t 156 " --> pdb=" O ILE t 153 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE t 159 " --> pdb=" O GLU t 156 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS t 163 " --> pdb=" O GLN t 160 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU t 168 " --> pdb=" O ILE t 165 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR t 171 " --> pdb=" O LEU t 168 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG t 172 " --> pdb=" O GLU t 169 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG t 174 " --> pdb=" O TYR t 171 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 22 Processing helix chain 'u' and resid 84 through 86 No H-bonds generated for 'chain 'u' and resid 84 through 86' Processing helix chain 'm' and resid 3 through 10 removed outlier: 3.619A pdb=" N LYS m 8 " --> pdb=" O ASN m 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 68 removed outlier: 3.625A pdb=" N ALA m 63 " --> pdb=" O GLY m 59 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR m 68 " --> pdb=" O SER m 64 " (cutoff:3.500A) Processing helix chain 'm' and resid 89 through 91 No H-bonds generated for 'chain 'm' and resid 89 through 91' Processing helix chain 'm' and resid 103 through 106 No H-bonds generated for 'chain 'm' and resid 103 through 106' Processing helix chain 'm' and resid 110 through 118 Processing helix chain 'j' and resid 65 through 67 No H-bonds generated for 'chain 'j' and resid 65 through 67' Processing helix chain 'h' and resid 15 through 21 Processing helix chain 'h' and resid 75 through 77 No H-bonds generated for 'chain 'h' and resid 75 through 77' Processing helix chain 'g' and resid 15 through 27 removed outlier: 3.641A pdb=" N GLU g 19 " --> pdb=" O ARG g 15 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 40 Processing helix chain 'k' and resid 55 through 60 removed outlier: 4.471A pdb=" N ASP k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LYS k 60 " --> pdb=" O THR k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 55 through 60' Processing helix chain 'k' and resid 105 through 108 No H-bonds generated for 'chain 'k' and resid 105 through 108' Processing helix chain 'e' and resid 15 through 27 removed outlier: 3.643A pdb=" N GLU e 19 " --> pdb=" O ARG e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 39 removed outlier: 3.993A pdb=" N ASP e 36 " --> pdb=" O LEU e 33 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL e 39 " --> pdb=" O ASP e 36 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 61 Processing helix chain 'l' and resid 6 through 14 Processing helix chain 'l' and resid 66 through 68 No H-bonds generated for 'chain 'l' and resid 66 through 68' Processing helix chain 'l' and resid 76 through 80 Processing helix chain 'l' and resid 82 through 84 No H-bonds generated for 'chain 'l' and resid 82 through 84' Processing helix chain 'i' and resid 13 through 22 Processing helix chain 'w' and resid 15 through 21 Processing helix chain 'w' and resid 75 through 77 No H-bonds generated for 'chain 'w' and resid 75 through 77' Processing helix chain 'x' and resid 65 through 67 No H-bonds generated for 'chain 'x' and resid 65 through 67' Processing helix chain 'y' and resid 6 through 14 Processing helix chain 'y' and resid 66 through 68 No H-bonds generated for 'chain 'y' and resid 66 through 68' Processing helix chain 'y' and resid 76 through 80 removed outlier: 3.970A pdb=" N ASN y 80 " --> pdb=" O LEU y 77 " (cutoff:3.500A) Processing helix chain 'y' and resid 82 through 84 No H-bonds generated for 'chain 'y' and resid 82 through 84' Processing helix chain 'z' and resid 3 through 9 removed outlier: 3.612A pdb=" N LYS z 8 " --> pdb=" O ASN z 5 " (cutoff:3.500A) Processing helix chain 'z' and resid 59 through 68 removed outlier: 3.624A pdb=" N ALA z 63 " --> pdb=" O GLY z 59 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR z 68 " --> pdb=" O SER z 64 " (cutoff:3.500A) Processing helix chain 'z' and resid 89 through 91 No H-bonds generated for 'chain 'z' and resid 89 through 91' Processing helix chain 'z' and resid 103 through 106 No H-bonds generated for 'chain 'z' and resid 103 through 106' Processing helix chain 'r' and resid 25 through 34 Processing helix chain 'r' and resid 78 through 138 removed outlier: 3.663A pdb=" N THR r 82 " --> pdb=" O PRO r 78 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU r 98 " --> pdb=" O GLU r 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU r 102 " --> pdb=" O LEU r 98 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU r 121 " --> pdb=" O ASP r 117 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA r 124 " --> pdb=" O LYS r 120 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN r 125 " --> pdb=" O LEU r 121 " (cutoff:3.500A) Proline residue: r 138 - end of helix Processing helix chain 'p' and resid 25 