Starting phenix.real_space_refine on Tue Mar 19 07:17:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w59_32317/03_2024/7w59_32317_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w59_32317/03_2024/7w59_32317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w59_32317/03_2024/7w59_32317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w59_32317/03_2024/7w59_32317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w59_32317/03_2024/7w59_32317_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w59_32317/03_2024/7w59_32317_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 430 5.49 5 Mg 9 5.21 5 S 319 5.16 5 C 56178 2.51 5 N 16771 2.21 5 O 18602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ASP 944": "OD1" <-> "OD2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A PHE 1495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1499": "OE1" <-> "OE2" Residue "A PHE 1561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1757": "OE1" <-> "OE2" Residue "A GLU 1760": "OE1" <-> "OE2" Residue "A PHE 1808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "E TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 201": "NH1" <-> "NH2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "L ASP 129": "OD1" <-> "OD2" Residue "L PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 41": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "O PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 273": "NH1" <-> "NH2" Residue "R GLU 309": "OE1" <-> "OE2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R GLU 318": "OE1" <-> "OE2" Residue "R GLU 326": "OE1" <-> "OE2" Residue "S PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 457": "NH1" <-> "NH2" Residue "V ARG 545": "NH1" <-> "NH2" Residue "V ARG 602": "NH1" <-> "NH2" Residue "W ASP 73": "OD1" <-> "OD2" Residue "W TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 232": "OE1" <-> "OE2" Residue "W TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 495": "NH1" <-> "NH2" Residue "b GLU 47": "OE1" <-> "OE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "X TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X GLU 68": "OE1" <-> "OE2" Residue "X PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 80": "NH1" <-> "NH2" Residue "X GLU 84": "OE1" <-> "OE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X GLU 106": "OE1" <-> "OE2" Residue "X GLU 114": "OE1" <-> "OE2" Residue "X TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 536": "OE1" <-> "OE2" Residue "I ARG 567": "NH1" <-> "NH2" Residue "I GLU 617": "OE1" <-> "OE2" Residue "I GLU 624": "OE1" <-> "OE2" Residue "I GLU 675": "OE1" <-> "OE2" Residue "I PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 698": "NH1" <-> "NH2" Residue "I ARG 727": "NH1" <-> "NH2" Residue "Y PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 420": "OD1" <-> "OD2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "f GLU 28": "OE1" <-> "OE2" Residue "f ARG 73": "NH1" <-> "NH2" Residue "e ARG 76": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "i GLU 47": "OE1" <-> "OE2" Residue "i GLU 75": "OE1" <-> "OE2" Residue "j ARG 61": "NH1" <-> "NH2" Residue "k ARG 61": "NH1" <-> "NH2" Residue "k GLU 68": "OE1" <-> "OE2" Residue "k ARG 102": "NH1" <-> "NH2" Residue "m GLU 28": "OE1" <-> "OE2" Residue "m ARG 73": "NH1" <-> "NH2" Residue "l ARG 76": "NH1" <-> "NH2" Residue "n ARG 32": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92315 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 16449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1984, 16449 Classifications: {'peptide': 1984} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 106, 'TRANS': 1877} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 6798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6798 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 808} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain: "4" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 7, 'rna3p': 5} Chain: "G" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1510 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 2, 'rna3p_pur': 30, 'rna3p_pyr': 41} Link IDs: {'rna2p': 10, 'rna3p': 71} Chain breaks: 2 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {' G%rna3p_pur:plan2': 7, ' C%rna3p_pyr:plan': 6, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 8, ' C%rna3p_pyr:plan2': 6, ' G%rna3p_pur:plan': 7, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 263 Chain: "J" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 3814 Classifications: {'peptide': 568} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 265} Link IDs: {'PTRANS': 17, 'TRANS': 550} Chain breaks: 19 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1442 Unresolved non-hydrogen dihedrals: 963 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 45, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 709 Chain: "L" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3015 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 12, 'TRANS': 424} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 767 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 9, 'PHE:plan': 1, 'GLU:plan': 26, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 343 Chain: "M" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1098 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "N" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "O" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2296 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 17, 'TRANS': 267} Chain: "P" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 953 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 2 Chain: "R" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2243 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 22, 'TRANS': 257} Chain breaks: 1 Chain: "S" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "T" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2454 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain: "U" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 422 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "V" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 2632 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 12, 'TRANS': 439} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1110 Unresolved non-hydrogen angles: 1430 Unresolved non-hydrogen dihedrals: 898 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 19, 'TYR:plan': 10, 'ASN:plan1': 23, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 37, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 611 Chain: "W" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4129 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 24, 'TRANS': 484} Chain: "B" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1768 Classifications: {'RNA': 84} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 31, 'rna3p_pyr': 38} Link IDs: {'rna2p': 14, 'rna3p': 69} Chain breaks: 1 Chain: "F" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2075 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 36} Link IDs: {'rna2p': 15, 'rna3p': 81} Chain: "H" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2966 Classifications: {'RNA': 140} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 14, 'rna3p_pur': 59, 'rna3p_pyr': 60} Link IDs: {'rna2p': 21, 'rna3p': 118} Chain breaks: 6 Chain: "b" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 616 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "I" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 3845 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 348} Link IDs: {'PTRANS': 16, 'TRANS': 600} Chain breaks: 20 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1422 Unresolved non-hydrogen angles: 1830 Unresolved non-hydrogen dihedrals: 1208 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 13, 'TYR:plan': 20, 'ASN:plan1': 13, 'TRP:plan': 10, 'ASP:plan': 25, 'PHE:plan': 14, 'GLU:plan': 35, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 901 Chain: "y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 390 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 150 Chain: "Y" Number of atoms: 3431 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 667, 3411 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 558} Link IDs: {'PTRANS': 36, 'TRANS': 630} Chain breaks: 1 Unresolved chain link angles: 33 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2000 Unresolved non-hydrogen angles: 2558 Unresolved non-hydrogen dihedrals: 1647 Unresolved non-hydrogen chiralities: 199 Planarities with less than four sites: {'GLN:plan1': 35, 'ASP:plan': 34, 'TYR:plan': 27, 'ASN:plan1': 14, 'TRP:plan': 4, 'HIS:plan': 10, 'PHE:plan': 22, 'GLU:plan': 43, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 1038 Conformer: "B" Number of residues, atoms: 667, 3411 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 558} Link IDs: {'PTRANS': 36, 'TRANS': 630} Chain breaks: 1 Unresolved chain link angles: 33 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2000 Unresolved non-hydrogen angles: 2558 Unresolved non-hydrogen dihedrals: 1647 Unresolved non-hydrogen chiralities: 199 Planarities with less than four sites: {'GLN:plan1': 35, 'ASP:plan': 34, 'TYR:plan': 27, 'ASN:plan1': 14, 'TRP:plan': 4, 'HIS:plan': 10, 'PHE:plan': 22, 'GLU:plan': 43, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 1038 bond proxies already assigned to first conformer: 3392 Chain: "a" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 640 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Chain: "c" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "d" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "f" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "e" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 652 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 577 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "v" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 711 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 6, 'TRANS': 137} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 655 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 295 Chain: "w" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 445 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 3, 'TRANS': 87} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 190 Chain: "u" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 1907 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 342} Link IDs: {'PTRANS': 12, 'TRANS': 373} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1244 Unresolved non-hydrogen angles: 1586 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 5, 'TYR:plan': 13, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 27, 'PHE:plan': 14, 'GLU:plan': 27, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 682 Chain: "x" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 124 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 22} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 Chain: "Q" Number of atoms: 6562 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1322, 6554 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 4578 Unresolved non-hydrogen angles: 5873 Unresolved non-hydrogen dihedrals: 3847 Unresolved non-hydrogen chiralities: 385 Planarities with less than four sites: {'GLN:plan1': 63, 'ARG:plan': 84, 'TYR:plan': 52, 'ASN:plan1': 70, 'TRP:plan': 15, 'HIS:plan': 42, 'PHE:plan': 76, 'GLU:plan': 97, 'ASP:plan': 62} Unresolved non-hydrogen planarities: 2621 Conformer: "B" Number of residues, atoms: 1322, 6554 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 4578 Unresolved non-hydrogen angles: 5873 Unresolved non-hydrogen dihedrals: 3847 Unresolved non-hydrogen chiralities: 385 Planarities with less than four sites: {'GLN:plan1': 63, 'ARG:plan': 84, 'TYR:plan': 52, 'ASN:plan1': 70, 'TRP:plan': 15, 'HIS:plan': 42, 'PHE:plan': 76, 'GLU:plan': 97, 'ASP:plan': 62} Unresolved non-hydrogen planarities: 2621 bond proxies already assigned to first conformer: 6533 Chain: "h" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 633 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 690 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "m" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "l" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 644 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "n" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 538 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1282 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "p" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 760 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "q" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 659 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 10, 'TRANS': 121} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "r" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 654 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 10, 'TRANS': 120} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "s" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 659 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 10, 'TRANS': 121} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "t" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 654 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 10, 'TRANS': 120} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "K" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 772 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 536 Unresolved non-hydrogen angles: 681 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 335 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36195 SG CYS N 105 69.241 179.621 117.770 1.00 47.34 S ATOM 36289 SG CYS N 117 69.482 176.180 116.146 1.00 48.90 S ATOM 36422 SG CYS N 134 68.525 175.964 119.538 1.00 56.23 S ATOM 36170 SG CYS N 102 69.646 182.983 120.007 1.00 50.90 S ATOM 36195 SG CYS N 105 69.241 179.621 117.770 1.00 47.34 S ATOM 36445 SG CYS N 137 66.756 181.274 121.072 1.00 54.91 S ATOM 36164 SG CYS N 101 64.477 181.989 118.362 1.00 52.08 S ATOM 36303 SG CYS N 119 65.457 177.953 115.876 1.00 50.52 S ATOM 36476 SG CYS N 142 63.767 180.880 115.137 1.00 54.53 S ATOM 36530 SG CYS O 24 77.076 143.967 120.160 1.00 55.59 S ATOM 36552 SG CYS O 27 76.211 148.267 121.378 1.00 53.59 S ATOM 36995 SG CYS O 81 79.547 146.988 121.126 1.00 54.08 S ATOM 37017 SG CYS O 84 75.624 145.388 123.167 1.00 55.92 S ATOM 36701 SG CYS O 45 89.978 150.921 130.185 1.00 50.36 S ATOM 36724 SG CYS O 48 93.120 149.500 129.762 1.00 52.73 S ATOM 36920 SG CYS O 71 91.911 149.437 126.341 1.00 50.95 S ATOM 36942 SG CYS O 74 89.385 147.493 127.790 1.00 49.99 S ATOM 37663 SG CYS O 165 62.789 163.028 134.572 1.00 86.47 S ATOM 37729 SG CYS O 173 60.423 166.003 133.959 1.00 90.25 S ATOM 37777 SG CYS O 179 62.495 164.396 130.857 1.00 81.02 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG Y 668 " occ=0.45 ... (8 atoms not shown) pdb=" CB BARG Y 668 " occ=0.55 residue: pdb=" N AMET Y 683 " occ=0.49 ... (8 atoms not shown) pdb=" CB BMET Y 683 " occ=0.51 residue: pdb=" N AGLN Y1030 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLN Y1030 " occ=0.50 residue: pdb=" N AGLU Y1039 " occ=0.54 ... (8 atoms not shown) pdb=" CB BGLU Y1039 " occ=0.46 residue: pdb=" N MET Q 79 " occ=0.50 ... (3 atoms not shown) pdb=" CB MET Q 79 " occ=0.50 residue: pdb=" N MET Q 326 " occ=0.58 ... (3 atoms not shown) pdb=" CB MET Q 326 " occ=0.58 Time building chain proxies: 40.05, per 1000 atoms: 0.43 Number of scatterers: 92315 At special positions: 0 Unit cell: (242.178, 327.81, 283.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 319 16.00 P 430 15.00 Mg 9 11.99 O 18602 8.00 N 16771 7.00 C 56178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 308 " distance=2.05 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 Atom "ATOM 57283 O4' A H 29 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.10 Conformation dependent library (CDL) restraints added in 14.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 134 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 117 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 137 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 102 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 119 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 142 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 101 " pdb=" ZN O 501 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 81 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 27 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 84 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 24 " pdb=" ZN O 502 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 71 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 48 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 45 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 74 " pdb=" ZN O 503 " pdb="ZN ZN O 503 " - pdb=" NE2 HIS O 183 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 179 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 173 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 165 " Number of angles added : 15 23728 Ramachandran restraints generated. 11864 Oldfield, 0 Emsley, 11864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22974 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 450 helices and 94 sheets defined 41.8% alpha, 12.1% beta 86 base pairs and 182 stacking pairs defined. Time for finding SS restraints: 32.01 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.514A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 63 through 72 removed outlier: 3.526A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.579A pdb=" N LYS A 85 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 86 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR A 88 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.639A pdb=" N LYS A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 removed outlier: 3.694A pdb=" N MET A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.621A pdb=" N THR A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 396 through 403 removed outlier: 4.495A pdb=" N ASN A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 441 through 459 removed outlier: 3.984A pdb=" N SER A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 489 through 510 removed outlier: 3.517A pdb=" N CYS A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 542 through 551 removed outlier: 3.803A pdb=" N CYS A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.533A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.602A pdb=" N ALA A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 596 through 616 removed outlier: 3.693A pdb=" N ILE A 602 " --> pdb=" O MET A 599 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 606 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 608 " --> pdb=" O CYS A 605 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 610 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 612 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 613 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.508A pdb=" N ARG A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 638 " --> pdb=" O TRP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 659 Proline residue: A 646 - end of helix removed outlier: 3.786A pdb=" N GLY A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 690 removed outlier: 3.553A pdb=" N ASP A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 716 removed outlier: 4.116A pdb=" N ARG A 707 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 709 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 710 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 714 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 716 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 733 through 752 removed outlier: 3.509A pdb=" N LEU A 740 " --> pdb=" O GLU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 762 removed outlier: 3.588A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 759 " --> pdb=" O HIS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 797 removed outlier: 3.691A pdb=" N LYS A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 819 removed outlier: 3.536A pdb=" N VAL A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.819A pdb=" N GLU A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 removed outlier: 3.757A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 887 removed outlier: 3.661A pdb=" N LEU A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 932 removed outlier: 3.905A pdb=" N ILE A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 924 " --> pdb=" O ALA A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 960 removed outlier: 3.561A pdb=" N VAL A 952 " --> pdb=" O PRO A 948 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR A 953 " --> pdb=" O PRO A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 987 No H-bonds generated for 'chain 'A' and resid 985 through 987' Processing helix chain 'A' and resid 990 through 998 removed outlier: 3.888A pdb=" N ARG A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1013 removed outlier: 3.868A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1053 removed outlier: 3.770A pdb=" N LEU A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A1052 " --> pdb=" O MET A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1077 through 1080 No H-bonds generated for 'chain 'A' and resid 1077 through 1080' Processing helix chain 'A' and resid 1103 through 1116 removed outlier: 3.665A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1125 No H-bonds generated for 'chain 'A' and resid 1123 through 1125' Processing helix chain 'A' and resid 1146 through 1160 removed outlier: 3.646A pdb=" N ALA A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A1159 " --> pdb=" O TRP A1155 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1249 removed outlier: 3.537A pdb=" N GLN A1238 " --> pdb=" O ASP A1234 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A1243 " --> pdb=" O ARG A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1266 Processing helix chain 'A' and resid 1271 through 1274 No H-bonds generated for 'chain 'A' and resid 1271 through 1274' Processing helix chain 'A' and resid 1277 through 1280 No H-bonds generated for 'chain 'A' and resid 1277 through 1280' Processing helix chain 'A' and resid 1282 through 1300 removed outlier: 3.800A pdb=" N ASP A1286 " --> pdb=" O GLN A1282 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A1295 " --> pdb=" O CYS A1291 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A1299 " --> pdb=" O ILE A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1310 No H-bonds generated for 'chain 'A' and resid 1308 through 1310' Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1340 through 1346 removed outlier: 4.260A pdb=" N LYS A1344 " --> pdb=" O LEU A1340 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A1345 " --> pdb=" O ARG A1341 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A1346 " --> pdb=" O TRP A1342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1346' Processing helix chain 'A' and resid 1368 through 1371 Processing helix chain 'A' and resid 1375 through 1398 removed outlier: 3.811A pdb=" N ILE A1380 " --> pdb=" O GLU A1376 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A1387 " --> pdb=" O GLN A1383 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1391 " --> pdb=" O ALA A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1411 No H-bonds generated for 'chain 'A' and resid 1409 through 1411' Processing helix chain 'A' and resid 1419 through 1423 Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1437 through 1445 removed outlier: 3.774A pdb=" N ASP A1441 " --> pdb=" O ARG A1437 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1461 No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1472 through 1475 No H-bonds generated for 'chain 'A' and resid 1472 through 1475' Processing helix chain 'A' and resid 1481 through 1487 removed outlier: 4.430A pdb=" N GLU A1486 " --> pdb=" O GLU A1482 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1493 No H-bonds generated for 'chain 'A' and resid 1491 through 1493' Processing helix chain 'A' and resid 1498 through 1500 No H-bonds generated for 'chain 'A' and resid 1498 through 1500' Processing helix chain 'A' and resid 1509 through 1514 Processing helix chain 'A' and resid 1520 through 1542 removed outlier: 4.114A pdb=" N SER A1524 " --> pdb=" O ASN A1520 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A1529 " --> pdb=" O GLY A1525 " (cutoff:3.500A) Proline residue: A1530 - end of helix removed outlier: 3.599A pdb=" N LEU A1536 " --> pdb=" O ARG A1532 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP A1537 " --> pdb=" O ARG A1533 " (cutoff:3.500A) Proline residue: A1540 - end of helix Processing helix chain 'A' and resid 1567 through 1576 removed outlier: 3.803A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1600 removed outlier: 3.883A pdb=" N GLN A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1677 through 1687 removed outlier: 4.574A pdb=" N ARG A1681 " --> pdb=" O GLU A1677 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A1682 " --> pdb=" O ARG A1678 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS A1683 " --> pdb=" O TYR A1679 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A1684 " --> pdb=" O ALA A1680 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A1685 " --> pdb=" O ARG A1681 " (cutoff:3.500A) Processing helix chain 'A' and resid 1723 through 1736 removed outlier: 3.783A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1731 " --> pdb=" O GLN A1727 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A1735 " --> pdb=" O ALA A1731 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1751 removed outlier: 3.724A pdb=" N ARG A1748 " --> pdb=" O ARG A1744 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1772 removed outlier: 3.679A pdb=" N LEU A1771 " --> pdb=" O TYR A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1827 Processing helix chain 'A' and resid 1833 through 1851 removed outlier: 3.825A pdb=" N TRP A1839 " --> pdb=" O GLN A1835 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A1842 " --> pdb=" O LYS A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1875 removed outlier: 3.815A pdb=" N LEU A1869 " --> pdb=" O LYS A1866 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) Proline residue: A1871 - end of helix removed outlier: 4.038A pdb=" N HIS A1875 " --> pdb=" O LEU A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1894 through 1898 Processing helix chain 'A' and resid 1900 through 1908 removed outlier: 3.748A pdb=" N ILE A1906 " --> pdb=" O PHE A1902 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU A1907 " --> pdb=" O GLY A1903 " (cutoff:3.500A) Processing helix chain 'A' and resid 1923 through 1925 No H-bonds generated for 'chain 'A' and resid 1923 through 1925' Processing helix chain 'A' and resid 1929 through 1945 removed outlier: 3.579A pdb=" N LEU A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1954 removed outlier: 3.745A pdb=" N ILE A1953 " --> pdb=" O ARG A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1973 through 1995 removed outlier: 3.780A pdb=" N ILE A1987 " --> pdb=" O LEU A1983 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1993 " --> pdb=" O ALA A1989 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS A1994 " --> pdb=" O ASP A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2001 No H-bonds generated for 'chain 'A' and resid 1999 through 2001' Processing helix chain 'A' and resid 2004 through 2011 removed outlier: 3.611A pdb=" N ILE A2010 " --> pdb=" O GLU A2006 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.817A pdb=" N TYR C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.531A pdb=" N ASP C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 153 removed outlier: 3.657A pdb=" N VAL C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 177 No H-bonds generated for 'chain 'C' and resid 174 through 177' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 215 through 221 removed outlier: 3.500A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.821A pdb=" N LYS C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 263 Processing helix chain 'C' and resid 271 through 290 removed outlier: 3.666A pdb=" N TYR C 275 " --> pdb=" O PRO C 271 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 290 " --> pdb=" O ASN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.842A pdb=" N ALA C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR C 327 " --> pdb=" O PHE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 4.247A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.587A pdb=" N PHE C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 374 through 387 removed outlier: 3.505A pdb=" N LYS C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 398 removed outlier: 3.666A pdb=" N ASP C 397 " --> pdb=" O PRO C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 412 through 423 removed outlier: 3.932A pdb=" N ARG C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 removed outlier: 3.650A pdb=" N ASP C 432 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 removed outlier: 5.182A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix removed outlier: 4.110A pdb=" N GLU C 450 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 467 removed outlier: 3.785A pdb=" N ASP C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 613 Proline residue: C 601 - end of helix removed outlier: 3.738A pdb=" N LEU C 607 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL C 610 " --> pdb=" O LEU C 607 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C 613 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 646 removed outlier: 3.619A pdb=" N ASP C 643 " --> pdb=" O CYS C 639 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 646 " --> pdb=" O HIS C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 701 removed outlier: 3.591A pdb=" N GLU C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 722 removed outlier: 3.794A pdb=" N GLY C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 730 Processing helix chain 'C' and resid 750 through 773 removed outlier: 4.806A pdb=" N VAL C 754 " --> pdb=" O PRO C 751 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ALA C 757 " --> pdb=" O VAL C 754 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY C 760 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 764 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN C 768 " --> pdb=" O SER C 765 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN C 771 " --> pdb=" O GLN C 768 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 773 " --> pdb=" O PHE C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 804 Processing helix chain 'C' and resid 807 through 821 removed outlier: 3.602A pdb=" N THR C 811 " --> pdb=" O GLN C 807 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 813 " --> pdb=" O ILE C 809 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 814 " --> pdb=" O PRO C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 852 removed outlier: 3.524A pdb=" N VAL C 843 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER C 844 " --> pdb=" O ASP C 841 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 845 " --> pdb=" O CYS C 842 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 852 " --> pdb=" O VAL C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 890 Processing helix chain 'C' and resid 926 through 940 removed outlier: 5.749A pdb=" N ALA C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG C 931 " --> pdb=" O HIS C 928 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 933 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 936 " --> pdb=" O PHE C 933 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 937 " --> pdb=" O MET C 934 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG C 939 " --> pdb=" O LYS C 936 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 199 removed outlier: 3.762A pdb=" N LEU J 195 " --> pdb=" O ALA J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 237 removed outlier: 3.819A pdb=" N ARG J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG J 228 " --> pdb=" O LYS J 224 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 254 removed outlier: 3.706A pdb=" N TYR J 248 " --> pdb=" O ASN J 244 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU J 252 " --> pdb=" O TYR J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 268 removed outlier: 3.507A pdb=" N SER J 263 " --> pdb=" O GLN J 259 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR J 265 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 287 removed outlier: 3.542A pdb=" N LEU J 280 " --> pdb=" O ILE J 276 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU J 284 " --> pdb=" O LEU J 280 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU J 286 " --> pdb=" O TYR J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 305 removed outlier: 4.184A pdb=" N ASN J 297 " --> pdb=" O ASN J 293 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR J 304 " --> pdb=" O ASP J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.706A pdb=" N LYS J 315 " --> pdb=" O GLN J 311 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR J 316 " --> pdb=" O PHE J 312 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 336 removed outlier: 3.641A pdb=" N GLN J 331 " --> pdb=" O ALA J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 355 removed outlier: 3.687A pdb=" N SER J 348 " --> pdb=" O GLN J 344 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR J 349 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 372 removed outlier: 3.683A pdb=" N ARG J 363 " --> pdb=" O VAL J 359 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR J 364 " --> pdb=" O ASP J 360 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE J 365 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU J 367 " --> pdb=" O ARG J 363 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU J 371 " --> pdb=" O GLU J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 388 Processing helix chain 'J' and resid 392 through 406 removed outlier: 3.760A pdb=" N LYS J 397 " --> pdb=" O ALA J 393 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR J 399 " --> pdb=" O ALA J 395 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU J 404 " --> pdb=" O GLU J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 425 Processing helix chain 'J' and resid 429 through 441 removed outlier: 3.906A pdb=" N VAL J 434 " --> pdb=" O GLU J 430 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE J 435 " --> pdb=" O ARG J 431 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA J 439 " --> pdb=" O ILE J 435 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU J 440 " --> pdb=" O TYR J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 466 removed outlier: 3.784A pdb=" N GLY J 463 " --> pdb=" O GLU J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 489 removed outlier: 3.615A pdb=" N GLU J 482 " --> pdb=" O PHE J 478 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN J 487 " --> pdb=" O GLU J 483 " (cutoff:3.500A) Proline residue: J 488 - end of helix Processing helix chain 'J' and resid 503 through 512 removed outlier: 4.130A pdb=" N GLU J 508 " --> pdb=" O ASP J 504 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU J 512 " --> pdb=" O GLU J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 521 through 533 removed outlier: 3.507A pdb=" N HIS J 529 " --> pdb=" O GLN J 525 " (cutoff:3.500A) Processing helix chain 'J' and resid 541 through 554 removed outlier: 4.202A pdb=" N GLU J 545 " --> pdb=" O ALA J 541 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU J 546 " --> pdb=" O LEU J 542 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU J 547 " --> pdb=" O TYR J 543 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA J 548 " --> pdb=" O GLU J 544 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP J 550 " --> pdb=" O LEU J 546 " (cutoff:3.500A) Proline residue: J 551 - end of helix Processing helix chain 'J' and resid 560 through 568 Proline residue: J 566 - end of helix Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 593 through 603 removed outlier: 3.951A pdb=" N THR J 598 " --> pdb=" O ARG J 594 " (cutoff:3.500A) Processing helix chain 'J' and resid 610 through 623 removed outlier: 3.500A pdb=" N ASP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 642 Processing helix chain 'J' and resid 649 through 659 removed outlier: 3.677A pdb=" N LEU J 653 " --> pdb=" O LEU J 649 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA J 659 " --> pdb=" O ASP J 655 " (cutoff:3.500A) Processing helix chain 'J' and resid 668 through 678 removed outlier: 3.669A pdb=" N MET J 674 " --> pdb=" O PRO J 670 " (cutoff:3.500A) Proline residue: J 675 - end of helix removed outlier: 3.675A pdb=" N LEU J 678 " --> pdb=" O MET J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 700 through 707 Processing helix chain 'J' and resid 719 through 730 Processing helix chain 'J' and resid 741 through 755 removed outlier: 3.691A pdb=" N LEU J 755 " --> pdb=" O ARG J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 765 through 774 Processing helix chain 'J' and resid 782 through 799 Processing helix chain 'L' and resid 13 through 25 removed outlier: 3.859A pdb=" N MET L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'L' and resid 43 through 52 removed outlier: 3.631A pdb=" N TYR L 51 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.587A pdb=" N GLU L 69 " --> pdb=" O ARG L 65 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS L 70 " --> pdb=" O GLU L 66 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU L 77 " --> pdb=" O HIS L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 Processing helix chain 'L' and resid 95 through 106 removed outlier: 4.230A pdb=" N TYR L 100 " --> pdb=" O CYS L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 158 removed outlier: 3.768A pdb=" N SER L 153 " --> pdb=" O LEU L 149 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 191 removed outlier: 3.691A pdb=" N GLN L 175 " --> pdb=" O ALA L 171 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU L 182 " --> pdb=" O GLU L 178 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA L 183 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS L 187 " --> pdb=" O ALA L 183 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU L 190 " --> pdb=" O GLN L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 211 No H-bonds generated for 'chain 'L' and resid 208 through 211' Processing helix chain 'L' and resid 244 through 248 Processing helix chain 'L' and resid 252 through 269 removed outlier: 3.500A pdb=" N GLU L 256 " --> pdb=" O ARG L 252 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS L 261 " --> pdb=" O GLY L 257 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 536 removed outlier: 3.598A pdb=" N GLU L 529 " --> pdb=" O ILE L 525 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG L 536 " --> pdb=" O LYS L 532 " (cutoff:3.500A) Processing helix chain 'L' and resid 569 through 589 removed outlier: 3.694A pdb=" N ILE L 575 " --> pdb=" O SER L 571 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS L 576 " --> pdb=" O GLU L 572 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS L 589 " --> pdb=" O TYR L 585 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 643 removed outlier: 3.926A pdb=" N GLU L 641 " --> pdb=" O VAL L 637 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 645 through 649 Processing helix chain 'L' and resid 691 through 799 removed outlier: 3.840A pdb=" N LEU L 696 " --> pdb=" O GLU L 693 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY L 701 " --> pdb=" O ILE L 698 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR L 704 " --> pdb=" O GLY L 701 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR L 705 " --> pdb=" O HIS L 702 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA L 707 " --> pdb=" O THR L 704 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA L 711 " --> pdb=" O LYS L 708 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS L 715 " --> pdb=" O LYS L 712 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS L 718 " --> pdb=" O LYS L 715 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE L 719 " --> pdb=" O LYS L 716 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU L 721 " --> pdb=" O LYS L 718 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY L 722 " --> pdb=" O ILE L 719 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY L 723 " --> pdb=" O LEU L 720 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN L 725 " --> pdb=" O GLY L 722 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET L 729 " --> pdb=" O SER L 726 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS L 733 " --> pdb=" O GLY L 730 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU L 735 " --> pdb=" O MET L 732 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP L 737 " --> pdb=" O GLN L 734 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TRP L 739 " --> pdb=" O ASN L 736 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP L 740 " --> pdb=" O ASP L 737 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE L 742 " --> pdb=" O TRP L 739 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN L 744 " --> pdb=" O GLN L 741 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU L 749 " --> pdb=" O HIS L 746 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR L 751 " --> pdb=" O GLU L 748 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 753 " --> pdb=" O ARG L 750 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU L 755 " --> pdb=" O PHE L 752 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP L 760 " --> pdb=" O LYS L 757 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER L 761 " --> pdb=" O HIS L 758 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE L 763 " --> pdb=" O ASP L 760 " (cutoff:3.500A) Proline residue: L 764 - end of helix removed outlier: 3.823A pdb=" N GLU L 768 " --> pdb=" O ARG L 765 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS L 769 " --> pdb=" O ARG L 766 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS L 771 " --> pdb=" O GLU L 768 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG L 776 " --> pdb=" O ASP L 773 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU L 779 " --> pdb=" O ARG L 776 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU L 781 " --> pdb=" O GLN L 778 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS L 782 " --> pdb=" O GLU L 779 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS L 786 " --> pdb=" O GLU L 783 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR L 788 " --> pdb=" O GLN L 785 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU L 791 " --> pdb=" O TYR L 788 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU L 792 " --> pdb=" O ALA L 789 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU L 794 " --> pdb=" O LEU L 791 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 141 removed outlier: 3.693A pdb=" N GLN M 134 " --> pdb=" O ALA M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 161 removed outlier: 3.605A pdb=" N GLU M 154 " --> pdb=" O GLU M 150 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS M 155 " --> pdb=" O ARG M 151 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY M 157 " --> pdb=" O ARG M 153 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU M 159 " --> pdb=" O LYS M 155 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE M 160 " --> pdb=" O HIS M 156 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE M 161 " --> pdb=" O GLY M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 194 removed outlier: 4.266A pdb=" N MET M 182 " --> pdb=" O GLU M 178 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN M 189 " --> pdb=" O ASP M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 226 removed outlier: 3.811A pdb=" N LYS M 217 " --> pdb=" O GLU M 213 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE M 218 " --> pdb=" O ARG M 214 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG M 224 " --> pdb=" O LYS M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 239 removed outlier: 4.052A pdb=" N GLU M 238 " --> pdb=" O LYS M 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 32 Proline residue: N 20 - end of helix removed outlier: 3.610A pdb=" N ASP N 23 " --> pdb=" O PRO N 20 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU N 25 " --> pdb=" O LEU N 22 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET N 29 " --> pdb=" O ASP N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 64 Processing helix chain 'N' and resid 72 through 80 removed outlier: 3.754A pdb=" N LYS N 80 " --> pdb=" O GLU N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 92 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 123 through 126 No H-bonds generated for 'chain 'N' and resid 123 through 126' Processing helix chain 'O' and resid 73 through 76 No H-bonds generated for 'chain 'O' and resid 73 through 76' Processing helix chain 'O' and resid 94 through 100 Processing helix chain 'O' and resid 111 through 127 removed outlier: 4.169A pdb=" N GLU O 115 " --> pdb=" O ASP O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 139 No H-bonds generated for 'chain 'O' and resid 137 through 139' Processing helix chain 'O' and resid 147 through 149 No H-bonds generated for 'chain 'O' and resid 147 through 149' Processing helix chain 'O' and resid 157 through 160 Processing helix chain 'O' and resid 192 through 194 No H-bonds generated for 'chain 'O' and resid 192 through 194' Processing helix chain 'O' and resid 198 through 203 Processing helix chain 'O' and resid 208 through 218 removed outlier: 3.796A pdb=" N LYS O 212 " --> pdb=" O PRO O 208 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU O 213 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU O 214 " --> pdb=" O ALA O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 249 Processing helix chain 'O' and resid 252 through 254 No H-bonds generated for 'chain 'O' and resid 252 through 254' Processing helix chain 'O' and resid 277 through 287 removed outlier: 3.789A pdb=" N GLU O 285 " --> pdb=" O GLU O 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 59 through 77 Processing helix chain 'P' and resid 206 through 208 No H-bonds generated for 'chain 'P' and resid 206 through 208' Processing helix chain 'P' and resid 218 through 227 removed outlier: 3.850A pdb=" N LYS P 226 " --> pdb=" O LYS P 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 101 removed outlier: 3.721A pdb=" N ILE R 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 98 through 101' Processing helix chain 'R' and resid 103 through 105 No H-bonds generated for 'chain 'R' and resid 103 through 105' Processing helix chain 'R' and resid 138 through 161 removed outlier: 3.616A pdb=" N VAL R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN R 157 " --> pdb=" O LYS R 153 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS R 158 " --> pdb=" O SER R 154 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 245 removed outlier: 3.527A pdb=" N GLU R 244 " --> pdb=" O LYS R 240 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP R 245 " --> pdb=" O GLU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 268 Processing helix chain 'R' and resid 282 through 334 removed outlier: 3.691A pdb=" N LEU R 287 " --> pdb=" O PHE R 284 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA R 288 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU R 289 " --> pdb=" O LYS R 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR R 292 " --> pdb=" O GLU R 289 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE R 293 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP R 295 " --> pdb=" O TYR R 292 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS R 297 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG R 299 " --> pdb=" O ARG R 296 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA R 301 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU R 303 " --> pdb=" O GLU R 300 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 44 removed outlier: 3.514A pdb=" N ASN S 38 " --> pdb=" O LYS S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 122 No H-bonds generated for 'chain 'S' and resid 120 through 122' Processing helix chain 'S' and resid 136 through 143 removed outlier: 3.511A pdb=" N ASN S 140 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG S 141 " --> pdb=" O GLY S 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 190 removed outlier: 3.552A pdb=" N TRP T 190 " --> pdb=" O LYS T 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 187 through 190' Processing helix chain 'T' and resid 460 through 462 No H-bonds generated for 'chain 'T' and resid 460 through 462' Processing helix chain 'U' and resid 56 through 80 Processing helix chain 'U' and resid 85 through 99 Processing helix chain 'V' and resid 150 through 172 Processing helix chain 'V' and resid 178 through 187 removed outlier: 3.522A pdb=" N GLN V 187 " --> pdb=" O GLN V 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 207 Processing helix chain 'V' and resid 209 through 225 removed outlier: 5.184A pdb=" N HIS V 213 " --> pdb=" O ILE V 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN V 223 " --> pdb=" O ALA V 220 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 246 Processing helix chain 'V' and resid 250 through 265 Processing helix chain 'V' and resid 272 through 283 Processing helix chain 'V' and resid 287 through 307 removed outlier: 3.551A pdb=" N GLU V 299 " --> pdb=" O GLY V 295 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU V 302 " --> pdb=" O LYS V 298 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS V 303 " --> pdb=" O GLU V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 309 through 324 Processing helix chain 'V' and resid 330 through 344 Processing helix chain 'V' and resid 362 through 364 No H-bonds generated for 'chain 'V' and resid 362 through 364' Processing helix chain 'V' and resid 380 through 383 Processing helix chain 'V' and resid 391 through 405 removed outlier: 3.578A pdb=" N GLU V 404 " --> pdb=" O ALA V 400 " (cutoff:3.500A) Processing helix chain 'V' and resid 453 through 463 removed outlier: 3.626A pdb=" N THR V 458 " --> pdb=" O SER V 454 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA V 462 " --> pdb=" O THR V 458 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 479 removed outlier: 3.632A pdb=" N LYS V 475 " --> pdb=" O GLU V 471 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU V 476 " --> pdb=" O CYS V 472 " (cutoff:3.500A) Processing helix chain 'V' and resid 483 through 499 removed outlier: 3.992A pdb=" N LYS V 487 " --> pdb=" O SER V 484 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU V 489 " --> pdb=" O THR V 486 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE V 493 " --> pdb=" O CYS V 490 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP V 495 " --> pdb=" O MET V 492 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS V 497 " --> pdb=" O LEU V 494 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA V 498 " --> pdb=" O ASP V 495 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN V 499 " --> pdb=" O CYS V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 506 through 516 removed outlier: 3.568A pdb=" N GLY V 512 " --> pdb=" O GLY V 508 " (cutoff:3.500A) Processing helix chain 'V' and resid 519 through 530 removed outlier: 4.103A pdb=" N GLU V 523 " --> pdb=" O LYS V 519 " (cutoff:3.500A) Processing helix chain 'V' and resid 533 through 535 No H-bonds generated for 'chain 'V' and resid 533 through 535' Processing helix chain 'V' and resid 541 through 557 removed outlier: 4.111A pdb=" N ASN V 546 " --> pdb=" O ASN V 542 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL V 547 " --> pdb=" O LYS V 543 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS V 549 " --> pdb=" O ARG V 545 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE V 551 " --> pdb=" O VAL V 547 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU V 554 " --> pdb=" O MET V 550 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU V 555 " --> pdb=" O PHE V 551 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR V 556 " --> pdb=" O ALA V 552 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR V 557 " --> pdb=" O HIS V 553 " (cutoff:3.500A) Processing helix chain 'V' and resid 563 through 565 No H-bonds generated for 'chain 'V' and resid 563 through 565' Processing helix chain 'V' and resid 577 through 594 removed outlier: 4.123A pdb=" N ILE V 581 " --> pdb=" O SER V 577 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE V 586 " --> pdb=" O PHE V 582 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU V 590 " --> pdb=" O PHE V 586 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR V 593 " --> pdb=" O GLU V 589 " (cutoff:3.500A) Processing helix chain 'V' and resid 599 through 602 No H-bonds generated for 'chain 'V' and resid 599 through 602' Processing helix chain 'V' and resid 621 through 634 removed outlier: 3.965A pdb=" N ILE V 628 " --> pdb=" O THR V 624 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE V 634 " --> pdb=" O PHE V 630 " (cutoff:3.500A) Processing helix chain 'V' and resid 641 through 644 No H-bonds generated for 'chain 'V' and resid 641 through 644' Processing helix chain 'W' and resid 85 through 89 removed outlier: 3.730A pdb=" N PHE W 89 " --> pdb=" O TYR W 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 85 through 89' Processing helix chain 'W' and resid 122 through 134 Processing helix chain 'W' and resid 156 through 161 Processing helix chain 'W' and resid 212 through 225 removed outlier: 3.926A pdb=" N ASP W 217 " --> pdb=" O GLN W 213 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU W 218 " --> pdb=" O LYS W 214 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG W 223 " --> pdb=" O ILE W 219 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN W 224 " --> pdb=" O THR W 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 12 removed outlier: 4.672A pdb=" N HIS b 12 " --> pdb=" O LYS b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 76 No H-bonds generated for 'chain 'b' and resid 74 through 76' Processing helix chain 'X' and resid 55 through 72 removed outlier: 3.518A pdb=" N GLN X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 78 Processing helix chain 'X' and resid 84 through 121 Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 35 through 45 Processing helix chain 'I' and resid 51 through 62 Processing helix chain 'I' and resid 72 through 84 Processing helix chain 'I' and resid 88 through 104 Processing helix chain 'I' and resid 110 through 121 Processing helix chain 'I' and resid 127 through 138 Processing helix chain 'I' and resid 146 through 157 Proline residue: I 150 - end of helix Processing helix chain 'I' and resid 162 through 174 Processing helix chain 'I' and resid 180 through 189 Processing helix chain 'I' and resid 195 through 204 Processing helix chain 'I' and resid 218 through 232 Proline residue: I 232 - end of helix Processing helix chain 'I' and resid 240 through 249 Processing helix chain 'I' and resid 254 through 267 Processing helix chain 'I' and resid 272 through 285 Processing helix chain 'I' and resid 290 through 311 Processing helix chain 'I' and resid 323 through 352 Proline residue: I 342 - end of helix removed outlier: 3.556A pdb=" N LEU I 349 " --> pdb=" O LEU I 345 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG I 351 " --> pdb=" O SER I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 369 removed outlier: 3.926A pdb=" N GLN I 368 " --> pdb=" O VAL I 364 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLY I 369 " --> pdb=" O ALA I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 383 Processing helix chain 'I' and resid 396 through 407 Processing helix chain 'I' and resid 411 through 422 Processing helix chain 'I' and resid 430 through 445 removed outlier: 4.157A pdb=" N SER I 434 " --> pdb=" O ASP I 430 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL I 435 " --> pdb=" O ASP I 431 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU I 444 " --> pdb=" O GLY I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 459 removed outlier: 3.521A pdb=" N LYS I 458 " --> pdb=" O ARG I 454 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA I 459 " --> pdb=" O LEU I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 496 Processing helix chain 'I' and resid 503 through 512 removed outlier: 3.732A pdb=" N TYR I 507 " --> pdb=" O THR I 503 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP I 508 " --> pdb=" O LYS I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 529 removed outlier: 3.586A pdb=" N ALA I 525 " --> pdb=" O VAL I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 547 Processing helix chain 'I' and resid 550 through 552 No H-bonds generated for 'chain 'I' and resid 550 through 552' Processing helix chain 'I' and resid 554 through 567 Processing helix chain 'I' and resid 574 through 583 removed outlier: 3.836A pdb=" N GLN I 582 " --> pdb=" O ASP I 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA I 583 " --> pdb=" O LEU I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 593 through 605 Processing helix chain 'I' and resid 610 through 619 removed outlier: 4.470A pdb=" N VAL I 615 " --> pdb=" O HIS I 611 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR I 616 " --> pdb=" O ALA I 612 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU I 617 " --> pdb=" O MET I 613 " (cutoff:3.500A) Processing helix chain 'I' and resid 625 through 639 Processing helix chain 'I' and resid 648 through 655 removed outlier: 3.908A pdb=" N GLN I 653 " --> pdb=" O GLY I 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 661 through 678 removed outlier: 4.248A pdb=" N GLU I 666 " --> pdb=" O GLU I 662 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU I 669 " --> pdb=" O ARG I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 682 through 694 Processing helix chain 'I' and resid 702 through 714 removed outlier: 3.508A pdb=" N PHE I 710 " --> pdb=" O THR I 706 " (cutoff:3.500A) Processing helix chain 'I' and resid 718 through 732 Processing helix chain 'y' and resid 19 through 29 Proline residue: y 28 - end of helix Processing helix chain 'y' and resid 57 through 67 Processing helix chain 'Y' and resid 397 through 407 Processing helix chain 'Y' and resid 558 through 563 Processing helix chain 'Y' and resid 566 through 580 removed outlier: 3.640A pdb=" N LYS Y 569 " --> pdb=" O PRO Y 566 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU Y 572 " --> pdb=" O LYS Y 569 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL Y 575 " --> pdb=" O GLU Y 572 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN Y 576 " --> pdb=" O GLN Y 573 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL Y 578 " --> pdb=" O VAL Y 575 " (cutoff:3.500A) Processing helix chain 'Y' and resid 594 through 604 removed outlier: 4.800A pdb=" N THR Y 599 " --> pdb=" O THR Y 595 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN Y 600 " --> pdb=" O THR Y 596 " (cutoff:3.500A) Processing helix chain 'Y' and resid 607 through 609 No H-bonds generated for 'chain 'Y' and resid 607 through 609' Processing helix chain 'Y' and resid 620 through 634 Processing helix chain 'Y' and resid 663 through 672 removed outlier: 3.504A pdb=" N ILE Y 672 " --> pdb=" O AARG Y 668 " (cutoff:3.500A) Processing helix chain 'Y' and resid 692 through 707 removed outlier: 3.819A pdb=" N GLN Y 706 " --> pdb=" O LYS Y 702 " (cutoff:3.500A) Processing helix chain 'Y' and resid 719 through 728 removed outlier: 4.775A pdb=" N VAL Y 723 " --> pdb=" O THR Y 719 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LYS Y 724 " --> pdb=" O LEU Y 720 " (cutoff:3.500A) Processing helix chain 'Y' and resid 756 through 770 Processing helix chain 'Y' and resid 783 through 800 removed outlier: 3.640A pdb=" N LEU Y 800 " --> pdb=" O ARG Y 796 " (cutoff:3.500A) Processing helix chain 'Y' and resid 818 through 825 removed outlier: 3.669A pdb=" N ARG Y 823 " --> pdb=" O GLU Y 819 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE Y 824 " --> pdb=" O MET Y 820 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE Y 825 " --> pdb=" O GLN Y 821 " (cutoff:3.500A) Processing helix chain 'Y' and resid 840 through 844 removed outlier: 3.644A pdb=" N THR Y 844 " --> pdb=" O ILE Y 841 " (cutoff:3.500A) Processing helix chain 'Y' and resid 881 through 892 removed outlier: 3.691A pdb=" N ARG Y 890 " --> pdb=" O GLN Y 886 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA Y 891 " --> pdb=" O ARG Y 887 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY Y 892 " --> pdb=" O ALA Y 888 " (cutoff:3.500A) Processing helix chain 'Y' and resid 905 through 910 Processing helix chain 'Y' and resid 919 through 921 No H-bonds generated for 'chain 'Y' and resid 919 through 921' Processing helix chain 'Y' and resid 926 through 935 Processing helix chain 'Y' and resid 951 through 964 Processing helix chain 'Y' and resid 975 through 982 removed outlier: 3.535A pdb=" N GLU Y 982 " --> pdb=" O ARG Y 978 " (cutoff:3.500A) Processing helix chain 'Y' and resid 987 through 998 removed outlier: 3.734A pdb=" N VAL Y 997 " --> pdb=" O LEU Y 993 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS Y 998 " --> pdb=" O ILE Y 994 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1002 through 1012 removed outlier: 3.627A pdb=" N THR Y1007 " --> pdb=" O GLU Y1003 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1025 through 1035 removed outlier: 3.634A pdb=" N LYS Y1034 " --> pdb=" O AGLN Y1030 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE Y1035 " --> pdb=" O LYS Y1031 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1041 through 1054 Processing helix chain 'Y' and resid 1059 through 1065 Processing helix chain 'Y' and resid 1069 through 1088 Processing helix chain 'Y' and resid 1101 through 1114 removed outlier: 7.025A pdb=" N ARG Y1113 " --> pdb=" O SER Y1109 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN Y1114 " --> pdb=" O GLY Y1110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1170 through 1176 removed outlier: 3.650A pdb=" N PHE Y1176 " --> pdb=" O LEU Y1173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1178 through 1180 No H-bonds generated for 'chain 'Y' and resid 1178 through 1180' Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 65 through 67 No H-bonds generated for 'chain 'a' and resid 65 through 67' Processing helix chain 'c' and resid 3 through 10 removed outlier: 3.958A pdb=" N LEU c 10 " --> pdb=" O PHE c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 64 No H-bonds generated for 'chain 'c' and resid 62 through 64' Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 28 through 38 removed outlier: 3.634A pdb=" N GLN d 34 " --> pdb=" O VAL d 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL d 36 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN d 38 " --> pdb=" O SER d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 105 No H-bonds generated for 'chain 'd' and resid 103 through 105' Processing helix chain 'f' and resid 7 through 14 Processing helix chain 'f' and resid 66 through 68 No H-bonds generated for 'chain 'f' and resid 66 through 68' Processing helix chain 'e' and resid 17 through 27 Processing helix chain 'e' and resid 81 through 83 No H-bonds generated for 'chain 'e' and resid 81 through 83' Processing helix chain 'g' and resid 10 through 12 No H-bonds generated for 'chain 'g' and resid 10 through 12' Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain 'v' and resid 40 through 42 No H-bonds generated for 'chain 'v' and resid 40 through 42' Processing helix chain 'v' and resid 54 through 67 Processing helix chain 'v' and resid 69 through 71 No H-bonds generated for 'chain 'v' and resid 69 through 71' Processing helix chain 'v' and resid 107 through 112 Processing helix chain 'v' and resid 116 through 141 removed outlier: 4.108A pdb=" N VAL v 121 " --> pdb=" O GLU v 117 " (cutoff:3.500A) Processing helix chain 'w' and resid 86 through 96 removed outlier: 4.766A pdb=" N GLU w 95 " --> pdb=" O ASP w 91 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR w 96 " --> pdb=" O LYS w 92 " (cutoff:3.500A) Processing helix chain 'w' and resid 124 through 134 Processing helix chain 'u' and resid 40 through 42 No H-bonds generated for 'chain 'u' and resid 40 through 42' Processing helix chain 'u' and resid 47 through 56 Processing helix chain 'u' and resid 63 through 74 removed outlier: 3.678A pdb=" N ILE u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS u 70 " --> pdb=" O GLN u 66 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN u 71 " --> pdb=" O ARG u 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 88 through 98 Processing helix chain 'u' and resid 116 through 129 Processing helix chain 'u' and resid 146 through 155 Processing helix chain 'u' and resid 164 through 172 Processing helix chain 'u' and resid 189 through 192 No H-bonds generated for 'chain 'u' and resid 189 through 192' Processing helix chain 'u' and resid 198 through 207 removed outlier: 4.171A pdb=" N TYR u 207 " --> pdb=" O ASP u 203 " (cutoff:3.500A) Processing helix chain 'u' and resid 223 through 231 removed outlier: 3.560A pdb=" N MET u 228 " --> pdb=" O GLU u 224 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR u 229 " --> pdb=" O ILE u 225 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN u 230 " --> pdb=" O LEU u 226 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS u 231 " --> pdb=" O GLU u 227 " (cutoff:3.500A) Processing helix chain 'u' and resid 243 through 245 No H-bonds generated for 'chain 'u' and resid 243 through 245' Processing helix chain 'u' and resid 261 through 275 removed outlier: 3.611A pdb=" N ASP u 266 " --> pdb=" O TRP u 263 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP u 273 " --> pdb=" O ASP u 270 " (cutoff:3.500A) Processing helix chain 'u' and resid 287 through 300 removed outlier: 3.501A pdb=" N ALA u 300 " --> pdb=" O LYS u 296 " (cutoff:3.500A) Processing helix chain 'u' and resid 313 through 325 Processing helix chain 'u' and resid 335 through 337 No H-bonds generated for 'chain 'u' and resid 335 through 337' Processing helix chain 'u' and resid 358 through 367 removed outlier: 3.579A pdb=" N ILE u 362 " --> pdb=" O ARG u 358 " (cutoff:3.500A) Processing helix chain 'u' and resid 370 through 372 No H-bonds generated for 'chain 'u' and resid 370 through 372' Processing helix chain 'u' and resid 383 through 396 Processing helix chain 'x' and resid 172 through 174 No H-bonds generated for 'chain 'x' and resid 172 through 174' Processing helix chain 'Q' and resid 20 through 30 Processing helix chain 'Q' and resid 43 through 52 Processing helix chain 'Q' and resid 61 through 69 Processing helix chain 'Q' and resid 72 through 75 No H-bonds generated for 'chain 'Q' and resid 72 through 75' Processing helix chain 'Q' and resid 88 through 103 Processing helix chain 'Q' and resid 110 through 114 Processing helix chain 'Q' and resid 116 through 131 Proline residue: Q 120 - end of helix removed outlier: 3.612A pdb=" N LYS Q 128 " --> pdb=" O HIS Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 156 Processing helix chain 'Q' and resid 160 through 170 removed outlier: 3.937A pdb=" N GLN Q 165 " --> pdb=" O LEU Q 161 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU Q 169 " --> pdb=" O GLN Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 177 Processing helix chain 'Q' and resid 180 through 189 Processing helix chain 'Q' and resid 191 through 205 removed outlier: 3.999A pdb=" N LYS Q 195 " --> pdb=" O LYS Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 219 Processing helix chain 'Q' and resid 221 through 235 Processing helix chain 'Q' and resid 244 through 261 Processing helix chain 'Q' and resid 264 through 276 removed outlier: 5.204A pdb=" N TRP Q 269 " --> pdb=" O PRO Q 265 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE Q 270 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR Q 272 " --> pdb=" O ARG Q 268 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE Q 273 " --> pdb=" O TRP Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 284 Processing helix chain 'Q' and resid 287 through 290 No H-bonds generated for 'chain 'Q' and resid 287 through 290' Processing helix chain 'Q' and resid 296 through 309 Processing helix chain 'Q' and resid 323 through 344 Processing helix chain 'Q' and resid 346 through 353 removed outlier: 5.090A pdb=" N ASP Q 350 " --> pdb=" O GLU Q 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 359 No H-bonds generated for 'chain 'Q' and resid 356 through 359' Processing helix chain 'Q' and resid 362 through 369 Processing helix chain 'Q' and resid 374 through 384 Processing helix chain 'Q' and resid 400 through 411 Processing helix chain 'Q' and resid 417 through 423 Processing helix chain 'Q' and resid 462 through 492 removed outlier: 3.512A pdb=" N TYR Q 479 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU Q 480 " --> pdb=" O GLU Q 476 " (cutoff:3.500A) Processing helix chain 'Q' and resid 547 through 553 Processing helix chain 'Q' and resid 583 through 587 Processing helix chain 'Q' and resid 631 through 644 Processing helix chain 'Q' and resid 649 through 651 No H-bonds generated for 'chain 'Q' and resid 649 through 651' Processing helix chain 'Q' and resid 661 through 663 No H-bonds generated for 'chain 'Q' and resid 661 through 663' Processing helix chain 'Q' and resid 666 through 678 Processing helix chain 'Q' and resid 685 through 692 removed outlier: 4.791A pdb=" N ASP Q 689 " --> pdb=" O ASP Q 685 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE Q 690 " --> pdb=" O TRP Q 686 " (cutoff:3.500A) Processing helix chain 'Q' and resid 702 through 704 No H-bonds generated for 'chain 'Q' and resid 702 through 704' Processing helix chain 'Q' and resid 721 through 727 Processing helix chain 'Q' and resid 791 through 793 No H-bonds generated for 'chain 'Q' and resid 791 through 793' Processing helix chain 'Q' and resid 804 through 814 Processing helix chain 'Q' and resid 829 through 843 Processing helix chain 'Q' and resid 856 through 868 removed outlier: 3.806A pdb=" N ALA Q 868 " --> pdb=" O GLU Q 864 " (cutoff:3.500A) Processing helix chain 'Q' and resid 873 through 875 No H-bonds generated for 'chain 'Q' and resid 873 through 875' Processing helix chain 'Q' and resid 894 through 918 Processing helix chain 'Q' and resid 929 through 943 removed outlier: 3.582A pdb=" N PHE Q 935 " --> pdb=" O ALA Q 932 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG Q 943 " --> pdb=" O VAL Q 940 " (cutoff:3.500A) Processing helix chain 'Q' and resid 945 through 951 Processing helix chain 'Q' and resid 961 through 966 removed outlier: 3.872A pdb=" N SER Q 965 " --> pdb=" O VAL Q 961 " (cutoff:3.500A) Processing helix chain 'Q' and resid 987 through 1016 removed outlier: 3.780A pdb=" N LEU Q1008 " --> pdb=" O ILE Q1004 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA Q1013 " --> pdb=" O GLU Q1009 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER Q1014 " --> pdb=" O GLU Q1010 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU Q1015 " --> pdb=" O PHE Q1011 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1020 through 1029 Processing helix chain 'Q' and resid 1039 through 1052 removed outlier: 5.525A pdb=" N HIS Q1047 " --> pdb=" O ALA Q1043 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASP Q1048 " --> pdb=" O LEU Q1044 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1064 through 1066 No H-bonds generated for 'chain 'Q' and resid 1064 through 1066' Processing helix chain 'Q' and resid 1069 through 1077 Proline residue: Q1075 - end of helix Processing helix chain 'Q' and resid 1108 through 1113 Processing helix chain 'Q' and resid 1119 through 1126 Processing helix chain 'Q' and resid 1141 through 1150 removed outlier: 4.198A pdb=" N LEU Q1146 " --> pdb=" O SER Q1142 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR Q1147 " --> pdb=" O LEU Q1143 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP Q1149 " --> pdb=" O ASN Q1145 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG Q1150 " --> pdb=" O LEU Q1146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1158 through 1162 Processing helix chain 'Q' and resid 1164 through 1166 No H-bonds generated for 'chain 'Q' and resid 1164 through 1166' Processing helix chain 'Q' and resid 1201 through 1217 Processing helix chain 'Q' and resid 1221 through 1223 No H-bonds generated for 'chain 'Q' and resid 1221 through 1223' Processing helix chain 'Q' and resid 1231 through 1244 Processing helix chain 'Q' and resid 1260 through 1262 No H-bonds generated for 'chain 'Q' and resid 1260 through 1262' Processing helix chain 'Q' and resid 1282 through 1285 Processing helix chain 'Q' and resid 1287 through 1295 Processing helix chain 'Q' and resid 1307 through 1311 Processing helix chain 'Q' and resid 1314 through 1325 Proline residue: Q1318 - end of helix removed outlier: 4.546A pdb=" N SER Q1321 " --> pdb=" O PRO Q1318 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR Q1324 " --> pdb=" O SER Q1321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1358 through 1375 removed outlier: 3.617A pdb=" N GLN Q1374 " --> pdb=" O MET Q1370 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 Processing helix chain 'h' and resid 65 through 67 No H-bonds generated for 'chain 'h' and resid 65 through 67' Processing helix chain 'i' and resid 7 through 12 removed outlier: 4.670A pdb=" N HIS i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 76 No H-bonds generated for 'chain 'i' and resid 74 through 76' Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.959A pdb=" N LEU j 10 " --> pdb=" O PHE j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 64 No H-bonds generated for 'chain 'j' and resid 62 through 64' Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'k' and resid 21 through 26 Processing helix chain 'k' and resid 28 through 38 removed outlier: 3.635A pdb=" N GLN k 34 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL k 36 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS k 37 " --> pdb=" O GLN k 34 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN k 38 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 105 No H-bonds generated for 'chain 'k' and resid 103 through 105' Processing helix chain 'm' and resid 7 through 14 Processing helix chain 'm' and resid 66 through 68 No H-bonds generated for 'chain 'm' and resid 66 through 68' Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'n' and resid 10 through 12 No H-bonds generated for 'chain 'n' and resid 10 through 12' Processing helix chain 'n' and resid 64 through 66 No H-bonds generated for 'chain 'n' and resid 64 through 66' Processing helix chain 'o' and resid 6 through 11 removed outlier: 3.512A pdb=" N GLN o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 40 Processing helix chain 'o' and resid 83 through 86 No H-bonds generated for 'chain 'o' and resid 83 through 86' Processing helix chain 'o' and resid 103 through 111 Proline residue: o 108 - end of helix removed outlier: 3.567A pdb=" N SER o 111 " --> pdb=" O PRO o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 124 through 127 Processing helix chain 'o' and resid 131 through 138 Processing helix chain 'o' and resid 152 through 160 Processing helix chain 'p' and resid 20 through 34 removed outlier: 4.194A pdb=" N GLN p 33 " --> pdb=" O ALA p 29 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE p 34 " --> pdb=" O LEU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 68 Processing helix chain 'p' and resid 89 through 95 Processing helix chain 'q' and resid 27 through 36 removed outlier: 3.723A pdb=" N LYS q 32 " --> pdb=" O ARG q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 133 removed outlier: 3.729A pdb=" N LEU q 87 " --> pdb=" O ASP q 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE q 90 " --> pdb=" O MET q 86 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU q 92 " --> pdb=" O HIS q 88 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN q 95 " --> pdb=" O THR q 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR q 98 " --> pdb=" O GLN q 94 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN q 101 " --> pdb=" O GLN q 97 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG q 115 " --> pdb=" O ASP q 111 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL q 116 " --> pdb=" O ALA q 112 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR q 125 " --> pdb=" O THR q 121 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR q 133 " --> pdb=" O GLU q 129 " (cutoff:3.500A) Processing helix chain 'r' and resid 27 through 36 Processing helix chain 'r' and resid 70 through 74 Processing helix chain 'r' and resid 76 through 132 removed outlier: 3.604A pdb=" N HIS r 88 " --> pdb=" O ALA r 84 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS r 122 " --> pdb=" O ALA r 118 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR r 125 " --> pdb=" O THR r 121 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA r 126 " --> pdb=" O LYS r 122 " (cutoff:3.500A) Processing helix chain 's' and resid 27 through 36 Processing helix chain 's' and resid 72 through 133 removed outlier: 3.629A pdb=" N ALA s 84 " --> pdb=" O ASP s 80 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR s 91 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN s 95 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU s 102 " --> pdb=" O THR s 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE s 117 " --> pdb=" O ALA s 113 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS s 122 " --> pdb=" O ALA s 118 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU s 129 " --> pdb=" O THR s 125 " (cutoff:3.500A) Processing helix chain 't' and resid 27 through 36 Processing helix chain 't' and resid 71 through 132 removed outlier: 3.708A pdb=" N LYS t 76 " --> pdb=" O PRO t 72 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU t 87 " --> pdb=" O ASP t 83 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU t 92 " --> pdb=" O HIS t 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG t 93 " --> pdb=" O SER t 89 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN t 95 " --> pdb=" O THR t 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU t 96 " --> pdb=" O LEU t 92 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN t 109 " --> pdb=" O HIS t 105 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS t 114 " --> pdb=" O HIS t 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG t 115 " --> pdb=" O ASP t 111 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA t 118 " --> pdb=" O CYS t 114 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG t 119 " --> pdb=" O ARG t 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 42 Processing helix chain 'K' and resid 66 through 77 Processing helix chain 'K' and resid 106 through 123 removed outlier: 3.572A pdb=" N GLU K 115 " --> pdb=" O MET K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 130 removed outlier: 4.038A pdb=" N HIS K 130 " --> pdb=" O LEU K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 204 removed outlier: 3.664A pdb=" N TYR K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN K 141 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS K 148 " --> pdb=" O HIS K 144 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN K 150 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN K 169 " --> pdb=" O TRP K 165 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 482 through 488 removed outlier: 3.591A pdb=" N TYR A 120 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 516 through 518 removed outlier: 3.549A pdb=" N LYS A 525 " --> pdb=" O HIS A 517 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 895 through 900 Processing sheet with id= D, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 7.273A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= F, first strand: chain 'A' and resid 1185 through 1188 removed outlier: 3.532A pdb=" N LEU A1197 " --> pdb=" O GLN A1227 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1334 through 1337 Processing sheet with id= H, first strand: chain 'A' and resid 1714 through 1716 removed outlier: 8.058A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1777 through 1780 removed outlier: 6.811A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 1788 through 1792 Processing sheet with id= K, first strand: chain 'A' and resid 1819 through 1821 removed outlier: 3.773A pdb=" N VAL A1915 " --> pdb=" O LEU A1819 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A1913 " --> pdb=" O ILE A1821 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 316 through 318 removed outlier: 9.581A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 229 " --> pdb=" O CYS C 256 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ARG C 130 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU C 199 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL C 132 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN C 201 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 134 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET C 203 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLY C 136 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 348 through 350 Processing sheet with id= N, first strand: chain 'C' and resid 524 through 526 removed outlier: 3.734A pdb=" N HIS C 477 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN C 548 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 530 through 534 removed outlier: 4.495A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 541 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.885A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 662 through 666 removed outlier: 3.520A pdb=" N HIS C 903 " --> pdb=" O TYR C 831 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 674 through 677 removed outlier: 4.784A pdb=" N CYS C 674 " --> pdb=" O MET C 687 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET C 687 " --> pdb=" O CYS C 674 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 685 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 688 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE C 791 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU C 690 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE C 789 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 831 through 839 removed outlier: 6.128A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 61 through 63 removed outlier: 4.367A pdb=" N ARG E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 346 " --> pdb=" O ARG E 350 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR E 352 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 69 through 74 removed outlier: 7.420A pdb=" N ALA E 84 " --> pdb=" O TYR E 70 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS E 72 " --> pdb=" O ALA E 82 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA E 82 " --> pdb=" O CYS E 72 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N PHE E 74 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR E 80 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA E 103 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN E 94 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN E 101 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.625A pdb=" N ALA E 127 " --> pdb=" O MET E 113 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU E 115 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE E 125 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR E 117 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET E 123 " --> pdb=" O TYR E 117 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS E 145 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP E 137 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG E 143 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 189 through 191 removed outlier: 4.259A pdb=" N THR E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 171 " --> pdb=" O THR E 175 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 196 through 201 removed outlier: 6.961A pdb=" N GLY E 211 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL E 199 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE E 209 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE E 201 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLN E 207 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 217 " --> pdb=" O MET E 231 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR E 229 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP E 221 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU E 227 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 240 through 243 removed outlier: 4.449A pdb=" N GLY E 240 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP E 263 " --> pdb=" O CYS E 273 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N CYS E 273 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 291 through 293 removed outlier: 3.539A pdb=" N ALA E 301 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR E 310 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP E 313 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE E 319 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 36 through 39 removed outlier: 3.648A pdb=" N ARG O 56 " --> pdb=" O THR O 37 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 299 through 302 removed outlier: 3.659A pdb=" N ASN O 299 " --> pdb=" O GLY O 237 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR O 260 " --> pdb=" O GLN O 273 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 174 through 179 Processing sheet with id= AD, first strand: chain 'S' and resid 13 through 17 removed outlier: 5.709A pdb=" N GLU S 26 " --> pdb=" O VAL S 132 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL S 132 " --> pdb=" O GLU S 26 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU S 98 " --> pdb=" O PHE S 129 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE S 97 " --> pdb=" O THR S 115 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 207 through 212 removed outlier: 6.584A pdb=" N GLY T 222 " --> pdb=" O ARG T 208 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE T 210 " --> pdb=" O VAL T 220 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL T 220 " --> pdb=" O ILE T 210 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL T 212 " --> pdb=" O TRP T 218 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TRP T 218 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR T 227 " --> pdb=" O SER T 223 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASP T 232 " --> pdb=" O LEU T 238 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU T 238 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 291 through 296 removed outlier: 6.784A pdb=" N CYS T 306 " --> pdb=" O TYR T 292 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU T 294 " --> pdb=" O VAL T 304 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL T 304 " --> pdb=" O LEU T 294 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU T 296 " --> pdb=" O VAL T 302 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL T 302 " --> pdb=" O LEU T 296 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS T 324 " --> pdb=" O ILE T 314 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP T 316 " --> pdb=" O SER T 322 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER T 322 " --> pdb=" O ASP T 316 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 333 through 337 removed outlier: 6.729A pdb=" N GLY T 348 " --> pdb=" O ALA T 334 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL T 336 " --> pdb=" O ILE T 346 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE T 346 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE T 345 " --> pdb=" O TRP T 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG T 355 " --> pdb=" O THR T 347 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL T 366 " --> pdb=" O LEU T 356 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASP T 358 " --> pdb=" O THR T 364 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR T 364 " --> pdb=" O ASP T 358 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'T' and resid 407 through 409 removed outlier: 3.979A pdb=" N GLN T 407 " --> pdb=" O GLN T 397 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA T 377 " --> pdb=" O GLY T 390 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'T' and resid 448 through 451 removed outlier: 4.009A pdb=" N GLN T 448 " --> pdb=" O LEU T 438 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR T 435 " --> pdb=" O ALA T 431 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA T 431 " --> pdb=" O THR T 435 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'T' and resid 194 through 200 removed outlier: 6.484A pdb=" N VAL T 488 " --> pdb=" O TYR T 197 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL T 199 " --> pdb=" O ILE T 486 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE T 486 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA T 467 " --> pdb=" O ALA T 480 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'T' and resid 249 through 254 removed outlier: 6.596A pdb=" N CYS T 264 " --> pdb=" O ARG T 250 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL T 252 " --> pdb=" O PHE T 262 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE T 262 " --> pdb=" O VAL T 252 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'T' and resid 270 through 274 removed outlier: 3.664A pdb=" N VAL T 270 " --> pdb=" O TYR T 284 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG T 282 " --> pdb=" O CYS T 272 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASP T 274 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL T 280 " --> pdb=" O ASP T 274 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'W' and resid 137 through 139 Processing sheet with id= AN, first strand: chain 'W' and resid 326 through 329 removed outlier: 3.685A pdb=" N ARG W 326 " --> pdb=" O LEU W 315 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS W 312 " --> pdb=" O SER W 308 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS W 314 " --> pdb=" O SER W 306 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU W 304 " --> pdb=" O TRP W 316 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA W 293 " --> pdb=" O CYS W 307 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'W' and resid 338 through 340 removed outlier: 3.705A pdb=" N CYS W 339 " --> pdb=" O LEU W 348 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER W 368 " --> pdb=" O LEU W 358 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP W 360 " --> pdb=" O CYS W 366 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N CYS W 366 " --> pdb=" O ASP W 360 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'W' and resid 379 through 381 Processing sheet with id= AQ, first strand: chain 'W' and resid 467 through 469 removed outlier: 3.645A pdb=" N THR W 468 " --> pdb=" O ALA W 477 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA W 477 " --> pdb=" O THR W 468 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'W' and resid 514 through 516 removed outlier: 4.093A pdb=" N ASP W 515 " --> pdb=" O ILE W 524 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE W 524 " --> pdb=" O ASP W 515 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER W 525 " --> pdb=" O ASN W 533 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP W 536 " --> pdb=" O LEU W 542 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU W 542 " --> pdb=" O ASP W 536 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'W' and resid 421 through 425 removed outlier: 6.827A pdb=" N THR W 436 " --> pdb=" O ASN W 422 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE W 424 " --> pdb=" O VAL W 434 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL W 434 " --> pdb=" O ILE W 424 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'W' and resid 441 through 445 removed outlier: 3.818A pdb=" N VAL W 444 " --> pdb=" O LYS W 454 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS W 454 " --> pdb=" O VAL W 444 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'b' and resid 64 through 68 removed outlier: 6.217A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG b 18 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL b 82 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE b 20 " --> pdb=" O MET b 80 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N MET b 80 " --> pdb=" O ILE b 20 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'b' and resid 70 through 72 removed outlier: 3.688A pdb=" N ALA b 33 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS b 43 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE b 31 " --> pdb=" O CYS b 43 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'y' and resid 78 through 81 Processing sheet with id= AX, first strand: chain 'Y' and resid 733 through 737 removed outlier: 6.593A pdb=" N LEU Y 713 " --> pdb=" O LEU Y 584 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL Y 586 " --> pdb=" O LEU Y 713 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL Y 715 " --> pdb=" O VAL Y 586 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLY Y 588 " --> pdb=" O VAL Y 715 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER Y 717 " --> pdb=" O GLY Y 588 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS Y 612 " --> pdb=" O ALA Y 680 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE Y 682 " --> pdb=" O LYS Y 612 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY Y 614 " --> pdb=" O ILE Y 682 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU Y 684 " --> pdb=" O GLY Y 614 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR Y 616 " --> pdb=" O LEU Y 684 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Y' and resid 744 through 748 removed outlier: 6.914A pdb=" N GLY Y 897 " --> pdb=" O GLU Y 745 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU Y 747 " --> pdb=" O GLY Y 897 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS Y 899 " --> pdb=" O LEU Y 747 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP Y 775 " --> pdb=" O TYR Y 852 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL Y 854 " --> pdb=" O ASP Y 775 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU Y 777 " --> pdb=" O VAL Y 854 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP Y 856 " --> pdb=" O LEU Y 777 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE Y 779 " --> pdb=" O ASP Y 856 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU Y 806 " --> pdb=" O ARG Y 833 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL Y 835 " --> pdb=" O GLU Y 806 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE Y 808 " --> pdb=" O VAL Y 835 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE Y 837 " --> pdb=" O ILE Y 808 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU Y 810 " --> pdb=" O ILE Y 837 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Y' and resid 859 through 866 removed outlier: 3.516A pdb=" N ILE Y 871 " --> pdb=" O ASN Y 866 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Y' and resid 1124 through 1126 Processing sheet with id= BB, first strand: chain 'Y' and resid 1153 through 1156 Processing sheet with id= BC, first strand: chain 'a' and resid 55 through 58 Processing sheet with id= BD, first strand: chain 'a' and resid 60 through 63 removed outlier: 6.830A pdb=" N SER a 44 " --> pdb=" O LEU a 32 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU a 32 " --> pdb=" O SER a 44 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'c' and resid 53 through 55 Processing sheet with id= BF, first strand: chain 'c' and resid 57 through 60 removed outlier: 6.031A pdb=" N LYS c 41 " --> pdb=" O ILE c 29 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE c 29 " --> pdb=" O LYS c 41 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'd' and resid 89 through 96 Processing sheet with id= BH, first strand: chain 'd' and resid 98 through 101 removed outlier: 6.583A pdb=" N GLU d 68 " --> pdb=" O VAL d 56 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL d 56 " --> pdb=" O GLU d 68 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'f' and resid 57 through 60 removed outlier: 3.573A pdb=" N GLY f 57 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR f 47 " --> pdb=" O LEU f 59 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'f' and resid 62 through 64 removed outlier: 3.672A pdb=" N SER f 35 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA f 45 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU f 33 " --> pdb=" O ALA f 45 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'e' and resid 70 through 75 removed outlier: 5.724A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N MET e 41 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU e 35 " --> pdb=" O MET e 41 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG e 30 " --> pdb=" O VAL e 90 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'e' and resid 77 through 79 removed outlier: 3.790A pdb=" N GLY e 49 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP e 59 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE e 47 " --> pdb=" O ASP e 59 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'g' and resid 67 through 72 removed outlier: 6.921A pdb=" N LYS g 20 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU g 70 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER g 18 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA g 72 " --> pdb=" O LYS g 16 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LYS g 16 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'g' and resid 45 through 48 removed outlier: 6.476A pdb=" N GLU g 47 " --> pdb=" O ASN g 56 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN g 56 " --> pdb=" O GLU g 47 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'v' and resid 46 through 51 Processing sheet with id= BP, first strand: chain 'w' and resid 145 through 148 removed outlier: 3.745A pdb=" N ASN w 101 " --> pdb=" O GLU w 120 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'u' and resid 237 through 239 Processing sheet with id= BR, first strand: chain 'u' and resid 400 through 402 removed outlier: 8.691A pdb=" N ASP u 401 " --> pdb=" O ILE u 251 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN u 253 " --> pdb=" O ASP u 401 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY u 375 " --> pdb=" O LYS u 252 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE u 254 " --> pdb=" O GLY u 375 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA u 377 " --> pdb=" O PHE u 254 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL u 256 " --> pdb=" O ALA u 377 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN u 379 " --> pdb=" O VAL u 256 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL u 258 " --> pdb=" O ASN u 379 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL u 381 " --> pdb=" O VAL u 258 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLN u 279 " --> pdb=" O SER u 347 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE u 349 " --> pdb=" O GLN u 279 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL u 281 " --> pdb=" O ILE u 349 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASN u 351 " --> pdb=" O VAL u 281 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE u 283 " --> pdb=" O ASN u 351 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER u 305 " --> pdb=" O ILE u 332 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id= BT, first strand: chain 'Q' and resid 511 through 513 removed outlier: 6.824A pdb=" N ARG Q 626 " --> pdb=" O GLN Q 598 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N MET Q 600 " --> pdb=" O THR Q 624 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR Q 624 " --> pdb=" O MET Q 600 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL Q 535 " --> pdb=" O LEU Q 629 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN Q 542 " --> pdb=" O ILE Q 514 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE Q 514 " --> pdb=" O ASN Q 542 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'Q' and resid 732 through 735 removed outlier: 3.608A pdb=" N PHE Q 747 " --> pdb=" O ASN Q 715 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN Q 715 " --> pdb=" O PHE Q 747 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE Q 749 " --> pdb=" O ASP Q 713 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP Q 713 " --> pdb=" O ILE Q 749 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'Q' and resid 817 through 822 removed outlier: 3.940A pdb=" N THR Q 853 " --> pdb=" O MET Q1037 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR Q1038 " --> pdb=" O LEU Q 879 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'Q' and resid 1177 through 1181 removed outlier: 6.781A pdb=" N LEU Q1301 " --> pdb=" O GLN Q1178 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE Q1180 " --> pdb=" O LEU Q1301 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE Q1303 " --> pdb=" O ILE Q1180 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'Q' and resid 1330 through 1332 Processing sheet with id= BY, first strand: chain 'h' and resid 55 through 58 Processing sheet with id= BZ, first strand: chain 'h' and resid 60 through 63 removed outlier: 6.831A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'i' and resid 64 through 68 removed outlier: 6.215A pdb=" N CYS i 45 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG i 18 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL i 82 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE i 20 " --> pdb=" O MET i 80 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET i 80 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'i' and resid 70 through 72 removed outlier: 3.689A pdb=" N ALA i 33 " --> pdb=" O ILE i 41 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS i 43 " --> pdb=" O PHE i 31 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE i 31 " --> pdb=" O CYS i 43 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'j' and resid 53 through 55 Processing sheet with id= CD, first strand: chain 'j' and resid 57 through 60 removed outlier: 6.031A pdb=" N LYS j 41 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE j 29 " --> pdb=" O LYS j 41 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'k' and resid 90 through 96 Processing sheet with id= CF, first strand: chain 'k' and resid 98 through 101 removed outlier: 6.583A pdb=" N GLU k 68 " --> pdb=" O VAL k 56 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL k 56 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'm' and resid 57 through 60 removed outlier: 3.571A pdb=" N GLY m 57 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR m 47 " --> pdb=" O LEU m 59 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'm' and resid 62 through 64 removed outlier: 3.672A pdb=" N SER m 35 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'l' and resid 70 through 75 removed outlier: 5.725A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG l 30 " --> pdb=" O VAL l 90 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'l' and resid 77 through 79 removed outlier: 3.790A pdb=" N GLY l 49 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP l 59 " --> pdb=" O ILE l 47 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE l 47 " --> pdb=" O ASP l 59 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'n' and resid 67 through 72 removed outlier: 6.920A pdb=" N LYS n 20 " --> pdb=" O ILE n 68 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA n 72 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LYS n 16 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'n' and resid 45 through 47 removed outlier: 6.475A pdb=" N GLU n 47 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASN n 56 " --> pdb=" O GLU n 47 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'o' and resid 14 through 16 removed outlier: 7.107A pdb=" N ALA o 46 " --> pdb=" O LEU o 24 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR o 68 " --> pdb=" O ILE o 47 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU o 92 " --> pdb=" O LEU o 69 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR o 117 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'p' and resid 80 through 83 removed outlier: 3.521A pdb=" N ASP p 39 " --> pdb=" O ILE p 55 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'r' and resid 15 through 17 Processing sheet with id= CP, first strand: chain 't' and resid 15 through 18 removed outlier: 4.178A pdb=" N HIS t 23 " --> pdb=" O SER t 18 " (cutoff:3.500A) 3628 hydrogen bonds defined for protein. 9715 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 213 hydrogen bonds 402 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 182 stacking parallelities Total time for adding SS restraints: 58.46 Time building geometry restraints manager: 32.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 743 1.22 - 1.38: 34181 1.38 - 1.53: 49677 1.53 - 1.68: 9437 1.68 - 1.84: 517 Bond restraints: 94555 Sorted by residual: bond pdb=" N PRO C 92 " pdb=" CA PRO C 92 " ideal model delta sigma weight residual 1.470 1.669 -0.199 1.23e-02 6.61e+03 2.61e+02 bond pdb=" N PRO Q 525 " pdb=" CA PRO Q 525 " ideal model delta sigma weight residual 1.469 1.671 -0.202 1.28e-02 6.10e+03 2.50e+02 bond pdb=" N PRO A 345 " pdb=" CA PRO A 345 " ideal model delta sigma weight residual 1.471 1.676 -0.205 1.32e-02 5.74e+03 2.42e+02 bond pdb=" C HIS T 191 " pdb=" N PRO T 192 " ideal model delta sigma weight residual 1.329 1.486 -0.156 1.18e-02 7.18e+03 1.76e+02 bond pdb=" C PRO A 942 " pdb=" O PRO A 942 " ideal model delta sigma weight residual 1.235 1.066 0.169 1.30e-02 5.92e+03 1.69e+02 ... (remaining 94550 not shown) Histogram of bond angle deviations from ideal: 84.69 - 98.75: 160 98.75 - 112.81: 53021 112.81 - 126.87: 75417 126.87 - 140.94: 1947 140.94 - 155.00: 5 Bond angle restraints: 130550 Sorted by residual: angle pdb=" PB ATP Q1501 " pdb=" O3B ATP Q1501 " pdb=" PG ATP Q1501 " ideal model delta sigma weight residual 139.87 114.08 25.79 1.00e+00 1.00e+00 6.65e+02 angle pdb=" C ASP A 344 " pdb=" N PRO A 345 " pdb=" CA PRO A 345 " ideal model delta sigma weight residual 119.28 142.03 -22.75 1.10e+00 8.26e-01 4.28e+02 angle pdb=" C LEU A 856 " pdb=" N ASN A 857 " pdb=" CA ASN A 857 " ideal model delta sigma weight residual 121.54 155.00 -33.46 1.91e+00 2.74e-01 3.07e+02 angle pdb=" C TRP Q 531 " pdb=" N PRO Q 532 " pdb=" CA PRO Q 532 " ideal model delta sigma weight residual 119.84 141.60 -21.76 1.25e+00 6.40e-01 3.03e+02 angle pdb=" C LYS Q 524 " pdb=" N PRO Q 525 " pdb=" CA PRO Q 525 " ideal model delta sigma weight residual 119.84 141.46 -21.62 1.25e+00 6.40e-01 2.99e+02 ... (remaining 130545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 55777 35.90 - 71.81: 1614 71.81 - 107.71: 166 107.71 - 143.61: 27 143.61 - 179.51: 17 Dihedral angle restraints: 57601 sinusoidal: 22364 harmonic: 35237 Sorted by residual: dihedral pdb=" C PHE T 400 " pdb=" N PHE T 400 " pdb=" CA PHE T 400 " pdb=" CB PHE T 400 " ideal model delta harmonic sigma weight residual -122.60 -161.16 38.56 0 2.50e+00 1.60e-01 2.38e+02 dihedral pdb=" N PHE T 400 " pdb=" C PHE T 400 " pdb=" CA PHE T 400 " pdb=" CB PHE T 400 " ideal model delta harmonic sigma weight residual 122.80 160.23 -37.43 0 2.50e+00 1.60e-01 2.24e+02 dihedral pdb=" C THR P 8 " pdb=" N THR P 8 " pdb=" CA THR P 8 " pdb=" CB THR P 8 " ideal model delta harmonic sigma weight residual -122.00 -155.87 33.87 0 2.50e+00 1.60e-01 1.84e+02 ... (remaining 57598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 15571 1.008 - 2.015: 7 2.015 - 3.023: 0 3.023 - 4.031: 0 4.031 - 5.038: 2 Chirality restraints: 15580 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 2.43 -4.77 2.00e-01 2.50e+01 5.68e+02 chirality pdb=" CA PHE T 400 " pdb=" N PHE T 400 " pdb=" C PHE T 400 " pdb=" CB PHE T 400 " both_signs ideal model delta sigma weight residual False 2.51 0.87 1.64 2.00e-01 2.50e+01 6.75e+01 ... (remaining 15577 not shown) Planarity restraints: 15700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A1507 " -0.085 2.00e-02 2.50e+03 1.61e-01 2.59e+02 pdb=" C SER A1507 " 0.278 2.00e-02 2.50e+03 pdb=" O SER A1507 " -0.108 2.00e-02 2.50e+03 pdb=" N GLY A1508 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 310 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.57e+02 pdb=" C LYS I 310 " 0.217 2.00e-02 2.50e+03 pdb=" O LYS I 310 " -0.080 2.00e-02 2.50e+03 pdb=" N MET I 311 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 83 " 0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C LYS I 83 " -0.216 2.00e-02 2.50e+03 pdb=" O LYS I 83 " 0.080 2.00e-02 2.50e+03 pdb=" N HIS I 84 " 0.069 2.00e-02 2.50e+03 ... (remaining 15697 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 42 2.06 - 2.77: 18171 2.77 - 3.48: 124998 3.48 - 4.19: 217789 4.19 - 4.90: 358833 Nonbonded interactions: 719833 Sorted by model distance: nonbonded pdb=" O6 G B 20 " pdb=" OP1 G B 24 " model vdw 1.346 3.040 nonbonded pdb=" OP1 A F 53 " pdb="MG MG F 201 " model vdw 1.359 2.170 nonbonded pdb=" O2' G G 24 " pdb=" OP1 G G 25 " model vdw 1.440 2.440 nonbonded pdb=" NZ LYS A1131 " pdb=" OE2 GLU A1193 " model vdw 1.463 2.520 nonbonded pdb=" NH2 ARG A 861 " pdb=" O4' A H 29 " model vdw 1.508 2.520 ... (remaining 719828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 3 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 56 or (resid 57 and (name N or name \ CA or name C or name O )) or resid 58 through 85)) selection = chain 'h' } ncs_group { reference = chain 'c' selection = chain 'j' } ncs_group { reference = (chain 'd' and (resid 20 through 76 or resid 89 through 116)) selection = chain 'k' } ncs_group { reference = (chain 'e' and resid 15 through 92) selection = chain 'l' } ncs_group { reference = chain 'f' selection = chain 'm' } ncs_group { reference = (chain 'g' and (resid 3 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 48 or (resid 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 76)) selection = chain 'n' } ncs_group { reference = (chain 'q' and resid 3 through 133) selection = chain 'r' selection = (chain 's' and resid 3 through 133) selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 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: 4.890 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: 0.120 Extract box with map and model: 16.920 Check model and map are aligned: 1.010 Set scattering table: 0.680 Process input model: 245.860 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 275.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 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 : 0.013 0.205 94555 Z= 0.846 Angle : 1.671 33.456 130550 Z= 1.080 Chirality : 0.112 5.038 15580 Planarity : 0.009 0.163 15700 Dihedral : 16.708 179.513 34624 Min Nonbonded Distance : 1.346 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.74 % Allowed : 5.59 % Favored : 93.67 % Rotamer: Outliers : 3.80 % Allowed : 5.46 % Favored : 90.74 % Cbeta Deviations : 1.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.07), residues: 11864 helix: -2.19 (0.06), residues: 4994 sheet: -1.09 (0.13), residues: 1538 loop : -1.86 (0.08), residues: 5332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.005 TRP A1498 HIS 0.027 0.004 HIS C 802 PHE 0.047 0.005 PHE A1071 TYR 0.050 0.005 TYR O 181 ARG 0.041 0.002 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23728 Ramachandran restraints generated. 11864 Oldfield, 0 Emsley, 11864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23728 Ramachandran restraints generated. 11864 Oldfield, 0 Emsley, 11864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1625 residues out of total 10769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1373 time to evaluate : 7.465 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 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable