Starting phenix.real_space_refine (version: dev) on Thu Feb 23 03:28:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh0_30677/02_2023/7dh0_30677_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh0_30677/02_2023/7dh0_30677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh0_30677/02_2023/7dh0_30677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh0_30677/02_2023/7dh0_30677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh0_30677/02_2023/7dh0_30677_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dh0_30677/02_2023/7dh0_30677_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.016 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 Process input model Symmetric amino acids flipped Residue "2 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 199": "NH1" <-> "NH2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "O ARG 77": "NH1" <-> "NH2" Residue "R PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 355": "NH1" <-> "NH2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "U PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 60": "NH1" <-> "NH2" Residue "1 ARG 195": "NH1" <-> "NH2" Residue "1 ARG 274": "NH1" <-> "NH2" Residue "6 TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 86": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 60091 Number of models: 1 Model: "" Number of chains: 57 Chain: "2" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2582 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 321} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "3" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 719 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 3447 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3439 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 434} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 97 Conformer: "B" Number of residues, atoms: 458, 3439 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'CIS': 3, 'PTRANS': 20, 'TRANS': 434} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 97 bond proxies already assigned to first conformer: 3516 Chain: "5" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 697 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 92} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1186 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 5, 'PTRANS': 3, 'TRANS': 163} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 94 Chain: "8" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2965 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'CIS': 6, 'PTRANS': 21, 'TRANS': 399} Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 172 Chain: "9" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1535 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 185} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 5183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5183 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'CIS': 4, 'PTRANS': 32, 'TRANS': 651} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3076 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 363} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1705 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 191} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1200 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 141} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1388 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 183 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PCIS': 3, 'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 115} 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: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 89} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 530 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 652 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 602 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 67} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "O" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 107} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "P" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 78} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1345 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 155} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2334 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Chain: "S" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2299 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 298} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 169 Chain: "T" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 942 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 131} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "U" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1019 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "V" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 596 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 55 Chain: "X" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 372 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "Y" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 409 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "Z" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 493 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 4, 'PTRANS': 3, 'TRANS': 66} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "a" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "b" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1032 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 4, 'PTRANS': 10, 'TRANS': 124} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "c" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 617 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "d" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 708 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 149 Chain: "f" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1156 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 204 Chain: "h" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 721 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 84} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "i" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 277 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "j" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 892 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "1" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2442 Classifications: {'peptide': 309} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 286} Chain breaks: 1 Chain: "6" Number of atoms: 4765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4765 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "g" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1351 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 159} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "e" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 864 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 15, 'TRANS': 122} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 224 Chain: "M" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 642 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "4" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13948 SG CYS A 137 68.458 63.649 48.076 1.00 81.76 S ATOM 24971 SG CYS E 123 93.119 74.035 53.005 1.00 65.43 S ATOM 24944 SG CYS E 119 90.196 70.176 47.088 1.00 84.29 S ATOM 28113 SG CYS I 115 84.871 55.323 31.605 1.00120.28 S Time building chain proxies: 25.95, per 1000 atoms: 0.43 Number of scatterers: 60091 At special positions: 0 Unit cell: (220.773, 238.938, 220.773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 393 16.00 P 11 15.00 O 10672 8.00 N 10216 7.00 C 38770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 66 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 56 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 46 " - pdb=" SG CYS Q 56 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 88 " - pdb=" SG CYS Q 100 " distance=2.03 Simple disulfide: pdb=" SG CYS T 18 " - pdb=" SG CYS T 75 " distance=2.03 Simple disulfide: pdb=" SG CYS T 95 " - pdb=" SG CYS T 115 " distance=2.02 Simple disulfide: pdb=" SG CYS d 59 " - pdb=" SG CYS d 90 " distance=2.02 Simple disulfide: pdb=" SG CYS g 113 " - pdb=" SG CYS g 125 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.63 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 9 301 " pdb="FE1 FES 9 301 " - pdb=" SG CYS 9 140 " pdb=" FES A 803 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 92 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 75 " pdb=" SF4 8 502 " pdb="FE2 SF4 8 502 " - pdb=" SG CYS 8 385 " pdb=" SF4 A 801 " pdb="FE4 SF4 A 801 " - pdb=" NE2 HIS A 124 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 137 " pdb="FE3 SF4 A 801 " - pdb=" SG CYS A 128 " pdb="FE3 SF4 A 801 " - pdb=" SG CYS A 131 " pdb=" SF4 A 802 " pdb="FE1 SF4 A 802 " - pdb=" SG CYS A 182 " pdb="FE3 SF4 A 802 " - pdb=" SG CYS A 179 " pdb="FE2 SF4 A 802 " - pdb=" SG CYS A 176 " pdb="FE4 SF4 A 802 " - pdb=" SG CYS A 226 " pdb=" SF4 D 301 " pdb="FE2 SF4 D 301 " - pdb=" SG CYS D 156 " pdb=" SF4 E 301 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 123 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 158 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 152 " pdb=" SF4 E 302 " pdb="FE2 SF4 E 302 " - pdb=" SG CYS E 119 " pdb="FE3 SF4 E 302 " - pdb=" SG CYS E 162 " pdb="FE1 SF4 E 302 " - pdb=" SG CYS E 113 " Number of angles added : 49 Zn2+ tetrahedral coordination pdb=" ZN I 300 " pdb="ZN ZN I 300 " - pdb=" NE2 HIS I 96 " pdb="ZN ZN I 300 " - pdb=" SG CYS I 115 " 15602 Ramachandran restraints generated. 7801 Oldfield, 0 Emsley, 7801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 314 helices and 19 sheets defined 38.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain '2' and resid 3 through 21 removed outlier: 4.109A pdb=" N ILE 2 7 " --> pdb=" O PRO 2 3 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE 2 8 " --> pdb=" O ILE 2 4 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE 2 13 " --> pdb=" O ILE 2 9 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET 2 14 " --> pdb=" O LEU 2 10 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE 2 19 " --> pdb=" O LEU 2 15 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 35 removed outlier: 4.123A pdb=" N PHE 2 33 " --> pdb=" O VAL 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 44 Processing helix chain '2' and resid 50 through 74 removed outlier: 5.195A pdb=" N LYS 2 58 " --> pdb=" O GLU 2 54 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR 2 62 " --> pdb=" O LYS 2 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN 2 63 " --> pdb=" O TYR 2 59 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR 2 65 " --> pdb=" O LEU 2 61 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET 2 71 " --> pdb=" O SER 2 67 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET 2 72 " --> pdb=" O MET 2 68 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA 2 73 " --> pdb=" O LEU 2 69 " (cutoff:3.500A) Processing helix chain '2' and resid 76 through 79 No H-bonds generated for 'chain '2' and resid 76 through 79' Processing helix chain '2' and resid 92 through 104 removed outlier: 3.607A pdb=" N LEU 2 97 " --> pdb=" O MET 2 93 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET 2 100 " --> pdb=" O MET 2 96 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA 2 101 " --> pdb=" O LEU 2 97 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET 2 104 " --> pdb=" O MET 2 100 " (cutoff:3.500A) Processing helix chain '2' and resid 112 through 119 removed outlier: 3.799A pdb=" N VAL 2 115 " --> pdb=" O HIS 2 112 " (cutoff:3.500A) Proline residue: 2 116 - end of helix Processing helix chain '2' and resid 130 through 145 removed outlier: 4.808A pdb=" N GLN 2 134 " --> pdb=" O LEU 2 131 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA 2 137 " --> pdb=" O GLN 2 134 " (cutoff:3.500A) Proline residue: 2 138 - end of helix removed outlier: 3.555A pdb=" N LEU 2 142 " --> pdb=" O MET 2 139 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR 2 143 " --> pdb=" O SER 2 140 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE 2 145 " --> pdb=" O LEU 2 142 " (cutoff:3.500A) Processing helix chain '2' and resid 153 through 165 removed outlier: 3.581A pdb=" N SER 2 158 " --> pdb=" O ILE 2 154 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE 2 162 " --> pdb=" O SER 2 158 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 2 163 " --> pdb=" O VAL 2 159 " (cutoff:3.500A) Processing helix chain '2' and resid 168 through 171 removed outlier: 3.851A pdb=" N ASN 2 171 " --> pdb=" O GLY 2 168 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 168 through 171' Processing helix chain '2' and resid 175 through 180 Processing helix chain '2' and resid 186 through 192 removed outlier: 3.503A pdb=" N MET 2 190 " --> pdb=" O HIS 2 186 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR 2 191 " --> pdb=" O MET 2 187 " (cutoff:3.500A) Processing helix chain '2' and resid 201 through 219 removed outlier: 4.096A pdb=" N MET 2 215 " --> pdb=" O MET 2 211 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE 2 216 " --> pdb=" O THR 2 212 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR 2 217 " --> pdb=" O SER 2 213 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 230 Processing helix chain '2' and resid 238 through 251 removed outlier: 3.605A pdb=" N VAL 2 242 " --> pdb=" O ILE 2 239 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE 2 244 " --> pdb=" O THR 2 241 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR 2 247 " --> pdb=" O ILE 2 244 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU 2 248 " --> pdb=" O LEU 2 245 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU 2 249 " --> pdb=" O ALA 2 246 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET 2 251 " --> pdb=" O LEU 2 248 " (cutoff:3.500A) Processing helix chain '2' and resid 261 through 270 removed outlier: 4.148A pdb=" N ILE 2 267 " --> pdb=" O LYS 2 263 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN 2 268 " --> pdb=" O TRP 2 264 " (cutoff:3.500A) Processing helix chain '2' and resid 277 through 285 Processing helix chain '2' and resid 297 through 300 No H-bonds generated for 'chain '2' and resid 297 through 300' Processing helix chain '2' and resid 340 through 343 No H-bonds generated for 'chain '2' and resid 340 through 343' Processing helix chain '3' and resid 8 through 21 removed outlier: 3.513A pdb=" N VAL 3 18 " --> pdb=" O ALA 3 14 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE 3 19 " --> pdb=" O THR 3 15 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE 3 20 " --> pdb=" O LEU 3 16 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 67 Processing helix chain '3' and resid 76 through 78 No H-bonds generated for 'chain '3' and resid 76 through 78' Processing helix chain '3' and resid 84 through 106 removed outlier: 3.566A pdb=" N ALA 3 91 " --> pdb=" O MET 3 87 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE 3 93 " --> pdb=" O THR 3 89 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU 3 94 " --> pdb=" O MET 3 90 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE 3 95 " --> pdb=" O ALA 3 91 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU 3 102 " --> pdb=" O LEU 3 98 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU 3 105 " --> pdb=" O SER 3 101 " (cutoff:3.500A) Processing helix chain '4' and resid 5 through 9 Processing helix chain '4' and resid 12 through 14 No H-bonds generated for 'chain '4' and resid 12 through 14' Processing helix chain '4' and resid 21 through 41 removed outlier: 4.060A pdb=" N ASN 4 26 " --> pdb=" O ILE 4 23 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR 4 28 " --> pdb=" O VAL 4 25 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS 4 30 " --> pdb=" O SER 4 27 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU 4 32 " --> pdb=" O ALA 4 29 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE 4 36 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER 4 38 " --> pdb=" O SER 4 35 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU 4 40 " --> pdb=" O THR 4 37 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU 4 41 " --> pdb=" O SER 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 68 through 71 No H-bonds generated for 'chain '4' and resid 68 through 71' Processing helix chain '4' and resid 73 through 80 removed outlier: 4.188A pdb=" N LEU 4 77 " --> pdb=" O LEU 4 73 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET 4 78 " --> pdb=" O PRO 4 74 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA 4 79 " --> pdb=" O LEU 4 75 " (cutoff:3.500A) Processing helix chain '4' and resid 89 through 108 removed outlier: 3.502A pdb=" N LEU 4 94 " --> pdb=" O THR 4 90 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE 4 95 " --> pdb=" O ARG 4 91 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU 4 99 " --> pdb=" O PHE 4 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN 4 103 " --> pdb=" O LEU 4 99 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU 4 104 " --> pdb=" O ILE 4 100 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE 4 105 " --> pdb=" O SER 4 101 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 4 106 " --> pdb=" O LEU 4 102 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 122 removed outlier: 4.043A pdb=" N ILE 4 120 " --> pdb=" O ILE 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 128 through 134 Processing helix chain '4' and resid 143 through 149 Processing helix chain '4' and resid 153 through 168 removed outlier: 3.777A pdb=" N LEU 4 158 " --> pdb=" O LEU 4 154 " (cutoff:3.500A) Proline residue: 4 159 - end of helix removed outlier: 3.604A pdb=" N VAL 4 162 " --> pdb=" O LEU 4 158 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE 4 165 " --> pdb=" O LEU 4 161 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR 4 166 " --> pdb=" O VAL 4 162 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 204 removed outlier: 3.520A pdb=" N CYS 4 199 " --> pdb=" O MET 4 195 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA 4 202 " --> pdb=" O ALA 4 198 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N PHE 4 203 " --> pdb=" O CYS 4 199 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET 4 204 " --> pdb=" O MET 4 200 " (cutoff:3.500A) Processing helix chain '4' and resid 216 through 219 No H-bonds generated for 'chain '4' and resid 216 through 219' Processing helix chain '4' and resid 230 through 238 removed outlier: 3.781A pdb=" N LEU 4 235 " --> pdb=" O LEU 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 241 through 246 Processing helix chain '4' and resid 259 through 273 removed outlier: 3.646A pdb=" N SER 4 265 " --> pdb=" O PHE 4 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET 4 269 " --> pdb=" O SER 4 265 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER 4 273 " --> pdb=" O MET 4 269 " (cutoff:3.500A) Processing helix chain '4' and resid 285 through 297 removed outlier: 3.676A pdb=" N SER 4 289 " --> pdb=" O LEU 4 285 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER 4 292 " --> pdb=" O TYR 4 288 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS 4 293 " --> pdb=" O SER 4 289 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET 4 294 " --> pdb=" O SER 4 290 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL 4 297 " --> pdb=" O HIS 4 293 " (cutoff:3.500A) Processing helix chain '4' and resid 299 through 302 No H-bonds generated for 'chain '4' and resid 299 through 302' Processing helix chain '4' and resid 309 through 331 removed outlier: 3.689A pdb=" N ALA 4 314 " --> pdb=" O MET 4 310 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET 4 316 " --> pdb=" O ALA 4 312 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE 4 317 " --> pdb=" O THR 4 313 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS 4 319 " --> pdb=" O LEU 4 315 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY 4 320 " --> pdb=" O MET 4 316 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER 4 324 " --> pdb=" O GLY 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 342 through 345 Processing helix chain '4' and resid 356 through 365 removed outlier: 3.513A pdb=" N LEU 4 360 " --> pdb=" O ALA 4 356 " (cutoff:3.500A) Processing helix chain '4' and resid 378 through 388 removed outlier: 4.648A pdb=" N SER 4 387 " --> pdb=" O MET 4 383 " (cutoff:3.500A) Processing helix chain '4' and resid 392 through 414 removed outlier: 3.619A pdb=" N MET 4 396 " --> pdb=" O THR 4 392 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN 4 399 " --> pdb=" O LEU 4 395 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET 4 400 " --> pdb=" O MET 4 396 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR 4 403 " --> pdb=" O ASN 4 399 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA 4 404 " --> pdb=" O MET 4 400 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 4 405 " --> pdb=" O VAL 4 401 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU 4 408 " --> pdb=" O ALA 4 404 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET 4 410 " --> pdb=" O TYR 4 406 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU 4 411 " --> pdb=" O SER 4 407 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET 4 413 " --> pdb=" O TYR 4 409 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR 4 414 " --> pdb=" O MET 4 410 " (cutoff:3.500A) Processing helix chain '4' and resid 431 through 435 Processing helix chain '4' and resid 441 through 447 removed outlier: 4.037A pdb=" N LEU 4 446 " --> pdb=" O LEU 4 442 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 6 No H-bonds generated for 'chain '5' and resid 3 through 6' Processing helix chain '5' and resid 10 through 14 removed outlier: 3.675A pdb=" N VAL 5 14 " --> pdb=" O ALA 5 11 " (cutoff:3.500A) Processing helix chain '5' and resid 17 through 19 No H-bonds generated for 'chain '5' and resid 17 through 19' Processing helix chain '5' and resid 26 through 36 removed outlier: 3.723A pdb=" N LEU 5 31 " --> pdb=" O SER 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 41 through 50 removed outlier: 4.102A pdb=" N THR 5 47 " --> pdb=" O MET 5 43 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) Processing helix chain '5' and resid 57 through 85 removed outlier: 3.896A pdb=" N ILE 5 61 " --> pdb=" O SER 5 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE 5 66 " --> pdb=" O ILE 5 62 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU 5 73 " --> pdb=" O CYS 5 69 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY 5 74 " --> pdb=" O GLU 5 70 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU 5 75 " --> pdb=" O ALA 5 71 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER 5 76 " --> pdb=" O ALA 5 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 5 79 " --> pdb=" O LEU 5 75 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR 5 84 " --> pdb=" O MET 5 80 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR 5 85 " --> pdb=" O VAL 5 81 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 20 removed outlier: 3.716A pdb=" N LEU 7 9 " --> pdb=" O ILE 7 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER 7 10 " --> pdb=" O VAL 7 6 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE 7 12 " --> pdb=" O ILE 7 8 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE 7 17 " --> pdb=" O PHE 7 13 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL 7 18 " --> pdb=" O VAL 7 14 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE 7 20 " --> pdb=" O GLY 7 16 " (cutoff:3.500A) Processing helix chain '7' and resid 25 through 27 No H-bonds generated for 'chain '7' and resid 25 through 27' Processing helix chain '7' and resid 30 through 44 removed outlier: 4.223A pdb=" N VAL 7 35 " --> pdb=" O LEU 7 31 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 59 removed outlier: 3.698A pdb=" N MET 7 55 " --> pdb=" O PHE 7 51 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 7 56 " --> pdb=" O LEU 7 52 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU 7 58 " --> pdb=" O LEU 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 64 through 70 Processing helix chain '7' and resid 95 through 107 removed outlier: 3.951A pdb=" N MET 7 99 " --> pdb=" O THR 7 95 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE 7 101 " --> pdb=" O LEU 7 97 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL 7 104 " --> pdb=" O GLU 7 100 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR 7 106 " --> pdb=" O PHE 7 102 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL 7 107 " --> pdb=" O MET 7 103 " (cutoff:3.500A) Processing helix chain '7' and resid 152 through 169 removed outlier: 3.507A pdb=" N VAL 7 156 " --> pdb=" O TRP 7 152 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 7 165 " --> pdb=" O LEU 7 161 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL 7 166 " --> pdb=" O LEU 7 162 " (cutoff:3.500A) Processing helix chain '8' and resid 66 through 70 Processing helix chain '8' and resid 73 through 76 No H-bonds generated for 'chain '8' and resid 73 through 76' Processing helix chain '8' and resid 79 through 83 removed outlier: 3.765A pdb=" N SER 8 83 " --> pdb=" O GLU 8 79 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 79 through 83' Processing helix chain '8' and resid 95 through 100 removed outlier: 3.939A pdb=" N SER 8 100 " --> pdb=" O GLY 8 96 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 133 No H-bonds generated for 'chain '8' and resid 130 through 133' Processing helix chain '8' and resid 138 through 149 removed outlier: 4.081A pdb=" N LEU 8 143 " --> pdb=" O VAL 8 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET 8 149 " --> pdb=" O GLY 8 145 " (cutoff:3.500A) Processing helix chain '8' and resid 163 through 175 removed outlier: 3.525A pdb=" N SER 8 167 " --> pdb=" O TYR 8 163 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN 8 168 " --> pdb=" O ASN 8 164 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU 8 169 " --> pdb=" O GLU 8 165 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN 8 170 " --> pdb=" O ALA 8 166 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL 8 171 " --> pdb=" O SER 8 167 " (cutoff:3.500A) Processing helix chain '8' and resid 212 through 215 No H-bonds generated for 'chain '8' and resid 212 through 215' Processing helix chain '8' and resid 246 through 249 No H-bonds generated for 'chain '8' and resid 246 through 249' Processing helix chain '8' and resid 251 through 256 Processing helix chain '8' and resid 296 through 301 removed outlier: 3.921A pdb=" N GLU 8 301 " --> pdb=" O LYS 8 297 " (cutoff:3.500A) Processing helix chain '8' and resid 331 through 333 No H-bonds generated for 'chain '8' and resid 331 through 333' Processing helix chain '8' and resid 339 through 344 Processing helix chain '8' and resid 363 through 376 removed outlier: 3.588A pdb=" N ARG 8 369 " --> pdb=" O LYS 8 365 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR 8 374 " --> pdb=" O LEU 8 370 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS 8 375 " --> pdb=" O ILE 8 371 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS 8 376 " --> pdb=" O GLU 8 372 " (cutoff:3.500A) Processing helix chain '8' and resid 389 through 401 removed outlier: 3.553A pdb=" N LYS 8 394 " --> pdb=" O ASP 8 390 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL 8 395 " --> pdb=" O TRP 8 391 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG 8 398 " --> pdb=" O LYS 8 394 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG 8 401 " --> pdb=" O ALA 8 397 " (cutoff:3.500A) Processing helix chain '8' and resid 408 through 416 Processing helix chain '8' and resid 426 through 439 removed outlier: 4.027A pdb=" N ALA 8 432 " --> pdb=" O GLY 8 428 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP 8 433 " --> pdb=" O ASP 8 429 " (cutoff:3.500A) Proline residue: 8 434 - end of helix Processing helix chain '8' and resid 449 through 457 Processing helix chain '9' and resid 57 through 67 removed outlier: 4.392A pdb=" N LYS 9 61 " --> pdb=" O PRO 9 57 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG 9 62 " --> pdb=" O GLU 9 58 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE 9 63 " --> pdb=" O ASN 9 59 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU 9 64 " --> pdb=" O TYR 9 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA 9 65 " --> pdb=" O LYS 9 61 " (cutoff:3.500A) Processing helix chain '9' and resid 79 through 90 removed outlier: 3.598A pdb=" N ASP 9 84 " --> pdb=" O LEU 9 80 " (cutoff:3.500A) Processing helix chain '9' and resid 95 through 104 removed outlier: 3.770A pdb=" N VAL 9 101 " --> pdb=" O ALA 9 97 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA 9 102 " --> pdb=" O MET 9 98 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU 9 103 " --> pdb=" O ASN 9 99 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE 9 104 " --> pdb=" O LYS 9 100 " (cutoff:3.500A) Processing helix chain '9' and resid 109 through 116 removed outlier: 4.308A pdb=" N GLU 9 114 " --> pdb=" O ARG 9 111 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA 9 116 " --> pdb=" O TYR 9 113 " (cutoff:3.500A) Processing helix chain '9' and resid 138 through 142 Processing helix chain '9' and resid 153 through 156 No H-bonds generated for 'chain '9' and resid 153 through 156' Processing helix chain '9' and resid 198 through 210 removed outlier: 3.981A pdb=" N ILE 9 205 " --> pdb=" O ILE 9 201 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP 9 206 " --> pdb=" O GLU 9 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 110 through 119 removed outlier: 3.549A pdb=" N GLU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.871A pdb=" N PHE A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 186 " --> pdb=" O CYS A 182 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 187' Processing helix chain 'A' and resid 219 through 222 removed outlier: 4.158A pdb=" N ILE A 222 " --> pdb=" O SER A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 222' Processing helix chain 'A' and resid 288 through 292 removed outlier: 4.140A pdb=" N PHE A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 292' Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 322 through 332 removed outlier: 3.905A pdb=" N VAL A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 353 No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 412 through 422 removed outlier: 3.503A pdb=" N ALA A 416 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 478 through 481 No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 486 through 501 removed outlier: 3.633A pdb=" N ALA A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 removed outlier: 4.511A pdb=" N ALA A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.577A pdb=" N ILE A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.570A pdb=" N GLU A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 removed outlier: 3.728A pdb=" N GLU A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 700 through 703 No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 705 through 715 removed outlier: 3.671A pdb=" N LYS A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 4.590A pdb=" N GLU B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 removed outlier: 4.231A pdb=" N ARG B 138 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 156 removed outlier: 3.597A pdb=" N LEU B 153 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 175 removed outlier: 3.699A pdb=" N TRP B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 removed outlier: 4.050A pdb=" N ASN B 182 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N HIS B 183 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA B 186 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 188 " --> pdb=" O MET B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 No H-bonds generated for 'chain 'B' and resid 190 through 193' Processing helix chain 'B' and resid 198 through 217 removed outlier: 4.118A pdb=" N MET B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 204 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU B 206 " --> pdb=" O TRP B 202 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 removed outlier: 4.201A pdb=" N ASN B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.784A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 282 through 285 No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 327 through 350 removed outlier: 3.531A pdb=" N LEU B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N CYS B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 341 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.811A pdb=" N ILE B 379 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU B 384 " --> pdb=" O HIS B 380 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 385 " --> pdb=" O HIS B 381 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 386 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 439 removed outlier: 5.002A pdb=" N LEU B 435 " --> pdb=" O HIS B 431 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 454 removed outlier: 3.969A pdb=" N ALA B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 63 Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.667A pdb=" N GLU C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 70 " --> pdb=" O TYR C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 70' Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.580A pdb=" N VAL C 95 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Proline residue: C 97 - end of helix Processing helix chain 'C' and resid 168 through 175 removed outlier: 3.840A pdb=" N ILE C 172 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 77 removed outlier: 3.868A pdb=" N ILE D 74 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASN D 75 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 100 removed outlier: 4.073A pdb=" N GLU D 95 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.827A pdb=" N ARG D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 140 " --> pdb=" O ALA D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 193 through 203 Processing helix chain 'E' and resid 52 through 62 removed outlier: 3.506A pdb=" N ARG E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR E 60 " --> pdb=" O ARG E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.556A pdb=" N VAL E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 122' Processing helix chain 'E' and resid 187 through 193 removed outlier: 4.213A pdb=" N ASN E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 206 removed outlier: 3.512A pdb=" N ALA E 203 " --> pdb=" O ALA E 199 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN E 206 " --> pdb=" O ALA E 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'G' and resid 71 through 74 No H-bonds generated for 'chain 'G' and resid 71 through 74' Processing helix chain 'G' and resid 132 through 141 removed outlier: 4.044A pdb=" N ALA G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN G 141 " --> pdb=" O PHE G 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 9 No H-bonds generated for 'chain 'H' and resid 6 through 9' Processing helix chain 'H' and resid 34 through 43 removed outlier: 3.685A pdb=" N LYS H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU H 42 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 55 No H-bonds generated for 'chain 'H' and resid 52 through 55' Processing helix chain 'H' and resid 59 through 68 removed outlier: 3.674A pdb=" N PHE H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.582A pdb=" N ALA H 78 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG H 81 " --> pdb=" O HIS H 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 74 No H-bonds generated for 'chain 'I' and resid 72 through 74' Processing helix chain 'J' and resid 4 through 25 removed outlier: 3.919A pdb=" N GLY J 8 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL J 11 " --> pdb=" O PRO J 7 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET J 12 " --> pdb=" O GLY J 8 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL J 14 " --> pdb=" O ALA J 10 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE J 17 " --> pdb=" O GLY J 13 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE J 18 " --> pdb=" O VAL J 14 " (cutoff:3.500A) Proline residue: J 19 - end of helix Processing helix chain 'J' and resid 27 through 30 No H-bonds generated for 'chain 'J' and resid 27 through 30' Processing helix chain 'J' and resid 42 through 54 removed outlier: 3.521A pdb=" N TYR J 46 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET J 48 " --> pdb=" O GLN J 44 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG J 53 " --> pdb=" O GLU J 49 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL J 54 " --> pdb=" O ARG J 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 40 removed outlier: 4.228A pdb=" N GLY K 32 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE K 37 " --> pdb=" O ARG K 34 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG K 40 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 89 No H-bonds generated for 'chain 'K' and resid 86 through 89' Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.699A pdb=" N VAL K 94 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU K 95 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER K 96 " --> pdb=" O ASN K 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 91 through 96' Processing helix chain 'L' and resid 19 through 26 Processing helix chain 'L' and resid 32 through 34 No H-bonds generated for 'chain 'L' and resid 32 through 34' Processing helix chain 'L' and resid 41 through 47 Processing helix chain 'L' and resid 80 through 83 No H-bonds generated for 'chain 'L' and resid 80 through 83' Processing helix chain 'N' and resid 23 through 37 removed outlier: 3.657A pdb=" N THR N 29 " --> pdb=" O LYS N 25 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL N 34 " --> pdb=" O LYS N 30 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS N 37 " --> pdb=" O ASP N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.977A pdb=" N GLN N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET N 58 " --> pdb=" O GLU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 69 Processing helix chain 'N' and resid 77 through 93 removed outlier: 3.946A pdb=" N LEU N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS N 93 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 32 No H-bonds generated for 'chain 'O' and resid 29 through 32' Processing helix chain 'O' and resid 34 through 47 removed outlier: 4.049A pdb=" N ALA O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) Proline residue: O 44 - end of helix removed outlier: 3.581A pdb=" N VAL O 47 " --> pdb=" O VAL O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 69 removed outlier: 3.510A pdb=" N ARG O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 94 removed outlier: 4.075A pdb=" N LEU O 90 " --> pdb=" O GLY O 86 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU O 91 " --> pdb=" O LYS O 87 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU O 92 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 106 No H-bonds generated for 'chain 'O' and resid 104 through 106' Processing helix chain 'O' and resid 118 through 123 removed outlier: 3.772A pdb=" N TYR O 123 " --> pdb=" O LEU O 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 14 removed outlier: 4.097A pdb=" N LEU P 11 " --> pdb=" O PHE P 7 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 25 No H-bonds generated for 'chain 'Q' and resid 22 through 25' Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 39 through 47 Processing helix chain 'Q' and resid 59 through 77 removed outlier: 3.533A pdb=" N GLU Q 69 " --> pdb=" O GLN Q 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS Q 77 " --> pdb=" O GLN Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 83 No H-bonds generated for 'chain 'Q' and resid 80 through 83' Processing helix chain 'Q' and resid 85 through 90 removed outlier: 3.850A pdb=" N ILE Q 89 " --> pdb=" O TYR Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 111 removed outlier: 4.817A pdb=" N CYS Q 110 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL Q 111 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 76 removed outlier: 4.029A pdb=" N TYR R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS R 72 " --> pdb=" O TYR R 68 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG R 75 " --> pdb=" O ASN R 71 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET R 76 " --> pdb=" O HIS R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 116 No H-bonds generated for 'chain 'R' and resid 114 through 116' Processing helix chain 'R' and resid 119 through 121 No H-bonds generated for 'chain 'R' and resid 119 through 121' Processing helix chain 'R' and resid 143 through 145 No H-bonds generated for 'chain 'R' and resid 143 through 145' Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 155 through 158 No H-bonds generated for 'chain 'R' and resid 155 through 158' Processing helix chain 'R' and resid 185 through 190 Processing helix chain 'R' and resid 213 through 216 No H-bonds generated for 'chain 'R' and resid 213 through 216' Processing helix chain 'R' and resid 242 through 253 removed outlier: 3.605A pdb=" N ILE R 249 " --> pdb=" O VAL R 245 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE R 250 " --> pdb=" O THR R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 283 removed outlier: 3.728A pdb=" N PHE R 281 " --> pdb=" O VAL R 277 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 283 " --> pdb=" O TYR R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 321 removed outlier: 3.592A pdb=" N GLU R 320 " --> pdb=" O ASP R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 352 No H-bonds generated for 'chain 'R' and resid 349 through 352' Processing helix chain 'S' and resid 27 through 31 removed outlier: 3.650A pdb=" N TYR S 31 " --> pdb=" O GLY S 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 27 through 31' Processing helix chain 'S' and resid 79 through 81 No H-bonds generated for 'chain 'S' and resid 79 through 81' Processing helix chain 'S' and resid 105 through 107 No H-bonds generated for 'chain 'S' and resid 105 through 107' Processing helix chain 'S' and resid 116 through 140 removed outlier: 3.782A pdb=" N GLN S 120 " --> pdb=" O SER S 116 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU S 128 " --> pdb=" O TYR S 124 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU S 135 " --> pdb=" O TYR S 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS S 137 " --> pdb=" O ASP S 133 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU S 138 " --> pdb=" O ALA S 134 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU S 139 " --> pdb=" O LEU S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 154 through 163 removed outlier: 3.744A pdb=" N GLU S 159 " --> pdb=" O PHE S 155 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA S 160 " --> pdb=" O VAL S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 181 removed outlier: 3.580A pdb=" N ASN S 176 " --> pdb=" O VAL S 172 " (cutoff:3.500A) Processing helix chain 'S' and resid 201 through 208 removed outlier: 4.138A pdb=" N ILE S 206 " --> pdb=" O GLN S 203 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN S 207 " --> pdb=" O SER S 204 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS S 208 " --> pdb=" O ARG S 205 " (cutoff:3.500A) Processing helix chain 'S' and resid 219 through 231 removed outlier: 4.102A pdb=" N ASP S 224 " --> pdb=" O ALA S 220 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE S 225 " --> pdb=" O TYR S 221 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS S 230 " --> pdb=" O GLU S 226 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 237 No H-bonds generated for 'chain 'S' and resid 234 through 237' Processing helix chain 'S' and resid 261 through 264 No H-bonds generated for 'chain 'S' and resid 261 through 264' Processing helix chain 'S' and resid 269 through 271 No H-bonds generated for 'chain 'S' and resid 269 through 271' Processing helix chain 'S' and resid 324 through 329 removed outlier: 3.772A pdb=" N TYR S 327 " --> pdb=" O GLY S 324 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA S 329 " --> pdb=" O LYS S 326 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 7 Processing helix chain 'T' and resid 18 through 42 removed outlier: 3.988A pdb=" N THR T 22 " --> pdb=" O CYS T 18 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER T 27 " --> pdb=" O TYR T 23 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE T 28 " --> pdb=" O ALA T 24 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY T 29 " --> pdb=" O THR T 25 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY T 33 " --> pdb=" O GLY T 29 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL T 35 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR T 39 " --> pdb=" O VAL T 35 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL T 41 " --> pdb=" O SER T 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA T 42 " --> pdb=" O ALA T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 80 removed outlier: 4.289A pdb=" N ALA T 65 " --> pdb=" O PHE T 61 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY T 71 " --> pdb=" O GLY T 67 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER T 74 " --> pdb=" O PHE T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 90 No H-bonds generated for 'chain 'T' and resid 87 through 90' Processing helix chain 'T' and resid 92 through 103 removed outlier: 4.018A pdb=" N ALA T 96 " --> pdb=" O ILE T 92 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY T 97 " --> pdb=" O GLY T 93 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE T 100 " --> pdb=" O ALA T 96 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU T 101 " --> pdb=" O GLY T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 128 removed outlier: 3.623A pdb=" N MET T 118 " --> pdb=" O ALA T 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY T 119 " --> pdb=" O CYS T 115 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU T 120 " --> pdb=" O ALA T 116 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR T 121 " --> pdb=" O TYR T 117 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU T 124 " --> pdb=" O LEU T 120 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL T 125 " --> pdb=" O THR T 121 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS T 126 " --> pdb=" O ALA T 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 15 removed outlier: 3.983A pdb=" N GLN U 12 " --> pdb=" O LYS U 8 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN U 13 " --> pdb=" O ARG U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 29 removed outlier: 4.086A pdb=" N VAL U 26 " --> pdb=" O GLY U 22 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG U 29 " --> pdb=" O ARG U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 88 No H-bonds generated for 'chain 'U' and resid 86 through 88' Processing helix chain 'V' and resid 37 through 49 removed outlier: 3.625A pdb=" N GLY V 41 " --> pdb=" O ALA V 37 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA V 42 " --> pdb=" O VAL V 38 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 70 removed outlier: 3.691A pdb=" N ALA V 67 " --> pdb=" O GLU V 63 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG V 68 " --> pdb=" O ASP V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 89 removed outlier: 3.819A pdb=" N ARG V 81 " --> pdb=" O ALA V 77 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG V 82 " --> pdb=" O GLU V 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 95 No H-bonds generated for 'chain 'V' and resid 92 through 95' Processing helix chain 'V' and resid 121 through 124 No H-bonds generated for 'chain 'V' and resid 121 through 124' Processing helix chain 'V' and resid 132 through 137 Processing helix chain 'W' and resid 77 through 89 removed outlier: 4.163A pdb=" N LEU W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU W 87 " --> pdb=" O VAL W 83 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS W 88 " --> pdb=" O LEU W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 125 removed outlier: 3.888A pdb=" N ALA W 121 " --> pdb=" O GLU W 117 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N MET W 122 " --> pdb=" O ILE W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 137 removed outlier: 3.714A pdb=" N ALA W 135 " --> pdb=" O ASP W 132 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU W 136 " --> pdb=" O ILE W 133 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS W 137 " --> pdb=" O ASP W 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 132 through 137' Processing helix chain 'W' and resid 141 through 152 removed outlier: 3.785A pdb=" N VAL W 145 " --> pdb=" O PRO W 141 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR W 147 " --> pdb=" O GLU W 143 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE W 148 " --> pdb=" O ILE W 144 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA W 149 " --> pdb=" O VAL W 145 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP W 150 " --> pdb=" O ASP W 146 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 33 removed outlier: 3.761A pdb=" N VAL X 21 " --> pdb=" O MET X 18 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR X 25 " --> pdb=" O PHE X 22 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG X 28 " --> pdb=" O TYR X 25 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN X 30 " --> pdb=" O ASP X 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP X 31 " --> pdb=" O ARG X 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU X 32 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 57 through 65 removed outlier: 3.617A pdb=" N PHE Y 64 " --> pdb=" O GLN Y 60 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 70 No H-bonds generated for 'chain 'Y' and resid 67 through 70' Processing helix chain 'Y' and resid 73 through 76 No H-bonds generated for 'chain 'Y' and resid 73 through 76' Processing helix chain 'Z' and resid 28 through 38 removed outlier: 3.697A pdb=" N VAL Z 32 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU Z 36 " --> pdb=" O GLN Z 33 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA Z 38 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 58 removed outlier: 3.869A pdb=" N ALA Z 58 " --> pdb=" O GLY Z 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 55 through 58' Processing helix chain 'Z' and resid 64 through 67 No H-bonds generated for 'chain 'Z' and resid 64 through 67' Processing helix chain 'Z' and resid 78 through 81 No H-bonds generated for 'chain 'Z' and resid 78 through 81' Processing helix chain 'a' and resid 31 through 33 No H-bonds generated for 'chain 'a' and resid 31 through 33' Processing helix chain 'a' and resid 37 through 51 removed outlier: 3.563A pdb=" N ARG a 42 " --> pdb=" O ALA a 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU a 43 " --> pdb=" O ILE a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 69 removed outlier: 3.502A pdb=" N THR a 69 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 92 removed outlier: 3.538A pdb=" N ALA a 91 " --> pdb=" O LEU a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 95 through 107 removed outlier: 3.866A pdb=" N TYR a 102 " --> pdb=" O LEU a 98 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR a 107 " --> pdb=" O TYR a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 117 Processing helix chain 'b' and resid 62 through 66 Processing helix chain 'b' and resid 69 through 92 removed outlier: 3.631A pdb=" N ILE b 75 " --> pdb=" O LEU b 71 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 78 " --> pdb=" O TYR b 74 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE b 80 " --> pdb=" O LEU b 76 " (cutoff:3.500A) Proline residue: b 81 - end of helix removed outlier: 4.129A pdb=" N ILE b 84 " --> pdb=" O ILE b 80 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY b 85 " --> pdb=" O PRO b 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE b 86 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN b 90 " --> pdb=" O ILE b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 119 through 125 removed outlier: 4.847A pdb=" N ARG b 123 " --> pdb=" O ARG b 119 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR b 124 " --> pdb=" O TRP b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 136 through 139 No H-bonds generated for 'chain 'b' and resid 136 through 139' Processing helix chain 'b' and resid 150 through 156 removed outlier: 4.227A pdb=" N LEU b 154 " --> pdb=" O ARG b 150 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU b 155 " --> pdb=" O LEU b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 176 through 178 No H-bonds generated for 'chain 'b' and resid 176 through 178' Processing helix chain 'c' and resid 6 through 9 removed outlier: 3.854A pdb=" N LYS c 9 " --> pdb=" O PRO c 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 6 through 9' Processing helix chain 'c' and resid 19 through 26 Processing helix chain 'c' and resid 78 through 90 removed outlier: 3.831A pdb=" N ILE c 82 " --> pdb=" O PRO c 78 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS c 89 " --> pdb=" O TYR c 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 48 removed outlier: 3.590A pdb=" N ASP d 48 " --> pdb=" O GLN d 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 44 through 48' Processing helix chain 'd' and resid 61 through 66 Processing helix chain 'd' and resid 68 through 72 Processing helix chain 'd' and resid 81 through 98 Processing helix chain 'd' and resid 101 through 108 Processing helix chain 'f' and resid 12 through 25 removed outlier: 3.915A pdb=" N VAL f 16 " --> pdb=" O HIS f 12 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU f 17 " --> pdb=" O GLN f 13 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU f 19 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS f 21 " --> pdb=" O LEU f 17 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG f 22 " --> pdb=" O ARG f 18 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU f 24 " --> pdb=" O TYR f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 48 removed outlier: 3.705A pdb=" N PHE f 40 " --> pdb=" O LYS f 36 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS f 42 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU f 43 " --> pdb=" O TYR f 39 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG f 47 " --> pdb=" O LEU f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 58 through 65 removed outlier: 3.649A pdb=" N LEU f 63 " --> pdb=" O LYS f 59 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU f 64 " --> pdb=" O ALA f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 116 through 130 removed outlier: 3.943A pdb=" N GLN f 124 " --> pdb=" O ALA f 120 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS f 126 " --> pdb=" O ARG f 122 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS f 127 " --> pdb=" O GLU f 123 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU f 128 " --> pdb=" O GLN f 124 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG f 129 " --> pdb=" O TRP f 125 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 143 removed outlier: 3.572A pdb=" N GLN f 141 " --> pdb=" O VAL f 137 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU f 142 " --> pdb=" O LYS f 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 86 Processing helix chain 'h' and resid 91 through 94 No H-bonds generated for 'chain 'h' and resid 91 through 94' Processing helix chain 'h' and resid 101 through 105 Processing helix chain 'h' and resid 112 through 129 removed outlier: 5.948A pdb=" N GLU h 116 " --> pdb=" O ARG h 113 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP h 117 " --> pdb=" O MET h 114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG h 119 " --> pdb=" O GLU h 116 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU h 121 " --> pdb=" O ALA h 118 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU h 125 " --> pdb=" O ALA h 122 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL h 126 " --> pdb=" O GLU h 123 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS h 127 " --> pdb=" O ARG h 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 72 removed outlier: 3.697A pdb=" N VAL i 52 " --> pdb=" O LEU i 48 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE i 59 " --> pdb=" O TRP i 55 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU i 64 " --> pdb=" O LYS i 60 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS i 70 " --> pdb=" O VAL i 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 29 through 48 removed outlier: 4.924A pdb=" N GLY j 35 " --> pdb=" O LEU j 31 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY j 38 " --> pdb=" O VAL j 34 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU j 43 " --> pdb=" O TYR j 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 61 No H-bonds generated for 'chain 'j' and resid 58 through 61' Processing helix chain 'j' and resid 64 through 95 removed outlier: 3.630A pdb=" N PHE j 70 " --> pdb=" O THR j 66 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS j 77 " --> pdb=" O TYR j 73 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG j 78 " --> pdb=" O TYR j 74 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN j 79 " --> pdb=" O LEU j 75 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET j 90 " --> pdb=" O ARG j 86 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE j 91 " --> pdb=" O ASP j 87 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER j 92 " --> pdb=" O HIS j 88 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR j 93 " --> pdb=" O ASP j 89 " (cutoff:3.500A) Processing helix chain 'j' and resid 98 through 100 No H-bonds generated for 'chain 'j' and resid 98 through 100' Processing helix chain '1' and resid 2 through 18 removed outlier: 3.506A pdb=" N ILE 1 6 " --> pdb=" O PHE 1 2 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE 1 11 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) Proline residue: 1 12 - end of helix removed outlier: 3.694A pdb=" N LEU 1 15 " --> pdb=" O ILE 1 11 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA 1 16 " --> pdb=" O PRO 1 12 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL 1 17 " --> pdb=" O ILE 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 21 through 31 removed outlier: 3.764A pdb=" N MET 1 31 " --> pdb=" O VAL 1 27 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 57 removed outlier: 3.944A pdb=" N ILE 1 53 " --> pdb=" O ILE 1 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS 1 54 " --> pdb=" O ALA 1 50 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU 1 55 " --> pdb=" O ASP 1 51 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE 1 56 " --> pdb=" O ALA 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 73 through 86 removed outlier: 3.677A pdb=" N LEU 1 79 " --> pdb=" O PRO 1 75 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA 1 82 " --> pdb=" O ALA 1 78 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU 1 83 " --> pdb=" O LEU 1 79 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP 1 86 " --> pdb=" O ALA 1 82 " (cutoff:3.500A) Processing helix chain '1' and resid 102 through 111 removed outlier: 4.262A pdb=" N LEU 1 111 " --> pdb=" O ALA 1 107 " (cutoff:3.500A) Processing helix chain '1' and resid 113 through 121 removed outlier: 3.867A pdb=" N LEU 1 117 " --> pdb=" O VAL 1 113 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP 1 118 " --> pdb=" O TYR 1 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER 1 119 " --> pdb=" O SER 1 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY 1 120 " --> pdb=" O ILE 1 116 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP 1 121 " --> pdb=" O LEU 1 117 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 113 through 121' Processing helix chain '1' and resid 126 through 139 removed outlier: 4.775A pdb=" N ALA 1 132 " --> pdb=" O ALA 1 128 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU 1 133 " --> pdb=" O LEU 1 129 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG 1 134 " --> pdb=" O ILE 1 130 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA 1 135 " --> pdb=" O GLY 1 131 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL 1 136 " --> pdb=" O ALA 1 132 " (cutoff:3.500A) Processing helix chain '1' and resid 144 through 157 removed outlier: 3.682A pdb=" N ILE 1 148 " --> pdb=" O VAL 1 144 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE 1 149 " --> pdb=" O THR 1 145 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL 1 153 " --> pdb=" O ILE 1 149 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 1 154 " --> pdb=" O LEU 1 150 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET 1 156 " --> pdb=" O SER 1 152 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 169 removed outlier: 3.639A pdb=" N GLN 1 169 " --> pdb=" O LEU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 179 through 192 removed outlier: 3.933A pdb=" N MET 1 183 " --> pdb=" O TRP 1 179 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET 1 184 " --> pdb=" O PRO 1 180 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER 1 188 " --> pdb=" O MET 1 184 " (cutoff:3.500A) Processing helix chain '1' and resid 222 through 241 removed outlier: 4.639A pdb=" N GLU 1 227 " --> pdb=" O PHE 1 223 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR 1 228 " --> pdb=" O PHE 1 224 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 1 231 " --> pdb=" O GLU 1 227 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE 1 232 " --> pdb=" O TYR 1 228 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET 1 233 " --> pdb=" O ALA 1 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU 1 241 " --> pdb=" O PHE 1 237 " (cutoff:3.500A) Processing helix chain '1' and resid 253 through 274 removed outlier: 3.651A pdb=" N ASN 1 258 " --> pdb=" O LEU 1 254 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 1 260 " --> pdb=" O THR 1 256 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE 1 261 " --> pdb=" O ILE 1 257 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS 1 262 " --> pdb=" O ASN 1 258 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU 1 265 " --> pdb=" O ILE 1 261 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU 1 266 " --> pdb=" O LYS 1 262 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE 1 270 " --> pdb=" O LEU 1 266 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU 1 271 " --> pdb=" O THR 1 267 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG 1 274 " --> pdb=" O PHE 1 270 " (cutoff:3.500A) Processing helix chain '1' and resid 283 through 290 removed outlier: 3.659A pdb=" N HIS 1 287 " --> pdb=" O ASP 1 283 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU 1 289 " --> pdb=" O LEU 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 293 through 311 removed outlier: 4.012A pdb=" N VAL 1 305 " --> pdb=" O CYS 1 301 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER 1 306 " --> pdb=" O MET 1 302 " (cutoff:3.500A) Proline residue: 1 308 - end of helix Processing helix chain '6' and resid 3 through 11 removed outlier: 4.062A pdb=" N LEU 6 7 " --> pdb=" O MET 6 3 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER 6 8 " --> pdb=" O PHE 6 4 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 22 Proline residue: 6 18 - end of helix removed outlier: 3.658A pdb=" N MET 6 21 " --> pdb=" O PRO 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 32 through 41 Processing helix chain '6' and resid 43 through 57 Proline residue: 6 50 - end of helix removed outlier: 3.916A pdb=" N MET 6 53 " --> pdb=" O ILE 6 49 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE 6 55 " --> pdb=" O THR 6 51 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS 6 56 " --> pdb=" O MET 6 52 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER 6 57 " --> pdb=" O MET 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 99 removed outlier: 3.821A pdb=" N ILE 6 90 " --> pdb=" O SER 6 86 " (cutoff:3.500A) Proline residue: 6 91 - end of helix removed outlier: 3.533A pdb=" N THR 6 97 " --> pdb=" O ALA 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 101 through 107 Processing helix chain '6' and resid 114 through 132 removed outlier: 3.905A pdb=" N PHE 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS 6 119 " --> pdb=" O ASN 6 115 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU 6 122 " --> pdb=" O PHE 6 118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU 6 123 " --> pdb=" O LYS 6 119 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU 6 131 " --> pdb=" O THR 6 127 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL 6 132 " --> pdb=" O MET 6 128 " (cutoff:3.500A) Processing helix chain '6' and resid 137 through 157 removed outlier: 3.580A pdb=" N GLU 6 145 " --> pdb=" O PHE 6 141 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY 6 148 " --> pdb=" O TRP 6 144 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET 6 150 " --> pdb=" O GLY 6 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER 6 151 " --> pdb=" O VAL 6 147 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU 6 153 " --> pdb=" O ILE 6 149 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TRP 6 157 " --> pdb=" O LEU 6 153 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 193 removed outlier: 3.587A pdb=" N ILE 6 172 " --> pdb=" O ALA 6 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU 6 173 " --> pdb=" O LEU 6 169 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR 6 174 " --> pdb=" O GLN 6 170 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN 6 175 " --> pdb=" O ALA 6 171 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG 6 176 " --> pdb=" O ILE 6 172 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE 6 177 " --> pdb=" O LEU 6 173 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY 6 178 " --> pdb=" O TYR 6 174 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY 6 181 " --> pdb=" O ILE 6 177 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE 6 182 " --> pdb=" O GLY 6 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE 6 183 " --> pdb=" O ASP 6 179 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU 6 184 " --> pdb=" O ILE 6 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP 6 188 " --> pdb=" O LEU 6 184 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE 6 189 " --> pdb=" O ALA 6 185 " (cutoff:3.500A) Processing helix chain '6' and resid 198 through 203 removed outlier: 3.649A pdb=" N PHE 6 202 " --> pdb=" O LEU 6 198 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 223 removed outlier: 3.598A pdb=" N ILE 6 214 " --> pdb=" O ASN 6 210 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY 6 215 " --> pdb=" O MET 6 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY 6 222 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS 6 223 " --> pdb=" O ALA 6 219 " (cutoff:3.500A) Processing helix chain '6' and resid 230 through 238 removed outlier: 3.999A pdb=" N LEU 6 233 " --> pdb=" O HIS 6 230 " (cutoff:3.500A) Proline residue: 6 234 - end of helix removed outlier: 4.404A pdb=" N MET 6 237 " --> pdb=" O PRO 6 234 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU 6 238 " --> pdb=" O SER 6 235 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 230 through 238' Processing helix chain '6' and resid 241 through 247 Processing helix chain '6' and resid 255 through 262 removed outlier: 3.844A pdb=" N LEU 6 259 " --> pdb=" O ALA 6 255 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU 6 260 " --> pdb=" O GLY 6 256 " (cutoff:3.500A) Processing helix chain '6' and resid 272 through 291 removed outlier: 3.860A pdb=" N ILE 6 276 " --> pdb=" O TYR 6 272 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE 6 283 " --> pdb=" O CYS 6 279 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR 6 285 " --> pdb=" O GLY 6 281 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU 6 286 " --> pdb=" O ALA 6 282 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE 6 287 " --> pdb=" O ILE 6 283 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR 6 288 " --> pdb=" O THR 6 284 " (cutoff:3.500A) Processing helix chain '6' and resid 298 through 318 removed outlier: 3.683A pdb=" N SER 6 305 " --> pdb=" O ILE 6 301 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER 6 307 " --> pdb=" O ALA 6 303 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU 6 312 " --> pdb=" O SER 6 308 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL 6 315 " --> pdb=" O GLY 6 311 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE 6 317 " --> pdb=" O MET 6 313 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY 6 318 " --> pdb=" O MET 6 314 " (cutoff:3.500A) Processing helix chain '6' and resid 322 through 350 removed outlier: 3.597A pdb=" N HIS 6 328 " --> pdb=" O LEU 6 324 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE 6 329 " --> pdb=" O ALA 6 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA 6 333 " --> pdb=" O ILE 6 329 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE 6 334 " --> pdb=" O CYS 6 330 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE 6 335 " --> pdb=" O THR 6 331 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS 6 336 " --> pdb=" O HIS 6 332 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA 6 337 " --> pdb=" O ALA 6 333 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET 6 338 " --> pdb=" O PHE 6 334 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET 6 341 " --> pdb=" O ALA 6 337 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE 6 346 " --> pdb=" O CYS 6 342 " (cutoff:3.500A) Processing helix chain '6' and resid 368 through 380 removed outlier: 3.523A pdb=" N ILE 6 374 " --> pdb=" O THR 6 370 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL 6 375 " --> pdb=" O THR 6 371 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY 6 376 " --> pdb=" O ALA 6 372 " (cutoff:3.500A) Processing helix chain '6' and resid 389 through 396 removed outlier: 4.742A pdb=" N LEU 6 394 " --> pdb=" O TYR 6 390 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE 6 395 " --> pdb=" O SER 6 391 " (cutoff:3.500A) Processing helix chain '6' and resid 409 through 412 No H-bonds generated for 'chain '6' and resid 409 through 412' Processing helix chain '6' and resid 414 through 430 removed outlier: 3.542A pdb=" N PHE 6 418 " --> pdb=" O ILE 6 414 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR 6 422 " --> pdb=" O PHE 6 418 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER 6 423 " --> pdb=" O THR 6 419 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR 6 424 " --> pdb=" O ALA 6 420 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG 6 425 " --> pdb=" O ILE 6 421 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE 6 426 " --> pdb=" O TYR 6 422 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE 6 427 " --> pdb=" O SER 6 423 " (cutoff:3.500A) Processing helix chain '6' and resid 448 through 462 removed outlier: 3.514A pdb=" N SER 6 453 " --> pdb=" O LEU 6 449 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE 6 459 " --> pdb=" O LYS 6 455 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY 6 460 " --> pdb=" O ARG 6 456 " (cutoff:3.500A) Processing helix chain '6' and resid 464 through 467 No H-bonds generated for 'chain '6' and resid 464 through 467' Processing helix chain '6' and resid 489 through 509 removed outlier: 3.703A pdb=" N GLY 6 497 " --> pdb=" O VAL 6 493 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE 6 498 " --> pdb=" O THR 6 494 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE 6 499 " --> pdb=" O ILE 6 495 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET 6 507 " --> pdb=" O GLU 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 529 through 547 removed outlier: 4.063A pdb=" N HIS 6 534 " --> pdb=" O PRO 6 530 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG 6 535 " --> pdb=" O THR 6 531 " (cutoff:3.500A) Proline residue: 6 538 - end of helix removed outlier: 3.868A pdb=" N ASN 6 541 " --> pdb=" O ALA 6 537 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU 6 542 " --> pdb=" O PRO 6 538 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER 6 545 " --> pdb=" O ASN 6 541 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN 6 546 " --> pdb=" O LEU 6 542 " (cutoff:3.500A) Processing helix chain '6' and resid 551 through 554 No H-bonds generated for 'chain '6' and resid 551 through 554' Processing helix chain '6' and resid 562 through 572 removed outlier: 3.701A pdb=" N ILE 6 566 " --> pdb=" O LEU 6 562 " (cutoff:3.500A) Processing helix chain '6' and resid 574 through 577 No H-bonds generated for 'chain '6' and resid 574 through 577' Processing helix chain '6' and resid 584 through 600 removed outlier: 3.505A pdb=" N LEU 6 589 " --> pdb=" O LYS 6 585 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER 6 590 " --> pdb=" O LEU 6 586 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 6 592 " --> pdb=" O PHE 6 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE 6 593 " --> pdb=" O LEU 6 589 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET 6 599 " --> pdb=" O ILE 6 595 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE 6 600 " --> pdb=" O LEU 6 596 " (cutoff:3.500A) Processing helix chain '6' and resid 603 through 605 No H-bonds generated for 'chain '6' and resid 603 through 605' Processing helix chain 'g' and resid 29 through 33 removed outlier: 3.779A pdb=" N LEU g 33 " --> pdb=" O ILE g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 58 removed outlier: 3.589A pdb=" N VAL g 41 " --> pdb=" O PHE g 37 " (cutoff:3.500A) Proline residue: g 44 - end of helix removed outlier: 4.050A pdb=" N LEU g 47 " --> pdb=" O ARG g 43 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL g 48 " --> pdb=" O PRO g 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS g 58 " --> pdb=" O ARG g 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 114 removed outlier: 4.298A pdb=" N GLU g 89 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG g 94 " --> pdb=" O MET g 90 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL g 98 " --> pdb=" O ARG g 94 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP g 99 " --> pdb=" O ASP g 95 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU g 101 " --> pdb=" O LYS g 97 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL g 103 " --> pdb=" O ASP g 99 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN g 104 " --> pdb=" O GLN g 100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS g 113 " --> pdb=" O ARG g 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 134 No H-bonds generated for 'chain 'g' and resid 132 through 134' Processing helix chain 'g' and resid 137 through 143 removed outlier: 4.664A pdb=" N ASP g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG g 142 " --> pdb=" O ALA g 138 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR g 143 " --> pdb=" O TYR g 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 137 through 143' Processing helix chain 'g' and resid 158 through 164 removed outlier: 3.972A pdb=" N ARG g 162 " --> pdb=" O LYS g 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 140 removed outlier: 3.616A pdb=" N GLY e 135 " --> pdb=" O LYS e 131 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE e 136 " --> pdb=" O HIS e 132 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL e 137 " --> pdb=" O LEU e 133 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE e 139 " --> pdb=" O GLY e 135 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 144 No H-bonds generated for 'chain 'e' and resid 142 through 144' Processing helix chain 'M' and resid 10 through 21 removed outlier: 3.946A pdb=" N ARG M 14 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL M 15 " --> pdb=" O ILE M 11 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR M 17 " --> pdb=" O ASP M 13 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS M 20 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 21 " --> pdb=" O TYR M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 54 removed outlier: 4.192A pdb=" N ALA M 53 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N MET M 54 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 68 Processing helix chain 'M' and resid 73 through 84 removed outlier: 3.657A pdb=" N LYS M 83 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '8' and resid 241 through 243 removed outlier: 6.883A pdb=" N ALA 8 153 " --> pdb=" O LEU 8 113 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL 8 115 " --> pdb=" O ALA 8 153 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR 8 155 " --> pdb=" O VAL 8 115 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE 8 196 " --> pdb=" O ILE 8 156 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE 8 158 " --> pdb=" O PHE 8 196 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL 8 198 " --> pdb=" O ILE 8 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '8' and resid 275 through 277 Processing sheet with id= C, first strand: chain '8' and resid 316 through 318 removed outlier: 4.057A pdb=" N ILE 8 355 " --> pdb=" O ILE 8 318 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '9' and resid 130 through 134 Processing sheet with id= E, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= F, first strand: chain 'A' and resid 198 through 200 Processing sheet with id= G, first strand: chain 'A' and resid 246 through 250 removed outlier: 3.793A pdb=" N ARG A 246 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 265 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 248 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 250 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG A 272 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 338 through 342 removed outlier: 6.286A pdb=" N MET A 544 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE A 341 " --> pdb=" O MET A 544 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE A 546 " --> pdb=" O ILE A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 428 through 432 removed outlier: 3.696A pdb=" N LEU A 402 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 432 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.027A pdb=" N VAL A 582 " --> pdb=" O TYR A 568 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 408 through 411 removed outlier: 3.611A pdb=" N LYS B 423 " --> pdb=" O TYR B 410 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 112 through 120 removed outlier: 6.755A pdb=" N ASN C 133 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU C 116 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL C 131 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA C 118 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU C 129 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 145 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 143 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER C 141 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU C 86 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 88 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 146 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR C 148 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 77 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 85 through 87 Processing sheet with id= N, first strand: chain 'E' and resid 100 through 103 Processing sheet with id= O, first strand: chain 'E' and resid 128 through 134 removed outlier: 3.717A pdb=" N THR E 129 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU E 133 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR E 142 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 78 through 81 removed outlier: 3.548A pdb=" N PHE G 80 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.550A pdb=" N GLU K 18 " --> pdb=" O ARG K 68 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 55 through 57 removed outlier: 6.578A pdb=" N GLN R 79 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET R 106 " --> pdb=" O VAL R 82 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 71 through 73 removed outlier: 6.955A pdb=" N GLY S 144 " --> pdb=" O LYS S 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= S 1212 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.40 Time building geometry restraints manager: 19.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 24643 1.39 - 1.62: 36201 1.62 - 1.84: 648 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 61572 Sorted by residual: bond pdb=" C1D NAP R 601 " pdb=" O4D NAP R 601 " ideal model delta sigma weight residual 1.375 1.630 -0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C1B NAP R 601 " pdb=" C2B NAP R 601 " ideal model delta sigma weight residual 1.528 1.293 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1D NAP R 601 " pdb=" C2D NAP R 601 " ideal model delta sigma weight residual 1.533 1.309 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1B NAP R 601 " pdb=" O4B NAP R 601 " ideal model delta sigma weight residual 1.400 1.615 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C4D NAP R 601 " pdb=" O4D NAP R 601 " ideal model delta sigma weight residual 1.447 1.298 0.149 2.00e-02 2.50e+03 5.56e+01 ... (remaining 61567 not shown) Histogram of bond angle deviations from ideal: 73.22 - 88.21: 74 88.21 - 103.19: 747 103.19 - 118.17: 46132 118.17 - 133.15: 36680 133.15 - 148.13: 191 Bond angle restraints: 83824 Sorted by residual: angle pdb=" S1 FES 9 301 " pdb="FE2 FES 9 301 " pdb=" S2 FES 9 301 " ideal model delta sigma weight residual 104.33 88.86 15.47 1.14e+00 7.69e-01 1.84e+02 angle pdb=" S1 FES 9 301 " pdb="FE1 FES 9 301 " pdb=" S2 FES 9 301 " ideal model delta sigma weight residual 104.33 88.90 15.43 1.20e+00 6.94e-01 1.65e+02 angle pdb=" N LYS e 77 " pdb=" CA LYS e 77 " pdb=" C LYS e 77 " ideal model delta sigma weight residual 111.28 97.44 13.84 1.09e+00 8.42e-01 1.61e+02 angle pdb="FE1 FES 9 301 " pdb=" S2 FES 9 301 " pdb="FE2 FES 9 301 " ideal model delta sigma weight residual 75.66 89.05 -13.39 1.14e+00 7.69e-01 1.38e+02 angle pdb="FE1 FES 9 301 " pdb=" S1 FES 9 301 " pdb="FE2 FES 9 301 " ideal model delta sigma weight residual 75.66 89.29 -13.63 1.20e+00 6.94e-01 1.29e+02 ... (remaining 83819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 36192 34.24 - 68.48: 392 68.48 - 102.71: 18 102.71 - 136.95: 0 136.95 - 171.19: 1 Dihedral angle restraints: 36603 sinusoidal: 13613 harmonic: 22990 Sorted by residual: dihedral pdb=" CA CYS D 186 " pdb=" C CYS D 186 " pdb=" N PRO D 187 " pdb=" CA PRO D 187 " ideal model delta harmonic sigma weight residual -180.00 -116.90 -63.10 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CA ALA h 81 " pdb=" C ALA h 81 " pdb=" N VAL h 82 " pdb=" CA VAL h 82 " ideal model delta harmonic sigma weight residual -180.00 -121.40 -58.60 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA PRO h 80 " pdb=" C PRO h 80 " pdb=" N ALA h 81 " pdb=" CA ALA h 81 " ideal model delta harmonic sigma weight residual 180.00 -122.19 -57.81 0 5.00e+00 4.00e-02 1.34e+02 ... (remaining 36600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 8124 0.083 - 0.167: 1214 0.167 - 0.250: 112 0.250 - 0.333: 20 0.333 - 0.417: 3 Chirality restraints: 9473 Sorted by residual: chirality pdb=" CA PRO S 200 " pdb=" N PRO S 200 " pdb=" C PRO S 200 " pdb=" CB PRO S 200 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C2B NAP R 601 " pdb=" C1B NAP R 601 " pdb=" C3B NAP R 601 " pdb=" O2B NAP R 601 " both_signs ideal model delta sigma weight residual False -2.75 -2.35 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CB ILE R 220 " pdb=" CA ILE R 220 " pdb=" CG1 ILE R 220 " pdb=" CG2 ILE R 220 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 9470 not shown) Planarity restraints: 10621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN e 115 " -0.030 2.00e-02 2.50e+03 6.37e-02 4.05e+01 pdb=" C ASN e 115 " 0.110 2.00e-02 2.50e+03 pdb=" O ASN e 115 " -0.043 2.00e-02 2.50e+03 pdb=" N ARG e 116 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR e 75 " -0.098 5.00e-02 4.00e+02 1.52e-01 3.70e+01 pdb=" N PRO e 76 " 0.263 5.00e-02 4.00e+02 pdb=" CA PRO e 76 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO e 76 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS W 106 " -0.024 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C LYS W 106 " 0.089 2.00e-02 2.50e+03 pdb=" O LYS W 106 " -0.035 2.00e-02 2.50e+03 pdb=" N ASP W 107 " -0.030 2.00e-02 2.50e+03 ... (remaining 10618 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 9 2.19 - 2.87: 20821 2.87 - 3.55: 81353 3.55 - 4.22: 131667 4.22 - 4.90: 211082 Nonbonded interactions: 444932 Sorted by model distance: nonbonded pdb=" OD1 ASP S 196 " pdb=" CB TYR S 246 " model vdw 1.514 3.440 nonbonded pdb=" O GLN B 87 " pdb=" CD PRO B 89 " model vdw 1.621 3.440 nonbonded pdb=" CE1 TYR 1 127 " pdb=" N GLY 1 210 " model vdw 1.644 3.420 nonbonded pdb=" O LEU R 170 " pdb=" CD1 ILE R 328 " model vdw 1.783 3.460 nonbonded pdb=" O THR e 70 " pdb=" N TYR e 72 " model vdw 1.963 2.520 ... (remaining 444927 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 'M' and (resid 6 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 or (resid 22 through 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 27 or (resid 28 and (n \ ame N or name CA or name C or name O or name CB )) or resid 29 through 30 or (re \ sid 31 and (name N or name CA or name C or name O or name CB )) or resid 32 thro \ ugh 34 or (resid 35 and (name N or name CA or name C or name O or name CB )) or \ resid 36 through 38 or (resid 39 and (name N or name CA or name C or name O or n \ ame CB )) or resid 43 through 44 or (resid 45 through 46 and (name N or name CA \ or name C or name O or name CB )) or resid 47 through 51 or (resid 52 through 53 \ and (name N or name CA or name C or name O or name CB )) or resid 54 through 55 \ or (resid 56 and (name N or name CA or name C or name O or name CB )) or resid \ 57 through 65 or (resid 66 through 67 and (name N or name CA or name C or name O \ or name CB )) or resid 68 through 69 or (resid 70 and (name N or name CA or nam \ e C or name O or name CB )) or resid 71 through 72 or (resid 73 and (name N or n \ ame CA or name C or name O or name CB )) or resid 74 or (resid 75 and (name N or \ name CA or name C or name O or name CB )) or resid 76 through 77 or (resid 78 a \ nd (name N or name CA or name C or name O or name CB )) or resid 79 through 81 o \ r (resid 82 and (name N or name CA or name C or name O or name CB )) or resid 83 \ or (resid 84 through 85 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'W' and resid 74 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 S 393 5.16 5 C 38770 2.51 5 N 10216 2.21 5 O 10672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.420 Check model and map are aligned: 0.650 Process input model: 124.040 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.400 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 0.255 61572 Z= 0.468 Angle : 1.274 21.134 83824 Z= 0.695 Chirality : 0.060 0.417 9473 Planarity : 0.008 0.152 10621 Dihedral : 11.241 171.191 21729 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.64 % Allowed : 16.29 % Favored : 83.06 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.93 % Twisted Proline : 1.97 % Twisted General : 0.57 % 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: -5.67 (0.07), residues: 7801 helix: -3.97 (0.05), residues: 2933 sheet: -2.90 (0.28), residues: 280 loop : -3.86 (0.08), residues: 4588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15602 Ramachandran restraints generated. 7801 Oldfield, 0 Emsley, 7801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15602 Ramachandran restraints generated. 7801 Oldfield, 0 Emsley, 7801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 6894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1253 time to evaluate : 5.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 1283 average time/residue: 0.5788 time to fit residues: 1238.3556 Evaluate side-chains 679 residues out of total 6894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 666 time to evaluate : 5.342 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.5010 time to fit residues: 18.4663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 648 optimal weight: 0.1980 chunk 582 optimal weight: 20.0000 chunk 322 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 392 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 601 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 366 optimal weight: 6.9990 chunk 448 optimal weight: 6.9990 chunk 697 optimal weight: 10.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 63 GLN 2 112 HIS 2 120 GLN ** 3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 138 ASN ** 4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 338 HIS 4 374 ASN ** 4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 91 GLN ** 8 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS A 572 HIS A 666 GLN B 79 ASN B 131 GLN B 160 ASN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 250 ASN ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 201 GLN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 GLN H 27 HIS H 34 HIS H 45 HIS K 22 HIS N 83 GLN P 52 ASN Q 35 GLN R 43 HIS R 84 HIS R 102 GLN R 169 HIS ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 143 GLN S 245 GLN U 59 HIS X 13 HIS Y 86 HIS ** c 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN 1 97 ASN 1 235 ASN 1 292 ASN ** 6 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 175 ASN 6 210 ASN 6 226 GLN 6 270 ASN 6 446 ASN 6 471 ASN ** 6 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 161 GLN e 94 HIS ** M 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 61572 Z= 0.257 Angle : 0.842 18.173 83824 Z= 0.420 Chirality : 0.046 0.235 9473 Planarity : 0.006 0.134 10621 Dihedral : 8.901 165.903 8728 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 15.74 % Favored : 83.83 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.96 % Twisted Proline : 1.53 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.08), residues: 7801 helix: -2.71 (0.07), residues: 2998 sheet: -2.67 (0.27), residues: 300 loop : -3.63 (0.08), residues: 4503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15602 Ramachandran restraints generated. 7801 Oldfield, 0 Emsley, 7801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15602 Ramachandran restraints generated. 7801 Oldfield, 0 Emsley, 7801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 6894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 860 time to evaluate : 5.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 864 average time/residue: 0.5529 time to fit residues: 820.7521 Evaluate side-chains 638 residues out of total 6894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 635 time to evaluate : 5.397 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.4564 time to fit residues: 10.7812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.7717 > 50: distance: 13 - 17: 23.311 distance: 17 - 18: 35.324 distance: 18 - 19: 28.881 distance: 18 - 21: 3.142 distance: 19 - 20: 13.005 distance: 19 - 22: 30.823 distance: 22 - 23: 23.787 distance: 23 - 24: 13.044 distance: 23 - 26: 15.878 distance: 24 - 25: 10.222 distance: 24 - 29: 10.191 distance: 26 - 27: 12.377 distance: 26 - 28: 3.054 distance: 29 - 30: 12.909 distance: 30 - 31: 15.242 distance: 30 - 33: 16.189 distance: 31 - 32: 17.592 distance: 31 - 35: 6.403 distance: 33 - 34: 17.311 distance: 35 - 36: 7.470 distance: 36 - 37: 16.197 distance: 36 - 39: 11.660 distance: 37 - 38: 20.912 distance: 37 - 44: 24.611 distance: 39 - 40: 8.112 distance: 40 - 41: 5.599 distance: 41 - 42: 22.613 distance: 41 - 43: 23.710 distance: 44 - 45: 3.302 distance: 45 - 46: 4.394 distance: 45 - 48: 32.109 distance: 46 - 47: 6.387 distance: 46 - 51: 3.178 distance: 48 - 49: 24.122 distance: 51 - 52: 11.619 distance: 51 - 57: 9.335 distance: 52 - 53: 8.840 distance: 52 - 55: 9.815 distance: 53 - 54: 5.908 distance: 53 - 58: 10.063 distance: 55 - 56: 11.375 distance: 56 - 57: 14.231 distance: 58 - 59: 10.387 distance: 60 - 61: 10.022 distance: 60 - 68: 9.687 distance: 62 - 63: 5.589 distance: 63 - 64: 9.653 distance: 63 - 65: 9.097 distance: 64 - 66: 5.080 distance: 65 - 67: 6.074 distance: 66 - 67: 15.753 distance: 68 - 69: 5.005 distance: 69 - 70: 11.605 distance: 69 - 72: 7.946 distance: 70 - 71: 14.750 distance: 70 - 77: 8.774 distance: 72 - 73: 4.617 distance: 73 - 74: 8.321 distance: 74 - 75: 4.566 distance: 77 - 78: 4.902 distance: 78 - 79: 5.859 distance: 78 - 81: 10.789 distance: 79 - 88: 6.196 distance: 80 - 109: 7.335 distance: 81 - 82: 10.382 distance: 82 - 83: 5.904 distance: 83 - 84: 8.306 distance: 84 - 85: 3.817 distance: 85 - 86: 3.020 distance: 85 - 87: 3.579 distance: 88 - 89: 7.159 distance: 89 - 92: 9.425 distance: 90 - 91: 9.703 distance: 91 - 117: 13.398 distance: 92 - 93: 9.880 distance: 93 - 94: 10.610 distance: 93 - 95: 4.227