through 34 Processing helix chain 'p' and resid 82 through 141 removed outlier: 3.503A pdb=" N SER p 104 " --> pdb=" O SER p 100 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR p 106 " --> pdb=" O LEU p 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU p 115 " --> pdb=" O THR p 111 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET p 128 " --> pdb=" O ALA p 124 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN p 131 " --> pdb=" O LEU p 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU p 132 " --> pdb=" O MET p 128 " (cutoff:3.500A) Proline residue: p 138 - end of helix removed outlier: 3.769A pdb=" N SER p 141 " --> pdb=" O LEU p 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 34 Processing helix chain 'q' and resid 78 through 142 removed outlier: 3.536A pdb=" N ALA q 90 " --> pdb=" O ASN q 86 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU q 105 " --> pdb=" O THR q 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL q 122 " --> pdb=" O ALA q 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA q 123 " --> pdb=" O ALA q 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET q 128 " --> pdb=" O ALA q 124 " (cutoff:3.500A) Proline residue: q 138 - end of helix Processing helix chain 'o' and resid 25 through 34 removed outlier: 3.707A pdb=" N GLN o 30 " --> pdb=" O SER o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 78 through 139 removed outlier: 3.512A pdb=" N LEU o 93 " --> pdb=" O ASP o 89 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU o 98 " --> pdb=" O GLU o 94 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR o 101 " --> pdb=" O LYS o 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER o 104 " --> pdb=" O SER o 100 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS o 107 " --> pdb=" O ASP o 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU o 121 " --> pdb=" O ASP o 117 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL o 122 " --> pdb=" O ALA o 118 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET o 128 " --> pdb=" O ALA o 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN o 131 " --> pdb=" O LEU o 127 " (cutoff:3.500A) Proline residue: o 138 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 557 through 563 Processing sheet with id= B, first strand: chain 'A' and resid 591 through 593 Processing sheet with id= C, first strand: chain 'A' and resid 968 through 973 Processing sheet with id= D, first strand: chain 'A' and resid 1246 through 1251 removed outlier: 3.570A pdb=" N THR A1052 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1160 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1089 through 1091 Processing sheet with id= F, first strand: chain 'A' and resid 1257 through 1261 removed outlier: 6.893A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1573 through 1575 removed outlier: 3.525A pdb=" N PHE A1574 " --> pdb=" O TYR A1826 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1826 " --> pdb=" O PHE A1574 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 1624 through 1626 Processing sheet with id= I, first strand: chain 'A' and resid 1783 through 1788 removed outlier: 3.525A pdb=" N ILE A1701 " --> pdb=" O PHE A1734 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A1680 " --> pdb=" O GLU A1704 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1709 through 1711 removed outlier: 3.769A pdb=" N LEU A1727 " --> pdb=" O VAL A1711 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1849 through 1852 removed outlier: 7.379A pdb=" N GLN A1932 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N VAL A1852 " --> pdb=" O GLN A1932 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE A1934 " --> pdb=" O VAL A1852 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 1877 through 1882 removed outlier: 3.629A pdb=" N PHE A1989 " --> pdb=" O LEU A1889 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 320 through 322 removed outlier: 3.583A pdb=" N PHE C 320 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN C 194 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.777A pdb=" N ASN C 358 " --> pdb=" O HIS C 355 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 536 through 538 removed outlier: 6.348A pdb=" N HIS C 471 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE C 488 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ILE C 561 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU C 545 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 541 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 474 through 477 Processing sheet with id= Q, first strand: chain 'C' and resid 668 through 670 Processing sheet with id= R, first strand: chain 'C' and resid 677 through 681 Processing sheet with id= S, first strand: chain 'C' and resid 727 through 729 Processing sheet with id= T, first strand: chain 'C' and resid 773 through 776 removed outlier: 6.311A pdb=" N SER C 709 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 926 through 931 removed outlier: 6.999A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 154 through 157 removed outlier: 3.513A pdb=" N THR O 176 " --> pdb=" O VAL O 166 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP O 168 " --> pdb=" O LEU O 174 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU O 174 " --> pdb=" O ASP O 168 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 215 through 217 removed outlier: 3.688A pdb=" N GLN O 215 " --> pdb=" O ASP O 210 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP O 187 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 227 through 232 removed outlier: 6.817A pdb=" N ALA O 242 " --> pdb=" O ARG O 228 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL O 230 " --> pdb=" O ALA O 240 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA O 240 " --> pdb=" O VAL O 230 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE O 232 " --> pdb=" O LEU O 238 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU O 238 " --> pdb=" O ILE O 232 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY O 243 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL O 247 " --> pdb=" O GLY O 243 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP O 252 " --> pdb=" O PRO O 258 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 269 through 274 removed outlier: 6.869A pdb=" N SER O 284 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL O 272 " --> pdb=" O VAL O 282 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL O 282 " --> pdb=" O VAL O 272 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL O 281 " --> pdb=" O TRP O 293 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASP O 294 " --> pdb=" O THR O 300 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR O 300 " --> pdb=" O ASP O 294 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 313 through 316 removed outlier: 3.643A pdb=" N ALA O 313 " --> pdb=" O ALA O 326 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR O 343 " --> pdb=" O SER O 333 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY O 335 " --> pdb=" O LEU O 341 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU O 341 " --> pdb=" O GLY O 335 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 353 through 358 removed outlier: 6.700A pdb=" N GLY O 367 " --> pdb=" O ASN O 354 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU O 356 " --> pdb=" O PHE O 365 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE O 365 " --> pdb=" O LEU O 356 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE O 358 " --> pdb=" O VAL O 363 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL O 363 " --> pdb=" O ILE O 358 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN O 385 " --> pdb=" O PHE O 375 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP O 377 " --> pdb=" O LYS O 383 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS O 383 " --> pdb=" O ASP O 377 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 129 through 136 removed outlier: 6.743A pdb=" N ILE O 425 " --> pdb=" O SER O 132 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL O 134 " --> pdb=" O ILE O 423 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE O 423 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER O 422 " --> pdb=" O GLU O 418 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'P' and resid 103 through 105 Processing sheet with id= AD, first strand: chain 'Q' and resid 26 through 28 Processing sheet with id= AE, first strand: chain 'Q' and resid 279 through 281 removed outlier: 3.646A pdb=" N GLY Q 279 " --> pdb=" O ILE Q 290 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 222 through 225 Processing sheet with id= AG, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= AH, first strand: chain 'n' and resid 168 through 170 removed outlier: 3.542A pdb=" N ARG n 200 " --> pdb=" O ILE n 189 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP n 191 " --> pdb=" O CYS n 198 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS n 198 " --> pdb=" O ASP n 191 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'n' and resid 230 through 234 Processing sheet with id= AJ, first strand: chain 'n' and resid 287 through 289 removed outlier: 4.306A pdb=" N GLU n 262 " --> pdb=" O PRO n 257 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'n' and resid 296 through 301 removed outlier: 6.839A pdb=" N SER n 311 " --> pdb=" O LEU n 297 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU n 299 " --> pdb=" O ILE n 309 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE n 309 " --> pdb=" O LEU n 299 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE n 308 " --> pdb=" O TRP n 320 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU n 321 " --> pdb=" O PRO n 327 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'n' and resid 341 through 344 removed outlier: 4.074A pdb=" N PHE n 341 " --> pdb=" O SER n 355 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'n' and resid 381 through 383 removed outlier: 3.648A pdb=" N TRP n 410 " --> pdb=" O SER n 400 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP n 402 " --> pdb=" O PHE n 408 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE n 408 " --> pdb=" O ASP n 402 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'n' and resid 153 through 158 removed outlier: 6.934A pdb=" N VAL n 453 " --> pdb=" O ILE n 155 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN n 157 " --> pdb=" O ILE n 451 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE n 451 " --> pdb=" O ASN n 157 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'a' and resid 30 through 32 removed outlier: 3.847A pdb=" N ALA a 72 " --> pdb=" O VAL a 32 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'a' and resid 92 through 94 removed outlier: 3.921A pdb=" N GLU a 92 " --> pdb=" O LEU a 99 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS a 97 " --> pdb=" O PHE a 94 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'b' and resid 126 through 128 removed outlier: 3.556A pdb=" N LEU b 79 " --> pdb=" O ASN b 100 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS b 55 " --> pdb=" O HIS b 77 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU b 79 " --> pdb=" O HIS b 55 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU b 57 " --> pdb=" O LEU b 79 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'u' and resid 58 through 61 removed outlier: 6.824A pdb=" N ILE u 37 " --> pdb=" O LEU u 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU u 31 " --> pdb=" O ILE u 37 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'u' and resid 80 through 82 removed outlier: 3.977A pdb=" N GLY u 45 " --> pdb=" O VAL u 53 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP u 55 " --> pdb=" O ILE u 43 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE u 43 " --> pdb=" O ASP u 55 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'm' and resid 79 through 83 removed outlier: 4.693A pdb=" N ASP m 42 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR m 28 " --> pdb=" O ASP m 42 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR m 23 " --> pdb=" O LEU m 19 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'j' and resid 44 through 46 removed outlier: 4.775A pdb=" N LYS j 24 " --> pdb=" O ILE j 46 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG j 23 " --> pdb=" O ILE j 19 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER j 70 " --> pdb=" O ASN j 18 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'j' and resid 60 through 63 removed outlier: 6.399A pdb=" N ASP j 41 " --> pdb=" O LEU j 29 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU j 29 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'h' and resid 66 through 68 Processing sheet with id= AX, first strand: chain 'h' and resid 51 through 54 Processing sheet with id= AY, first strand: chain 'g' and resid 84 through 91 removed outlier: 3.557A pdb=" N VAL g 44 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL g 103 " --> pdb=" O SER g 47 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 93 through 96 removed outlier: 6.582A pdb=" N GLU g 70 " --> pdb=" O VAL g 58 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL g 58 " --> pdb=" O GLU g 70 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'k' and resid 77 through 83 removed outlier: 3.709A pdb=" N ARG k 80 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS k 48 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU k 47 " --> pdb=" O GLN k 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN k 33 " --> pdb=" O GLU k 47 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG k 28 " --> pdb=" O THR k 24 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'e' and resid 84 through 90 removed outlier: 3.673A pdb=" N VAL e 103 " --> pdb=" O SER e 47 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'e' and resid 93 through 96 removed outlier: 6.743A pdb=" N GLU e 70 " --> pdb=" O VAL e 58 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL e 58 " --> pdb=" O GLU e 70 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 's' and resid 77 through 83 removed outlier: 5.065A pdb=" N GLU s 47 " --> pdb=" O GLN s 33 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN s 33 " --> pdb=" O GLU s 47 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'l' and resid 56 through 59 removed outlier: 3.562A pdb=" N PHE l 71 " --> pdb=" O GLU l 22 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'l' and resid 61 through 64 removed outlier: 6.241A pdb=" N ARG l 45 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU l 33 " --> pdb=" O ARG l 45 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'i' and resid 89 through 91 Processing sheet with id= BH, first strand: chain 'i' and resid 80 through 82 removed outlier: 3.977A pdb=" N GLY i 45 " --> pdb=" O VAL i 53 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP i 55 " --> pdb=" O ILE i 43 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE i 43 " --> pdb=" O ASP i 55 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'w' and resid 66 through 68 Processing sheet with id= BJ, first strand: chain 'w' and resid 51 through 54 Processing sheet with id= BK, first strand: chain 'x' and resid 71 through 73 removed outlier: 6.709A pdb=" N VAL x 39 " --> pdb=" O ARG x 30 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'y' and resid 56 through 59 removed outlier: 3.580A pdb=" N PHE y 71 " --> pdb=" O GLU y 22 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'y' and resid 61 through 63 removed outlier: 6.104A pdb=" N ARG y 45 " --> pdb=" O LEU y 33 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU y 33 " --> pdb=" O ARG y 45 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'z' and resid 79 through 83 removed outlier: 4.693A pdb=" N ASP z 42 " --> pdb=" O THR z 28 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR z 28 " --> pdb=" O ASP z 42 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR z 23 " --> pdb=" O LEU z 19 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'r' and resid 13 through 16 removed outlier: 4.413A pdb=" N THR r 21 " --> pdb=" O SER r 16 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'p' and resid 13 through 15 Processing sheet with id= BQ, first strand: chain 'q' and resid 13 through 15 Processing sheet with id= BR, first strand: chain 'o' and resid 13 through 15 2906 hydrogen bonds defined for protein. 8076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 325 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 306 stacking parallelities Total time for adding SS restraints: 48.57 Time building geometry restraints manager: 28.42 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: 17759 1.33 - 1.45: 19498 1.45 - 1.57: 42731 1.57 - 1.70: 1096 1.70 - 1.82: 395 Bond restraints: 81479 Sorted by residual: bond pdb=" O3' G L1120 " pdb=" P U L1121 " ideal model delta sigma weight residual 1.607 1.541 0.066 1.50e-02 4.44e+03 1.96e+01 bond pdb=" N ASP H 67 " pdb=" CA ASP H 67 " ideal model delta sigma weight residual 1.453 1.494 -0.040 9.20e-03 1.18e+04 1.91e+01 bond pdb=" N VAL k 53 " pdb=" CA VAL k 53 " ideal model delta sigma weight residual 1.460 1.491 -0.030 7.60e-03 1.73e+04 1.60e+01 bond pdb=" N VAL H 38 " pdb=" CA VAL H 38 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.06e-02 8.90e+03 1.46e+01 bond pdb=" C5 IHP A3000 " pdb=" O15 IHP A3000 " ideal model delta sigma weight residual 1.389 1.464 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 81474 not shown) Histogram of bond angle deviations from ideal: 96.17 - 104.12: 2882 104.12 - 112.07: 41524 112.07 - 120.02: 34010 120.02 - 127.97: 33142 127.97 - 135.92: 1323 Bond angle restraints: 112881 Sorted by residual: angle pdb=" C MET b 43 " pdb=" N PRO b 44 " pdb=" CA PRO b 44 " ideal model delta sigma weight residual 119.28 128.71 -9.43 1.10e+00 8.26e-01 7.35e+01 angle pdb=" C THR b 4 " pdb=" N PRO b 5 " pdb=" CA PRO b 5 " ideal model delta sigma weight residual 118.85 127.43 -8.58 1.09e+00 8.42e-01 6.20e+01 angle pdb=" C4' U D 96 " pdb=" C3' U D 96 " pdb=" O3' U D 96 " ideal model delta sigma weight residual 113.00 101.40 11.60 1.50e+00 4.44e-01 5.98e+01 angle pdb=" N SER v 681 " pdb=" CA SER v 681 " pdb=" C SER v 681 " ideal model delta sigma weight residual 113.16 105.07 8.09 1.24e+00 6.50e-01 4.25e+01 angle pdb=" C ALA b 11 " pdb=" N PRO b 12 " pdb=" CA PRO b 12 " ideal model delta sigma weight residual 119.84 127.94 -8.10 1.25e+00 6.40e-01 4.20e+01 ... (remaining 112876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 48201 35.87 - 71.74: 1811 71.74 - 107.61: 190 107.61 - 143.48: 25 143.48 - 179.35: 11 Dihedral angle restraints: 50238 sinusoidal: 23950 harmonic: 26288 Sorted by residual: dihedral pdb=" O4' C D 164 " pdb=" C1' C D 164 " pdb=" N1 C D 164 " pdb=" C2 C D 164 " ideal model delta sinusoidal sigma weight residual -128.00 49.72 -177.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U E 89 " pdb=" C1' U E 89 " pdb=" N1 U E 89 " pdb=" C2 U E 89 " ideal model delta sinusoidal sigma weight residual -128.00 46.92 -174.92 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C D 79 " pdb=" C1' C D 79 " pdb=" N1 C D 79 " pdb=" C2 C D 79 " ideal model delta sinusoidal sigma weight residual 200.00 76.88 123.12 1 1.50e+01 4.44e-03 6.60e+01 ... (remaining 50235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 13460 1.032 - 2.065: 0 2.065 - 3.097: 0 3.097 - 4.129: 0 4.129 - 5.162: 2 Chirality restraints: 13462 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.64 -5.16 2.00e-01 2.50e+01 6.66e+02 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 2.62 -4.96 2.00e-01 2.50e+01 6.15e+02 chirality pdb=" C3' C D 95 " pdb=" C4' C D 95 " pdb=" O3' C D 95 " pdb=" C2' C D 95 " both_signs ideal model delta sigma weight residual False -2.74 -2.27 -0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 13459 not shown) Planarity restraints: 12409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 34 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.67e+01 pdb=" N PRO H 35 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO H 35 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO H 35 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR g 42 " -0.084 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO g 43 " 0.223 5.00e-02 4.00e+02 pdb=" CA PRO g 43 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO g 43 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA c 222 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO c 223 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO c 223 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO c 223 " 0.064 5.00e-02 4.00e+02 ... (remaining 12406 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 379 2.50 - 3.10: 53509 3.10 - 3.70: 125351 3.70 - 4.30: 179320 4.30 - 4.90: 279540 Nonbonded interactions: 638099 Sorted by model distance: nonbonded pdb=" O2' U L1154 " pdb=" C5' C L1155 " model vdw 1.903 3.440 nonbonded pdb=" O ASN R 147 " pdb=" OG SER R 148 " model vdw 2.040 2.440 nonbonded pdb=" O2' A E 49 " pdb=" OP1 G E 50 " model vdw 2.072 2.440 nonbonded pdb=" O2B GTP C1500 " pdb="MG MG C1501 " model vdw 2.078 2.170 nonbonded pdb=" OP1 G E 78 " pdb="MG MG E 200 " model vdw 2.095 2.170 ... (remaining 638094 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 'e' selection = chain 'g' } ncs_group { reference = chain 'h' selection = chain 'w' } ncs_group { reference = (chain 'i' and (resid 10 through 31 or (resid 32 through 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 37 or (resid 38 and (na \ me N or name CA or name C or name O or name CB )) or resid 39 through 53 or (res \ id 54 through 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 through 92)) selection = chain 'u' } ncs_group { reference = chain 'j' selection = chain 'x' } ncs_group { reference = (chain 'k' and resid 3 through 102) selection = chain 's' } ncs_group { reference = (chain 'l' and (resid 5 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 36 or (resid 37 and (nam \ e N or name CA or name C or name O or name CB )) or resid 38 through 85)) selection = chain 'y' } ncs_group { reference = (chain 'm' and resid 1 through 108) selection = chain 'z' } ncs_group { reference = (chain 'o' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 or resid \ 65 through 139)) selection = (chain 'p' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 or resid \ 65 through 139)) selection = (chain 'q' and (resid 1 through 52 or resid 57 through 58 or (resid 59 through 6 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 61 or (resid \ 76 and (name N or name CA or name C or name O or name CB )) or resid 77 through \ 139)) selection = (chain 'r' and (resid 1 through 52 or resid 57 through 61 or resid 65 through 13 \ 9)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 16.390 Check model and map are aligned: 1.020 Set scattering table: 0.660 Process input model: 209.460 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.470 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: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 235.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 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 : 0.007 0.092 81479 Z= 0.426 Angle : 0.937 11.621 112881 Z= 0.578 Chirality : 0.085 5.162 13462 Planarity : 0.007 0.129 12409 Dihedral : 17.092 179.347 33050 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.59 % Favored : 94.90 % Rotamer: Outliers : 3.03 % Allowed : 5.25 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.07), residues: 8730 helix: -2.91 (0.06), residues: 3932 sheet: -0.45 (0.15), residues: 1054 loop : -1.82 (0.09), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP d 205 HIS 0.019 0.002 HIS A2038 PHE 0.057 0.003 PHE R 72 TYR 0.068 0.003 TYR d 105 ARG 0.017 0.001 ARG A 851 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17460 Ramachandran restraints generated. 8730 Oldfield, 0 Emsley, 8730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 8148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1311 time to evaluate : 6.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable