Starting phenix.real_space_refine on Thu Mar 21 00:30:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x36_22019/03_2024/6x36_22019_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x36_22019/03_2024/6x36_22019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x36_22019/03_2024/6x36_22019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x36_22019/03_2024/6x36_22019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x36_22019/03_2024/6x36_22019_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x36_22019/03_2024/6x36_22019_neut.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 4 Type Number sf(0) Gaussians S 540 5.16 5 C 63896 2.51 5 N 17884 2.21 5 O 17844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 799": "OE1" <-> "OE2" Residue "B ARG 844": "NH1" <-> "NH2" Residue "B PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1271": "NH1" <-> "NH2" Residue "B ARG 1290": "NH1" <-> "NH2" Residue "B TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1594": "NH1" <-> "NH2" Residue "B ARG 1607": "NH1" <-> "NH2" Residue "B ARG 1656": "NH1" <-> "NH2" Residue "B PHE 1662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1721": "OE1" <-> "OE2" Residue "B ARG 1725": "NH1" <-> "NH2" Residue "B ARG 1743": "NH1" <-> "NH2" Residue "B PHE 1783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1828": "NH1" <-> "NH2" Residue "B ASP 1857": "OD1" <-> "OD2" Residue "B TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2000": "NH1" <-> "NH2" Residue "B ARG 2141": "NH1" <-> "NH2" Residue "B PHE 2338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3644": "NH1" <-> "NH2" Residue "B PHE 3701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3881": "NH1" <-> "NH2" Residue "B ARG 3899": "NH1" <-> "NH2" Residue "B ARG 3979": "NH1" <-> "NH2" Residue "B TYR 4172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4671": "NH1" <-> "NH2" Residue "B ARG 4701": "NH1" <-> "NH2" Residue "B ARG 4858": "NH1" <-> "NH2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 469": "NH1" <-> "NH2" Residue "E ARG 474": "NH1" <-> "NH2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 683": "NH1" <-> "NH2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 799": "OE1" <-> "OE2" Residue "E ARG 844": "NH1" <-> "NH2" Residue "E PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1271": "NH1" <-> "NH2" Residue "E ARG 1290": "NH1" <-> "NH2" Residue "E TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1594": "NH1" <-> "NH2" Residue "E ARG 1607": "NH1" <-> "NH2" Residue "E ARG 1656": "NH1" <-> "NH2" Residue "E PHE 1662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1721": "OE1" <-> "OE2" Residue "E ARG 1725": "NH1" <-> "NH2" Residue "E ARG 1743": "NH1" <-> "NH2" Residue "E PHE 1783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1828": "NH1" <-> "NH2" Residue "E ASP 1857": "OD1" <-> "OD2" Residue "E TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2000": "NH1" <-> "NH2" Residue "E ARG 2141": "NH1" <-> "NH2" Residue "E PHE 2338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 3644": "NH1" <-> "NH2" Residue "E PHE 3701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 3881": "NH1" <-> "NH2" Residue "E ARG 3899": "NH1" <-> "NH2" Residue "E ARG 3979": "NH1" <-> "NH2" Residue "E TYR 4172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 4671": "NH1" <-> "NH2" Residue "E ARG 4701": "NH1" <-> "NH2" Residue "E ARG 4858": "NH1" <-> "NH2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 266": "NH1" <-> "NH2" Residue "H TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 426": "NH1" <-> "NH2" Residue "H TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 469": "NH1" <-> "NH2" Residue "H ARG 474": "NH1" <-> "NH2" Residue "H ARG 553": "NH1" <-> "NH2" Residue "H TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 683": "NH1" <-> "NH2" Residue "H TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 799": "OE1" <-> "OE2" Residue "H ARG 844": "NH1" <-> "NH2" Residue "H PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1271": "NH1" <-> "NH2" Residue "H ARG 1290": "NH1" <-> "NH2" Residue "H TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1594": "NH1" <-> "NH2" Residue "H ARG 1607": "NH1" <-> "NH2" Residue "H ARG 1656": "NH1" <-> "NH2" Residue "H PHE 1662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1721": "OE1" <-> "OE2" Residue "H ARG 1725": "NH1" <-> "NH2" Residue "H ARG 1743": "NH1" <-> "NH2" Residue "H PHE 1783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1828": "NH1" <-> "NH2" Residue "H ASP 1857": "OD1" <-> "OD2" Residue "H TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 2000": "NH1" <-> "NH2" Residue "H ARG 2141": "NH1" <-> "NH2" Residue "H PHE 2338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 3644": "NH1" <-> "NH2" Residue "H PHE 3701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 3881": "NH1" <-> "NH2" Residue "H ARG 3899": "NH1" <-> "NH2" Residue "H ARG 3979": "NH1" <-> "NH2" Residue "H TYR 4172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 4669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 4671": "NH1" <-> "NH2" Residue "H ARG 4701": "NH1" <-> "NH2" Residue "H ARG 4858": "NH1" <-> "NH2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I GLU 15": "OE1" <-> "OE2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K GLU 139": "OE1" <-> "OE2" Residue "K ARG 178": "NH1" <-> "NH2" Residue "K TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 426": "NH1" <-> "NH2" Residue "K TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 469": "NH1" <-> "NH2" Residue "K ARG 474": "NH1" <-> "NH2" Residue "K ARG 553": "NH1" <-> "NH2" Residue "K TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 683": "NH1" <-> "NH2" Residue "K TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 799": "OE1" <-> "OE2" Residue "K ARG 844": "NH1" <-> "NH2" Residue "K PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1271": "NH1" <-> "NH2" Residue "K ARG 1290": "NH1" <-> "NH2" Residue "K TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1594": "NH1" <-> "NH2" Residue "K ARG 1607": "NH1" <-> "NH2" Residue "K ARG 1656": "NH1" <-> "NH2" Residue "K PHE 1662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1721": "OE1" <-> "OE2" Residue "K ARG 1725": "NH1" <-> "NH2" Residue "K ARG 1743": "NH1" <-> "NH2" Residue "K PHE 1783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1828": "NH1" <-> "NH2" Residue "K ASP 1857": "OD1" <-> "OD2" Residue "K TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 2000": "NH1" <-> "NH2" Residue "K ARG 2141": "NH1" <-> "NH2" Residue "K PHE 2338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 3644": "NH1" <-> "NH2" Residue "K PHE 3701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 3881": "NH1" <-> "NH2" Residue "K ARG 3899": "NH1" <-> "NH2" Residue "K ARG 3979": "NH1" <-> "NH2" Residue "K TYR 4172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 4669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 4671": "NH1" <-> "NH2" Residue "K ARG 4701": "NH1" <-> "NH2" Residue "K ARG 4858": "NH1" <-> "NH2" Residue "L GLU 12": "OE1" <-> "OE2" Residue "L GLU 15": "OE1" <-> "OE2" Time to flip residues: 0.30s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 100164 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 697 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 23573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3529, 23573 Classifications: {'peptide': 3529} Incomplete info: {'truncation_to_alanine': 1350} Link IDs: {'PTRANS': 140, 'TRANS': 3388} Chain breaks: 63 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 4402 Unresolved non-hydrogen angles: 5664 Unresolved non-hydrogen dihedrals: 3342 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 62, 'ARG:plan': 97, 'TYR:plan': 18, 'ASN:plan1': 38, 'TRP:plan': 5, 'HIS:plan': 27, 'PHE:plan': 21, 'GLU:plan': 188, 'ASP:plan': 116, 'UNK:plan-1': 344} Unresolved non-hydrogen planarities: 2723 Chain: "C" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 771 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 188 Chain: "D" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 697 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "E" Number of atoms: 23573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3529, 23573 Classifications: {'peptide': 3529} Incomplete info: {'truncation_to_alanine': 1350} Link IDs: {'PTRANS': 140, 'TRANS': 3388} Chain breaks: 63 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 4402 Unresolved non-hydrogen angles: 5664 Unresolved non-hydrogen dihedrals: 3342 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 62, 'ARG:plan': 97, 'TYR:plan': 18, 'ASN:plan1': 38, 'TRP:plan': 5, 'HIS:plan': 27, 'PHE:plan': 21, 'GLU:plan': 188, 'ASP:plan': 116, 'UNK:plan-1': 344} Unresolved non-hydrogen planarities: 2723 Chain: "F" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 771 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 188 Chain: "G" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 697 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 23573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3529, 23573 Classifications: {'peptide': 3529} Incomplete info: {'truncation_to_alanine': 1350} Link IDs: {'PTRANS': 140, 'TRANS': 3388} Chain breaks: 63 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 4402 Unresolved non-hydrogen angles: 5664 Unresolved non-hydrogen dihedrals: 3342 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 62, 'ARG:plan': 97, 'TYR:plan': 18, 'ASN:plan1': 38, 'TRP:plan': 5, 'HIS:plan': 27, 'PHE:plan': 21, 'GLU:plan': 188, 'ASP:plan': 116, 'UNK:plan-1': 344} Unresolved non-hydrogen planarities: 2723 Chain: "I" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 771 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 188 Chain: "J" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 697 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "K" Number of atoms: 23573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3529, 23573 Classifications: {'peptide': 3529} Incomplete info: {'truncation_to_alanine': 1350} Link IDs: {'PTRANS': 140, 'TRANS': 3388} Chain breaks: 63 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 4402 Unresolved non-hydrogen angles: 5664 Unresolved non-hydrogen dihedrals: 3342 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 62, 'ARG:plan': 97, 'TYR:plan': 18, 'ASN:plan1': 38, 'TRP:plan': 5, 'HIS:plan': 27, 'PHE:plan': 21, 'GLU:plan': 188, 'ASP:plan': 116, 'UNK:plan-1': 344} Unresolved non-hydrogen planarities: 2723 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 771 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 188 Time building chain proxies: 39.43, per 1000 atoms: 0.39 Number of scatterers: 100164 At special positions: 0 Unit cell: (295.39, 295.39, 187.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 540 16.00 O 17844 8.00 N 17884 7.00 C 63896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.68 Conformation dependent library (CDL) restraints added in 14.5 seconds 26648 Ramachandran restraints generated. 13324 Oldfield, 0 Emsley, 13324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28384 Finding SS restraints... Secondary structure from input PDB file: 620 helices and 104 sheets defined 61.7% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.86 Creating SS restraints... Processing helix chain 'A' and resid 56 through 66 Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.770A pdb=" N ILE B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.676A pdb=" N SER B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 460 through 481 Processing helix chain 'B' and resid 482 through 496 removed outlier: 3.862A pdb=" N LEU B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 Processing helix chain 'B' and resid 512 through 531 removed outlier: 4.369A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.664A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 4.245A pdb=" N LEU B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 552 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.801A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 removed outlier: 4.288A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.528A pdb=" N ILE B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 606 removed outlier: 4.284A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 812 through 815 removed outlier: 3.857A pdb=" N VAL B 815 " --> pdb=" O HIS B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 815' Processing helix chain 'B' and resid 871 through 889 removed outlier: 3.529A pdb=" N ALA B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 Processing helix chain 'B' and resid 943 through 949 removed outlier: 4.116A pdb=" N GLU B 947 " --> pdb=" O ASP B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 960 Processing helix chain 'B' and resid 978 through 1004 Processing helix chain 'B' and resid 1018 through 1022 removed outlier: 3.990A pdb=" N VAL B1022 " --> pdb=" O PRO B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1050 removed outlier: 3.595A pdb=" N LYS B1032 " --> pdb=" O ASP B1028 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B1033 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1444 through 1446 No H-bonds generated for 'chain 'B' and resid 1444 through 1446' Processing helix chain 'B' and resid 1465 through 1469 Processing helix chain 'B' and resid 1574 through 1580 removed outlier: 3.846A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1654 removed outlier: 3.659A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1650 through 1654' Processing helix chain 'B' and resid 1656 through 1674 removed outlier: 3.754A pdb=" N GLN B1660 " --> pdb=" O ARG B1656 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS B1674 " --> pdb=" O TYR B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1689 removed outlier: 3.642A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1699 removed outlier: 3.894A pdb=" N LEU B1694 " --> pdb=" O ASP B1690 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B1695 " --> pdb=" O GLN B1691 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1719 removed outlier: 4.061A pdb=" N HIS B1719 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1720 through 1731 Processing helix chain 'B' and resid 1804 through 1826 Processing helix chain 'B' and resid 1830 through 1834 removed outlier: 4.072A pdb=" N SER B1834 " --> pdb=" O VAL B1831 " (cutoff:3.500A) Processing helix chain 'B' and resid 1839 through 1853 Processing helix chain 'B' and resid 1856 through 1868 Processing helix chain 'B' and resid 1933 through 1982 removed outlier: 3.844A pdb=" N ASP B1968 " --> pdb=" O GLU B1964 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS B1969 " --> pdb=" O ARG B1965 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B1974 " --> pdb=" O LEU B1970 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY B1979 " --> pdb=" O ARG B1975 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE B1980 " --> pdb=" O ASP B1976 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B1982 " --> pdb=" O TYR B1978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1988 through 2001 removed outlier: 5.126A pdb=" N GLU B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N PHE B1999 " --> pdb=" O ARG B1995 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B2000 " --> pdb=" O THR B1996 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER B2001 " --> pdb=" O ARG B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2010 Processing helix chain 'B' and resid 2028 through 2044 removed outlier: 3.931A pdb=" N LEU B2032 " --> pdb=" O ILE B2028 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B2044 " --> pdb=" O LEU B2040 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2110 removed outlier: 3.888A pdb=" N ASP B2110 " --> pdb=" O TRP B2106 " (cutoff:3.500A) Processing helix chain 'B' and resid 2114 through 2130 removed outlier: 3.514A pdb=" N VAL B2118 " --> pdb=" O SER B2114 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2139 removed outlier: 3.611A pdb=" N GLU B2134 " --> pdb=" O ASP B2130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2140 through 2142 No H-bonds generated for 'chain 'B' and resid 2140 through 2142' Processing helix chain 'B' and resid 2146 through 2148 No H-bonds generated for 'chain 'B' and resid 2146 through 2148' Processing helix chain 'B' and resid 2149 through 2169 removed outlier: 3.736A pdb=" N ILE B2168 " --> pdb=" O ARG B2164 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL B2169 " --> pdb=" O SER B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2188 removed outlier: 3.707A pdb=" N ASN B2188 " --> pdb=" O GLY B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2190 through 2195 Processing helix chain 'B' and resid 2195 through 2202 removed outlier: 3.573A pdb=" N LEU B2202 " --> pdb=" O LEU B2198 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2217 Processing helix chain 'B' and resid 2226 through 2244 removed outlier: 4.127A pdb=" N SER B2244 " --> pdb=" O PHE B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2244 through 2254 Processing helix chain 'B' and resid 2254 through 2263 Processing helix chain 'B' and resid 2272 through 2282 removed outlier: 4.178A pdb=" N VAL B2276 " --> pdb=" O THR B2272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B2277 " --> pdb=" O PRO B2273 " (cutoff:3.500A) Processing helix chain 'B' and resid 2284 through 2290 Processing helix chain 'B' and resid 2292 through 2309 Processing helix chain 'B' and resid 2313 through 2318 Processing helix chain 'B' and resid 2325 through 2339 removed outlier: 3.570A pdb=" N ALA B2339 " --> pdb=" O PHE B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2355 Processing helix chain 'B' and resid 2355 through 2360 Processing helix chain 'B' and resid 2378 through 2384 Processing helix chain 'B' and resid 2425 through 2437 removed outlier: 3.534A pdb=" N LEU B2434 " --> pdb=" O LEU B2430 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS B2437 " --> pdb=" O LEU B2433 " (cutoff:3.500A) Processing helix chain 'B' and resid 2448 through 2455 removed outlier: 3.653A pdb=" N LEU B2452 " --> pdb=" O LYS B2448 " (cutoff:3.500A) Processing helix chain 'B' and resid 2455 through 2461 removed outlier: 3.840A pdb=" N LEU B2461 " --> pdb=" O ILE B2457 " (cutoff:3.500A) Processing helix chain 'B' and resid 2498 through 2509 removed outlier: 3.927A pdb=" N ASP B2508 " --> pdb=" O VAL B2504 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG B2509 " --> pdb=" O LEU B2505 " (cutoff:3.500A) Processing helix chain 'B' and resid 2549 through 2567 removed outlier: 3.713A pdb=" N CYS B2556 " --> pdb=" O ASN B2552 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU B2557 " --> pdb=" O ARG B2553 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B2560 " --> pdb=" O CYS B2556 " (cutoff:3.500A) Proline residue: B2561 - end of helix Processing helix chain 'B' and resid 2580 through 2593 Processing helix chain 'B' and resid 2597 through 2613 removed outlier: 3.518A pdb=" N ARG B2613 " --> pdb=" O MET B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2619 through 2629 Processing helix chain 'B' and resid 2642 through 2653 Processing helix chain 'B' and resid 2665 through 2682 Processing helix chain 'B' and resid 2689 through 2700 removed outlier: 3.505A pdb=" N UNK B2700 " --> pdb=" O UNK B2696 " (cutoff:3.500A) Processing helix chain 'B' and resid 2957 through 2978 Processing helix chain 'B' and resid 3000 through 3018 Processing helix chain 'B' and resid 3033 through 3046 Processing helix chain 'B' and resid 3052 through 3062 Processing helix chain 'B' and resid 3147 through 3166 Processing helix chain 'B' and resid 3181 through 3193 Processing helix chain 'B' and resid 3203 through 3216 Processing helix chain 'B' and resid 3226 through 3238 Processing helix chain 'B' and resid 3279 through 3288 Processing helix chain 'B' and resid 3293 through 3308 Processing helix chain 'B' and resid 3321 through 3335 Processing helix chain 'B' and resid 3347 through 3358 Processing helix chain 'B' and resid 3366 through 3384 Processing helix chain 'B' and resid 3399 through 3418 Proline residue: B3411 - end of helix Processing helix chain 'B' and resid 3420 through 3425 Processing helix chain 'B' and resid 3431 through 3449 Processing helix chain 'B' and resid 3449 through 3461 Processing helix chain 'B' and resid 3510 through 3526 Processing helix chain 'B' and resid 3535 through 3544 Processing helix chain 'B' and resid 3549 through 3555 Processing helix chain 'B' and resid 3566 through 3574 Processing helix chain 'B' and resid 3587 through 3603 Processing helix chain 'B' and resid 3629 through 3634 Processing helix chain 'B' and resid 3636 through 3640 removed outlier: 4.424A pdb=" N ASN B3639 " --> pdb=" O PRO B3636 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B3640 " --> pdb=" O LEU B3637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3636 through 3640' Processing helix chain 'B' and resid 3643 through 3661 removed outlier: 3.901A pdb=" N ILE B3658 " --> pdb=" O LYS B3654 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU B3659 " --> pdb=" O ALA B3655 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B3660 " --> pdb=" O ALA B3656 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B3661 " --> pdb=" O TRP B3657 " (cutoff:3.500A) Processing helix chain 'B' and resid 3664 through 3676 removed outlier: 3.702A pdb=" N ARG B3668 " --> pdb=" O SER B3664 " (cutoff:3.500A) Processing helix chain 'B' and resid 3692 through 3707 removed outlier: 3.598A pdb=" N THR B3704 " --> pdb=" O HIS B3700 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B3705 " --> pdb=" O PHE B3701 " (cutoff:3.500A) Processing helix chain 'B' and resid 3715 through 3730 Processing helix chain 'B' and resid 3748 through 3767 Processing helix chain 'B' and resid 3769 through 3782 removed outlier: 3.962A pdb=" N MET B3773 " --> pdb=" O GLY B3769 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N MET B3777 " --> pdb=" O MET B3773 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B3778 " --> pdb=" O VAL B3774 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B3782 " --> pdb=" O ILE B3778 " (cutoff:3.500A) Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.065A pdb=" N SER B3798 " --> pdb=" O LYS B3794 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B3799 " --> pdb=" O LEU B3795 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B3800 " --> pdb=" O GLY B3796 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3819 removed outlier: 4.206A pdb=" N GLN B3808 " --> pdb=" O ASN B3804 " (cutoff:3.500A) Processing helix chain 'B' and resid 3822 through 3833 removed outlier: 3.940A pdb=" N SER B3826 " --> pdb=" O GLY B3822 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B3827 " --> pdb=" O PHE B3823 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B3833 " --> pdb=" O ALA B3829 " (cutoff:3.500A) Processing helix chain 'B' and resid 3838 through 3850 Processing helix chain 'B' and resid 3872 through 3887 removed outlier: 3.772A pdb=" N CYS B3887 " --> pdb=" O LEU B3883 " (cutoff:3.500A) Processing helix chain 'B' and resid 3892 through 3900 removed outlier: 3.542A pdb=" N TYR B3897 " --> pdb=" O ASP B3893 " (cutoff:3.500A) Processing helix chain 'B' and resid 3909 through 3932 Processing helix chain 'B' and resid 3942 through 3963 removed outlier: 4.314A pdb=" N LYS B3948 " --> pdb=" O ARG B3944 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B3949 " --> pdb=" O ASN B3945 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET B3950 " --> pdb=" O PHE B3946 " (cutoff:3.500A) Processing helix chain 'B' and resid 3969 through 3977 Processing helix chain 'B' and resid 3983 through 3999 Processing helix chain 'B' and resid 4009 through 4025 removed outlier: 3.678A pdb=" N LEU B4025 " --> pdb=" O MET B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4034 through 4046 removed outlier: 3.812A pdb=" N GLN B4038 " --> pdb=" O MET B4034 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B4041 " --> pdb=" O ARG B4037 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B4044 " --> pdb=" O VAL B4040 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU B4045 " --> pdb=" O ASP B4041 " (cutoff:3.500A) Processing helix chain 'B' and resid 4046 through 4066 removed outlier: 3.534A pdb=" N ILE B4053 " --> pdb=" O ASN B4049 " (cutoff:3.500A) Processing helix chain 'B' and resid 4069 through 4078 Processing helix chain 'B' and resid 4084 through 4090 removed outlier: 3.813A pdb=" N PHE B4088 " --> pdb=" O SER B4084 " (cutoff:3.500A) Processing helix chain 'B' and resid 4123 through 4128 removed outlier: 4.258A pdb=" N GLN B4128 " --> pdb=" O ALA B4124 " (cutoff:3.500A) Processing helix chain 'B' and resid 4131 through 4146 Processing helix chain 'B' and resid 4152 through 4154 No H-bonds generated for 'chain 'B' and resid 4152 through 4154' Processing helix chain 'B' and resid 4155 through 4170 removed outlier: 3.695A pdb=" N LEU B4161 " --> pdb=" O ASN B4157 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B4165 " --> pdb=" O LEU B4161 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU B4167 " --> pdb=" O GLU B4163 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR B4168 " --> pdb=" O SER B4164 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B4169 " --> pdb=" O ILE B4165 " (cutoff:3.500A) Processing helix chain 'B' and resid 4193 through 4201 removed outlier: 3.508A pdb=" N GLU B4201 " --> pdb=" O ARG B4197 " (cutoff:3.500A) Processing helix chain 'B' and resid 4202 through 4218 Processing helix chain 'B' and resid 4222 through 4241 Processing helix chain 'B' and resid 4316 through 4331 Processing helix chain 'B' and resid 4544 through 4556 Processing helix chain 'B' and resid 4556 through 4577 removed outlier: 3.575A pdb=" N PHE B4577 " --> pdb=" O PHE B4573 " (cutoff:3.500A) Processing helix chain 'B' and resid 4636 through 4681 removed outlier: 4.371A pdb=" N ARG B4642 " --> pdb=" O GLU B4638 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS B4643 " --> pdb=" O PRO B4639 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL B4664 " --> pdb=" O ASN B4660 " (cutoff:3.500A) Proline residue: B4665 - end of helix Processing helix chain 'B' and resid 4694 through 4701 Processing helix chain 'B' and resid 4702 through 4706 removed outlier: 3.763A pdb=" N ASN B4705 " --> pdb=" O LEU B4702 " (cutoff:3.500A) Processing helix chain 'B' and resid 4708 through 4712 removed outlier: 4.166A pdb=" N ASN B4712 " --> pdb=" O PHE B4709 " (cutoff:3.500A) Processing helix chain 'B' and resid 4717 through 4724 Processing helix chain 'B' and resid 4732 through 4737 removed outlier: 3.705A pdb=" N ALA B4736 " --> pdb=" O ARG B4732 " (cutoff:3.500A) Processing helix chain 'B' and resid 4764 through 4768 Processing helix chain 'B' and resid 4770 through 4783 Processing helix chain 'B' and resid 4784 through 4803 Processing helix chain 'B' and resid 4807 through 4817 Processing helix chain 'B' and resid 4818 through 4829 Processing helix chain 'B' and resid 4831 through 4857 Processing helix chain 'B' and resid 4876 through 4889 Processing helix chain 'B' and resid 4894 through 4898 removed outlier: 3.544A pdb=" N ASP B4897 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4907 through 4925 removed outlier: 3.567A pdb=" N ARG B4911 " --> pdb=" O TYR B4907 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B4925 " --> pdb=" O PHE B4921 " (cutoff:3.500A) Processing helix chain 'B' and resid 4927 through 4955 removed outlier: 4.375A pdb=" N GLN B4931 " --> pdb=" O LEU B4927 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B4953 " --> pdb=" O ARG B4949 " (cutoff:3.500A) Processing helix chain 'B' and resid 4963 through 4969 removed outlier: 3.500A pdb=" N THR B4969 " --> pdb=" O TYR B4965 " (cutoff:3.500A) Processing helix chain 'B' and resid 4972 through 4996 removed outlier: 3.702A pdb=" N HIS B4976 " --> pdb=" O ARG B4972 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B4981 " --> pdb=" O THR B4977 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR B4986 " --> pdb=" O ASN B4982 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N MET B4987 " --> pdb=" O LEU B4983 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B4988 " --> pdb=" O ALA B4984 " (cutoff:3.500A) Processing helix chain 'B' and resid 5002 through 5014 removed outlier: 3.678A pdb=" N MET B5011 " --> pdb=" O TYR B5007 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B5014 " --> pdb=" O LYS B5010 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 21 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 65 through 90 Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.672A pdb=" N ASP C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'D' and resid 56 through 66 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.769A pdb=" N ILE E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 84 Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 394 through 421 removed outlier: 3.675A pdb=" N SER E 398 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 452 Processing helix chain 'E' and resid 460 through 481 Processing helix chain 'E' and resid 482 through 496 removed outlier: 3.861A pdb=" N LEU E 486 " --> pdb=" O GLY E 482 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 496 " --> pdb=" O ASP E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 508 Processing helix chain 'E' and resid 512 through 531 removed outlier: 4.370A pdb=" N LYS E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 541 removed outlier: 3.664A pdb=" N CYS E 537 " --> pdb=" O ASN E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 552 removed outlier: 4.245A pdb=" N LEU E 547 " --> pdb=" O ASN E 543 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP E 552 " --> pdb=" O VAL E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 571 removed outlier: 3.802A pdb=" N ILE E 560 " --> pdb=" O ALA E 556 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER E 571 " --> pdb=" O VAL E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 577 removed outlier: 4.287A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 594 removed outlier: 3.530A pdb=" N ILE E 583 " --> pdb=" O GLN E 579 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 606 removed outlier: 4.283A pdb=" N LEU E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 626 Processing helix chain 'E' and resid 812 through 815 removed outlier: 3.857A pdb=" N VAL E 815 " --> pdb=" O HIS E 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 812 through 815' Processing helix chain 'E' and resid 871 through 889 removed outlier: 3.529A pdb=" N ALA E 875 " --> pdb=" O ARG E 871 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 936 Processing helix chain 'E' and resid 943 through 949 removed outlier: 4.115A pdb=" N GLU E 947 " --> pdb=" O ASP E 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 955 through 960 Processing helix chain 'E' and resid 978 through 1004 Processing helix chain 'E' and resid 1018 through 1022 removed outlier: 3.990A pdb=" N VAL E1022 " --> pdb=" O PRO E1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1050 removed outlier: 3.595A pdb=" N LYS E1032 " --> pdb=" O ASP E1028 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E1033 " --> pdb=" O GLU E1029 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER E1034 " --> pdb=" O ALA E1030 " (cutoff:3.500A) Processing helix chain 'E' and resid 1444 through 1446 No H-bonds generated for 'chain 'E' and resid 1444 through 1446' Processing helix chain 'E' and resid 1465 through 1469 Processing helix chain 'E' and resid 1574 through 1580 removed outlier: 3.845A pdb=" N ALA E1578 " --> pdb=" O PRO E1574 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET E1579 " --> pdb=" O LEU E1575 " (cutoff:3.500A) Processing helix chain 'E' and resid 1650 through 1654 removed outlier: 3.658A pdb=" N SER E1654 " --> pdb=" O ILE E1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1650 through 1654' Processing helix chain 'E' and resid 1656 through 1674 removed outlier: 3.755A pdb=" N GLN E1660 " --> pdb=" O ARG E1656 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS E1674 " --> pdb=" O TYR E1670 " (cutoff:3.500A) Processing helix chain 'E' and resid 1678 through 1689 removed outlier: 3.642A pdb=" N ALA E1684 " --> pdb=" O ARG E1680 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER E1687 " --> pdb=" O HIS E1683 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS E1688 " --> pdb=" O ALA E1684 " (cutoff:3.500A) Processing helix chain 'E' and resid 1690 through 1699 removed outlier: 3.894A pdb=" N LEU E1694 " --> pdb=" O ASP E1690 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E1695 " --> pdb=" O GLN E1691 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E1699 " --> pdb=" O LEU E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1704 through 1719 removed outlier: 4.062A pdb=" N HIS E1719 " --> pdb=" O LEU E1715 " (cutoff:3.500A) Processing helix chain 'E' and resid 1720 through 1731 Processing helix chain 'E' and resid 1804 through 1826 Processing helix chain 'E' and resid 1830 through 1834 removed outlier: 4.072A pdb=" N SER E1834 " --> pdb=" O VAL E1831 " (cutoff:3.500A) Processing helix chain 'E' and resid 1839 through 1853 Processing helix chain 'E' and resid 1856 through 1868 Processing helix chain 'E' and resid 1933 through 1982 removed outlier: 3.845A pdb=" N ASP E1968 " --> pdb=" O GLU E1964 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS E1969 " --> pdb=" O ARG E1965 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN E1974 " --> pdb=" O LEU E1970 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY E1979 " --> pdb=" O ARG E1975 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE E1980 " --> pdb=" O ASP E1976 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET E1982 " --> pdb=" O TYR E1978 " (cutoff:3.500A) Processing helix chain 'E' and resid 1988 through 2001 removed outlier: 5.124A pdb=" N GLU E1998 " --> pdb=" O ARG E1994 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE E1999 " --> pdb=" O ARG E1995 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E2000 " --> pdb=" O THR E1996 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER E2001 " --> pdb=" O ARG E1997 " (cutoff:3.500A) Processing helix chain 'E' and resid 2002 through 2010 Processing helix chain 'E' and resid 2028 through 2044 removed outlier: 3.931A pdb=" N LEU E2032 " --> pdb=" O ILE E2028 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E2044 " --> pdb=" O LEU E2040 " (cutoff:3.500A) Processing helix chain 'E' and resid 2094 through 2110 removed outlier: 3.889A pdb=" N ASP E2110 " --> pdb=" O TRP E2106 " (cutoff:3.500A) Processing helix chain 'E' and resid 2114 through 2130 removed outlier: 3.515A pdb=" N VAL E2118 " --> pdb=" O SER E2114 " (cutoff:3.500A) Processing helix chain 'E' and resid 2130 through 2139 removed outlier: 3.610A pdb=" N GLU E2134 " --> pdb=" O ASP E2130 " (cutoff:3.500A) Processing helix chain 'E' and resid 2140 through 2142 No H-bonds generated for 'chain 'E' and resid 2140 through 2142' Processing helix chain 'E' and resid 2146 through 2148 No H-bonds generated for 'chain 'E' and resid 2146 through 2148' Processing helix chain 'E' and resid 2149 through 2169 removed outlier: 3.736A pdb=" N ILE E2168 " --> pdb=" O ARG E2164 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL E2169 " --> pdb=" O SER E2165 " (cutoff:3.500A) Processing helix chain 'E' and resid 2172 through 2188 removed outlier: 3.706A pdb=" N ASN E2188 " --> pdb=" O GLY E2184 " (cutoff:3.500A) Processing helix chain 'E' and resid 2190 through 2195 Processing helix chain 'E' and resid 2195 through 2202 removed outlier: 3.574A pdb=" N LEU E2202 " --> pdb=" O LEU E2198 " (cutoff:3.500A) Processing helix chain 'E' and resid 2203 through 2217 Processing helix chain 'E' and resid 2226 through 2244 removed outlier: 4.126A pdb=" N SER E2244 " --> pdb=" O PHE E2240 " (cutoff:3.500A) Processing helix chain 'E' and resid 2244 through 2254 Processing helix chain 'E' and resid 2254 through 2263 Processing helix chain 'E' and resid 2272 through 2282 removed outlier: 4.179A pdb=" N VAL E2276 " --> pdb=" O THR E2272 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA E2277 " --> pdb=" O PRO E2273 " (cutoff:3.500A) Processing helix chain 'E' and resid 2284 through 2290 Processing helix chain 'E' and resid 2292 through 2309 Processing helix chain 'E' and resid 2313 through 2318 Processing helix chain 'E' and resid 2325 through 2339 removed outlier: 3.571A pdb=" N ALA E2339 " --> pdb=" O PHE E2335 " (cutoff:3.500A) Processing helix chain 'E' and resid 2347 through 2355 Processing helix chain 'E' and resid 2355 through 2360 Processing helix chain 'E' and resid 2378 through 2384 Processing helix chain 'E' and resid 2425 through 2437 removed outlier: 3.534A pdb=" N LEU E2434 " --> pdb=" O LEU E2430 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N CYS E2437 " --> pdb=" O LEU E2433 " (cutoff:3.500A) Processing helix chain 'E' and resid 2448 through 2455 removed outlier: 3.653A pdb=" N LEU E2452 " --> pdb=" O LYS E2448 " (cutoff:3.500A) Processing helix chain 'E' and resid 2455 through 2461 removed outlier: 3.840A pdb=" N LEU E2461 " --> pdb=" O ILE E2457 " (cutoff:3.500A) Processing helix chain 'E' and resid 2498 through 2509 removed outlier: 3.928A pdb=" N ASP E2508 " --> pdb=" O VAL E2504 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG E2509 " --> pdb=" O LEU E2505 " (cutoff:3.500A) Processing helix chain 'E' and resid 2549 through 2567 removed outlier: 3.712A pdb=" N CYS E2556 " --> pdb=" O ASN E2552 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU E2557 " --> pdb=" O ARG E2553 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E2560 " --> pdb=" O CYS E2556 " (cutoff:3.500A) Proline residue: E2561 - end of helix Processing helix chain 'E' and resid 2580 through 2593 Processing helix chain 'E' and resid 2597 through 2613 removed outlier: 3.518A pdb=" N ARG E2613 " --> pdb=" O MET E2609 " (cutoff:3.500A) Processing helix chain 'E' and resid 2619 through 2629 Processing helix chain 'E' and resid 2642 through 2653 Processing helix chain 'E' and resid 2665 through 2682 Processing helix chain 'E' and resid 2689 through 2700 removed outlier: 3.505A pdb=" N UNK E2700 " --> pdb=" O UNK E2696 " (cutoff:3.500A) Processing helix chain 'E' and resid 2957 through 2978 Processing helix chain 'E' and resid 3000 through 3018 Processing helix chain 'E' and resid 3033 through 3046 Processing helix chain 'E' and resid 3052 through 3062 Processing helix chain 'E' and resid 3147 through 3166 Processing helix chain 'E' and resid 3181 through 3193 Processing helix chain 'E' and resid 3203 through 3216 Processing helix chain 'E' and resid 3226 through 3238 Processing helix chain 'E' and resid 3279 through 3288 Processing helix chain 'E' and resid 3293 through 3308 Processing helix chain 'E' and resid 3321 through 3335 Processing helix chain 'E' and resid 3347 through 3358 Processing helix chain 'E' and resid 3366 through 3384 Processing helix chain 'E' and resid 3399 through 3418 Proline residue: E3411 - end of helix Processing helix chain 'E' and resid 3420 through 3425 Processing helix chain 'E' and resid 3431 through 3449 Processing helix chain 'E' and resid 3449 through 3461 Processing helix chain 'E' and resid 3510 through 3526 Processing helix chain 'E' and resid 3535 through 3544 Processing helix chain 'E' and resid 3549 through 3555 Processing helix chain 'E' and resid 3566 through 3574 Processing helix chain 'E' and resid 3587 through 3603 Processing helix chain 'E' and resid 3629 through 3634 Processing helix chain 'E' and resid 3636 through 3640 removed outlier: 4.423A pdb=" N ASN E3639 " --> pdb=" O PRO E3636 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E3640 " --> pdb=" O LEU E3637 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3636 through 3640' Processing helix chain 'E' and resid 3643 through 3661 removed outlier: 3.899A pdb=" N ILE E3658 " --> pdb=" O LYS E3654 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU E3659 " --> pdb=" O ALA E3655 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR E3660 " --> pdb=" O ALA E3656 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E3661 " --> pdb=" O TRP E3657 " (cutoff:3.500A) Processing helix chain 'E' and resid 3664 through 3676 removed outlier: 3.702A pdb=" N ARG E3668 " --> pdb=" O SER E3664 " (cutoff:3.500A) Processing helix chain 'E' and resid 3692 through 3707 removed outlier: 3.599A pdb=" N THR E3704 " --> pdb=" O HIS E3700 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA E3705 " --> pdb=" O PHE E3701 " (cutoff:3.500A) Processing helix chain 'E' and resid 3715 through 3730 Processing helix chain 'E' and resid 3748 through 3767 Processing helix chain 'E' and resid 3769 through 3782 removed outlier: 3.964A pdb=" N MET E3773 " --> pdb=" O GLY E3769 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N MET E3777 " --> pdb=" O MET E3773 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE E3778 " --> pdb=" O VAL E3774 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS E3782 " --> pdb=" O ILE E3778 " (cutoff:3.500A) Processing helix chain 'E' and resid 3786 through 3800 removed outlier: 4.065A pdb=" N SER E3798 " --> pdb=" O LYS E3794 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E3799 " --> pdb=" O LEU E3795 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E3800 " --> pdb=" O GLY E3796 " (cutoff:3.500A) Processing helix chain 'E' and resid 3804 through 3819 removed outlier: 4.206A pdb=" N GLN E3808 " --> pdb=" O ASN E3804 " (cutoff:3.500A) Processing helix chain 'E' and resid 3822 through 3833 removed outlier: 3.940A pdb=" N SER E3826 " --> pdb=" O GLY E3822 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE E3827 " --> pdb=" O PHE E3823 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E3833 " --> pdb=" O ALA E3829 " (cutoff:3.500A) Processing helix chain 'E' and resid 3838 through 3850 Processing helix chain 'E' and resid 3872 through 3887 removed outlier: 3.771A pdb=" N CYS E3887 " --> pdb=" O LEU E3883 " (cutoff:3.500A) Processing helix chain 'E' and resid 3892 through 3900 removed outlier: 3.541A pdb=" N TYR E3897 " --> pdb=" O ASP E3893 " (cutoff:3.500A) Processing helix chain 'E' and resid 3909 through 3932 Processing helix chain 'E' and resid 3942 through 3963 removed outlier: 4.313A pdb=" N LYS E3948 " --> pdb=" O ARG E3944 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA E3949 " --> pdb=" O ASN E3945 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET E3950 " --> pdb=" O PHE E3946 " (cutoff:3.500A) Processing helix chain 'E' and resid 3969 through 3977 Processing helix chain 'E' and resid 3983 through 3999 Processing helix chain 'E' and resid 4009 through 4025 removed outlier: 3.679A pdb=" N LEU E4025 " --> pdb=" O MET E4021 " (cutoff:3.500A) Processing helix chain 'E' and resid 4034 through 4046 removed outlier: 3.811A pdb=" N GLN E4038 " --> pdb=" O MET E4034 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP E4041 " --> pdb=" O ARG E4037 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL E4044 " --> pdb=" O VAL E4040 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU E4045 " --> pdb=" O ASP E4041 " (cutoff:3.500A) Processing helix chain 'E' and resid 4046 through 4066 removed outlier: 3.534A pdb=" N ILE E4053 " --> pdb=" O ASN E4049 " (cutoff:3.500A) Processing helix chain 'E' and resid 4069 through 4078 Processing helix chain 'E' and resid 4084 through 4090 removed outlier: 3.813A pdb=" N PHE E4088 " --> pdb=" O SER E4084 " (cutoff:3.500A) Processing helix chain 'E' and resid 4123 through 4128 removed outlier: 4.257A pdb=" N GLN E4128 " --> pdb=" O ALA E4124 " (cutoff:3.500A) Processing helix chain 'E' and resid 4131 through 4146 Processing helix chain 'E' and resid 4152 through 4154 No H-bonds generated for 'chain 'E' and resid 4152 through 4154' Processing helix chain 'E' and resid 4155 through 4170 removed outlier: 3.696A pdb=" N LEU E4161 " --> pdb=" O ASN E4157 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E4165 " --> pdb=" O LEU E4161 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU E4167 " --> pdb=" O GLU E4163 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR E4168 " --> pdb=" O SER E4164 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE E4169 " --> pdb=" O ILE E4165 " (cutoff:3.500A) Processing helix chain 'E' and resid 4193 through 4201 removed outlier: 3.509A pdb=" N GLU E4201 " --> pdb=" O ARG E4197 " (cutoff:3.500A) Processing helix chain 'E' and resid 4202 through 4218 Processing helix chain 'E' and resid 4222 through 4241 Processing helix chain 'E' and resid 4316 through 4331 Processing helix chain 'E' and resid 4544 through 4556 Processing helix chain 'E' and resid 4556 through 4577 removed outlier: 3.574A pdb=" N PHE E4577 " --> pdb=" O PHE E4573 " (cutoff:3.500A) Processing helix chain 'E' and resid 4636 through 4681 removed outlier: 4.370A pdb=" N ARG E4642 " --> pdb=" O GLU E4638 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS E4643 " --> pdb=" O PRO E4639 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL E4664 " --> pdb=" O ASN E4660 " (cutoff:3.500A) Proline residue: E4665 - end of helix Processing helix chain 'E' and resid 4694 through 4701 Processing helix chain 'E' and resid 4702 through 4706 removed outlier: 3.762A pdb=" N ASN E4705 " --> pdb=" O LEU E4702 " (cutoff:3.500A) Processing helix chain 'E' and resid 4708 through 4712 removed outlier: 4.167A pdb=" N ASN E4712 " --> pdb=" O PHE E4709 " (cutoff:3.500A) Processing helix chain 'E' and resid 4717 through 4724 Processing helix chain 'E' and resid 4732 through 4737 removed outlier: 3.704A pdb=" N ALA E4736 " --> pdb=" O ARG E4732 " (cutoff:3.500A) Processing helix chain 'E' and resid 4764 through 4768 Processing helix chain 'E' and resid 4770 through 4783 Processing helix chain 'E' and resid 4784 through 4803 Processing helix chain 'E' and resid 4807 through 4817 Processing helix chain 'E' and resid 4818 through 4829 Processing helix chain 'E' and resid 4831 through 4857 Processing helix chain 'E' and resid 4876 through 4889 Processing helix chain 'E' and resid 4894 through 4898 removed outlier: 3.545A pdb=" N ASP E4897 " --> pdb=" O GLY E4894 " (cutoff:3.500A) Processing helix chain 'E' and resid 4907 through 4925 removed outlier: 3.568A pdb=" N ARG E4911 " --> pdb=" O TYR E4907 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E4925 " --> pdb=" O PHE E4921 " (cutoff:3.500A) Processing helix chain 'E' and resid 4927 through 4955 removed outlier: 4.374A pdb=" N GLN E4931 " --> pdb=" O LEU E4927 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E4953 " --> pdb=" O ARG E4949 " (cutoff:3.500A) Processing helix chain 'E' and resid 4963 through 4969 Processing helix chain 'E' and resid 4972 through 4996 removed outlier: 3.702A pdb=" N HIS E4976 " --> pdb=" O ARG E4972 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS E4981 " --> pdb=" O THR E4977 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR E4986 " --> pdb=" O ASN E4982 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N MET E4987 " --> pdb=" O LEU E4983 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE E4988 " --> pdb=" O ALA E4984 " (cutoff:3.500A) Processing helix chain 'E' and resid 5002 through 5014 removed outlier: 3.678A pdb=" N MET E5011 " --> pdb=" O TYR E5007 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU E5014 " --> pdb=" O LYS E5010 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 65 through 90 Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 118 through 127 removed outlier: 3.674A pdb=" N ASP F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 148 Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.769A pdb=" N ILE H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 84 Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 394 through 421 removed outlier: 3.675A pdb=" N SER H 398 " --> pdb=" O GLN H 394 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 452 Processing helix chain 'H' and resid 460 through 481 Processing helix chain 'H' and resid 482 through 496 removed outlier: 3.862A pdb=" N LEU H 486 " --> pdb=" O GLY H 482 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL H 496 " --> pdb=" O ASP H 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 508 Processing helix chain 'H' and resid 512 through 531 removed outlier: 4.369A pdb=" N LYS H 516 " --> pdb=" O ALA H 512 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU H 517 " --> pdb=" O GLU H 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 541 removed outlier: 3.664A pdb=" N CYS H 537 " --> pdb=" O ASN H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 543 through 552 removed outlier: 4.244A pdb=" N LEU H 547 " --> pdb=" O ASN H 543 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP H 552 " --> pdb=" O VAL H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 556 through 571 removed outlier: 3.802A pdb=" N ILE H 560 " --> pdb=" O ALA H 556 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER H 571 " --> pdb=" O VAL H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 571 through 577 removed outlier: 4.287A pdb=" N LEU H 575 " --> pdb=" O SER H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 579 through 594 removed outlier: 3.529A pdb=" N ILE H 583 " --> pdb=" O GLN H 579 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 606 removed outlier: 4.283A pdb=" N LEU H 600 " --> pdb=" O ASN H 596 " (cutoff:3.500A) Processing helix chain 'H' and resid 614 through 626 Processing helix chain 'H' and resid 812 through 815 removed outlier: 3.856A pdb=" N VAL H 815 " --> pdb=" O HIS H 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 812 through 815' Processing helix chain 'H' and resid 871 through 889 removed outlier: 3.528A pdb=" N ALA H 875 " --> pdb=" O ARG H 871 " (cutoff:3.500A) Processing helix chain 'H' and resid 914 through 936 Processing helix chain 'H' and resid 943 through 949 removed outlier: 4.115A pdb=" N GLU H 947 " --> pdb=" O ASP H 943 " (cutoff:3.500A) Processing helix chain 'H' and resid 955 through 960 Processing helix chain 'H' and resid 978 through 1004 Processing helix chain 'H' and resid 1018 through 1022 removed outlier: 3.991A pdb=" N VAL H1022 " --> pdb=" O PRO H1019 " (cutoff:3.500A) Processing helix chain 'H' and resid 1028 through 1050 removed outlier: 3.596A pdb=" N LYS H1032 " --> pdb=" O ASP H1028 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG H1033 " --> pdb=" O GLU H1029 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER H1034 " --> pdb=" O ALA H1030 " (cutoff:3.500A) Processing helix chain 'H' and resid 1444 through 1446 No H-bonds generated for 'chain 'H' and resid 1444 through 1446' Processing helix chain 'H' and resid 1465 through 1469 Processing helix chain 'H' and resid 1574 through 1580 removed outlier: 3.845A pdb=" N ALA H1578 " --> pdb=" O PRO H1574 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET H1579 " --> pdb=" O LEU H1575 " (cutoff:3.500A) Processing helix chain 'H' and resid 1650 through 1654 removed outlier: 3.659A pdb=" N SER H1654 " --> pdb=" O ILE H1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1650 through 1654' Processing helix chain 'H' and resid 1656 through 1674 removed outlier: 3.754A pdb=" N GLN H1660 " --> pdb=" O ARG H1656 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS H1674 " --> pdb=" O TYR H1670 " (cutoff:3.500A) Processing helix chain 'H' and resid 1678 through 1689 removed outlier: 3.641A pdb=" N ALA H1684 " --> pdb=" O ARG H1680 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER H1687 " --> pdb=" O HIS H1683 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS H1688 " --> pdb=" O ALA H1684 " (cutoff:3.500A) Processing helix chain 'H' and resid 1690 through 1699 removed outlier: 3.894A pdb=" N LEU H1694 " --> pdb=" O ASP H1690 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU H1695 " --> pdb=" O GLN H1691 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU H1699 " --> pdb=" O LEU H1695 " (cutoff:3.500A) Processing helix chain 'H' and resid 1704 through 1719 removed outlier: 4.061A pdb=" N HIS H1719 " --> pdb=" O LEU H1715 " (cutoff:3.500A) Processing helix chain 'H' and resid 1720 through 1731 Processing helix chain 'H' and resid 1804 through 1826 Processing helix chain 'H' and resid 1830 through 1834 removed outlier: 4.072A pdb=" N SER H1834 " --> pdb=" O VAL H1831 " (cutoff:3.500A) Processing helix chain 'H' and resid 1839 through 1853 Processing helix chain 'H' and resid 1856 through 1868 Processing helix chain 'H' and resid 1933 through 1982 removed outlier: 3.845A pdb=" N ASP H1968 " --> pdb=" O GLU H1964 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS H1969 " --> pdb=" O ARG H1965 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN H1974 " --> pdb=" O LEU H1970 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY H1979 " --> pdb=" O ARG H1975 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE H1980 " --> pdb=" O ASP H1976 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET H1982 " --> pdb=" O TYR H1978 " (cutoff:3.500A) Processing helix chain 'H' and resid 1988 through 2001 removed outlier: 5.125A pdb=" N GLU H1998 " --> pdb=" O ARG H1994 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE H1999 " --> pdb=" O ARG H1995 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG H2000 " --> pdb=" O THR H1996 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER H2001 " --> pdb=" O ARG H1997 " (cutoff:3.500A) Processing helix chain 'H' and resid 2002 through 2010 Processing helix chain 'H' and resid 2028 through 2044 removed outlier: 3.931A pdb=" N LEU H2032 " --> pdb=" O ILE H2028 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY H2044 " --> pdb=" O LEU H2040 " (cutoff:3.500A) Processing helix chain 'H' and resid 2094 through 2110 removed outlier: 3.889A pdb=" N ASP H2110 " --> pdb=" O TRP H2106 " (cutoff:3.500A) Processing helix chain 'H' and resid 2114 through 2130 removed outlier: 3.514A pdb=" N VAL H2118 " --> pdb=" O SER H2114 " (cutoff:3.500A) Processing helix chain 'H' and resid 2130 through 2139 removed outlier: 3.610A pdb=" N GLU H2134 " --> pdb=" O ASP H2130 " (cutoff:3.500A) Processing helix chain 'H' and resid 2140 through 2142 No H-bonds generated for 'chain 'H' and resid 2140 through 2142' Processing helix chain 'H' and resid 2146 through 2148 No H-bonds generated for 'chain 'H' and resid 2146 through 2148' Processing helix chain 'H' and resid 2149 through 2169 removed outlier: 3.735A pdb=" N ILE H2168 " --> pdb=" O ARG H2164 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL H2169 " --> pdb=" O SER H2165 " (cutoff:3.500A) Processing helix chain 'H' and resid 2172 through 2188 removed outlier: 3.706A pdb=" N ASN H2188 " --> pdb=" O GLY H2184 " (cutoff:3.500A) Processing helix chain 'H' and resid 2190 through 2195 Processing helix chain 'H' and resid 2195 through 2202 removed outlier: 3.574A pdb=" N LEU H2202 " --> pdb=" O LEU H2198 " (cutoff:3.500A) Processing helix chain 'H' and resid 2203 through 2217 Processing helix chain 'H' and resid 2226 through 2244 removed outlier: 4.126A pdb=" N SER H2244 " --> pdb=" O PHE H2240 " (cutoff:3.500A) Processing helix chain 'H' and resid 2244 through 2254 Processing helix chain 'H' and resid 2254 through 2263 Processing helix chain 'H' and resid 2272 through 2282 removed outlier: 4.179A pdb=" N VAL H2276 " --> pdb=" O THR H2272 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA H2277 " --> pdb=" O PRO H2273 " (cutoff:3.500A) Processing helix chain 'H' and resid 2284 through 2290 Processing helix chain 'H' and resid 2292 through 2309 Processing helix chain 'H' and resid 2313 through 2318 Processing helix chain 'H' and resid 2325 through 2339 removed outlier: 3.571A pdb=" N ALA H2339 " --> pdb=" O PHE H2335 " (cutoff:3.500A) Processing helix chain 'H' and resid 2347 through 2355 Processing helix chain 'H' and resid 2355 through 2360 Processing helix chain 'H' and resid 2378 through 2384 Processing helix chain 'H' and resid 2425 through 2437 removed outlier: 3.533A pdb=" N LEU H2434 " --> pdb=" O LEU H2430 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N CYS H2437 " --> pdb=" O LEU H2433 " (cutoff:3.500A) Processing helix chain 'H' and resid 2448 through 2455 removed outlier: 3.653A pdb=" N LEU H2452 " --> pdb=" O LYS H2448 " (cutoff:3.500A) Processing helix chain 'H' and resid 2455 through 2461 removed outlier: 3.839A pdb=" N LEU H2461 " --> pdb=" O ILE H2457 " (cutoff:3.500A) Processing helix chain 'H' and resid 2498 through 2509 removed outlier: 3.929A pdb=" N ASP H2508 " --> pdb=" O VAL H2504 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG H2509 " --> pdb=" O LEU H2505 " (cutoff:3.500A) Processing helix chain 'H' and resid 2549 through 2567 removed outlier: 3.714A pdb=" N CYS H2556 " --> pdb=" O ASN H2552 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU H2557 " --> pdb=" O ARG H2553 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU H2560 " --> pdb=" O CYS H2556 " (cutoff:3.500A) Proline residue: H2561 - end of helix Processing helix chain 'H' and resid 2580 through 2593 Processing helix chain 'H' and resid 2597 through 2613 removed outlier: 3.517A pdb=" N ARG H2613 " --> pdb=" O MET H2609 " (cutoff:3.500A) Processing helix chain 'H' and resid 2619 through 2629 Processing helix chain 'H' and resid 2642 through 2653 Processing helix chain 'H' and resid 2665 through 2682 Processing helix chain 'H' and resid 2689 through 2700 removed outlier: 3.505A pdb=" N UNK H2700 " --> pdb=" O UNK H2696 " (cutoff:3.500A) Processing helix chain 'H' and resid 2957 through 2978 Processing helix chain 'H' and resid 3000 through 3018 Processing helix chain 'H' and resid 3033 through 3046 Processing helix chain 'H' and resid 3052 through 3062 Processing helix chain 'H' and resid 3147 through 3166 Processing helix chain 'H' and resid 3181 through 3193 Processing helix chain 'H' and resid 3203 through 3216 Processing helix chain 'H' and resid 3226 through 3238 Processing helix chain 'H' and resid 3279 through 3288 Processing helix chain 'H' and resid 3293 through 3308 Processing helix chain 'H' and resid 3321 through 3335 Processing helix chain 'H' and resid 3347 through 3358 Processing helix chain 'H' and resid 3366 through 3384 Processing helix chain 'H' and resid 3399 through 3418 Proline residue: H3411 - end of helix Processing helix chain 'H' and resid 3420 through 3425 Processing helix chain 'H' and resid 3431 through 3449 Processing helix chain 'H' and resid 3449 through 3461 Processing helix chain 'H' and resid 3510 through 3526 Processing helix chain 'H' and resid 3535 through 3544 Processing helix chain 'H' and resid 3549 through 3555 Processing helix chain 'H' and resid 3566 through 3574 Processing helix chain 'H' and resid 3587 through 3603 Processing helix chain 'H' and resid 3629 through 3634 Processing helix chain 'H' and resid 3636 through 3640 removed outlier: 4.423A pdb=" N ASN H3639 " --> pdb=" O PRO H3636 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU H3640 " --> pdb=" O LEU H3637 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3636 through 3640' Processing helix chain 'H' and resid 3643 through 3661 removed outlier: 3.899A pdb=" N ILE H3658 " --> pdb=" O LYS H3654 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU H3659 " --> pdb=" O ALA H3655 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR H3660 " --> pdb=" O ALA H3656 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU H3661 " --> pdb=" O TRP H3657 " (cutoff:3.500A) Processing helix chain 'H' and resid 3664 through 3676 removed outlier: 3.702A pdb=" N ARG H3668 " --> pdb=" O SER H3664 " (cutoff:3.500A) Processing helix chain 'H' and resid 3692 through 3707 removed outlier: 3.600A pdb=" N THR H3704 " --> pdb=" O HIS H3700 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA H3705 " --> pdb=" O PHE H3701 " (cutoff:3.500A) Processing helix chain 'H' and resid 3715 through 3730 Processing helix chain 'H' and resid 3748 through 3767 Processing helix chain 'H' and resid 3769 through 3782 removed outlier: 3.963A pdb=" N MET H3773 " --> pdb=" O GLY H3769 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N MET H3777 " --> pdb=" O MET H3773 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE H3778 " --> pdb=" O VAL H3774 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS H3782 " --> pdb=" O ILE H3778 " (cutoff:3.500A) Processing helix chain 'H' and resid 3786 through 3800 removed outlier: 4.064A pdb=" N SER H3798 " --> pdb=" O LYS H3794 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE H3799 " --> pdb=" O LEU H3795 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H3800 " --> pdb=" O GLY H3796 " (cutoff:3.500A) Processing helix chain 'H' and resid 3804 through 3819 removed outlier: 4.206A pdb=" N GLN H3808 " --> pdb=" O ASN H3804 " (cutoff:3.500A) Processing helix chain 'H' and resid 3822 through 3833 removed outlier: 3.942A pdb=" N SER H3826 " --> pdb=" O GLY H3822 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE H3827 " --> pdb=" O PHE H3823 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR H3833 " --> pdb=" O ALA H3829 " (cutoff:3.500A) Processing helix chain 'H' and resid 3838 through 3850 Processing helix chain 'H' and resid 3872 through 3887 removed outlier: 3.772A pdb=" N CYS H3887 " --> pdb=" O LEU H3883 " (cutoff:3.500A) Processing helix chain 'H' and resid 3892 through 3900 removed outlier: 3.541A pdb=" N TYR H3897 " --> pdb=" O ASP H3893 " (cutoff:3.500A) Processing helix chain 'H' and resid 3909 through 3932 Processing helix chain 'H' and resid 3942 through 3963 removed outlier: 4.314A pdb=" N LYS H3948 " --> pdb=" O ARG H3944 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA H3949 " --> pdb=" O ASN H3945 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET H3950 " --> pdb=" O PHE H3946 " (cutoff:3.500A) Processing helix chain 'H' and resid 3969 through 3977 Processing helix chain 'H' and resid 3983 through 3999 Processing helix chain 'H' and resid 4009 through 4025 removed outlier: 3.679A pdb=" N LEU H4025 " --> pdb=" O MET H4021 " (cutoff:3.500A) Processing helix chain 'H' and resid 4034 through 4046 removed outlier: 3.812A pdb=" N GLN H4038 " --> pdb=" O MET H4034 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP H4041 " --> pdb=" O ARG H4037 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL H4044 " --> pdb=" O VAL H4040 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU H4045 " --> pdb=" O ASP H4041 " (cutoff:3.500A) Processing helix chain 'H' and resid 4046 through 4066 removed outlier: 3.533A pdb=" N ILE H4053 " --> pdb=" O ASN H4049 " (cutoff:3.500A) Processing helix chain 'H' and resid 4069 through 4078 Processing helix chain 'H' and resid 4084 through 4090 removed outlier: 3.814A pdb=" N PHE H4088 " --> pdb=" O SER H4084 " (cutoff:3.500A) Processing helix chain 'H' and resid 4123 through 4128 removed outlier: 4.258A pdb=" N GLN H4128 " --> pdb=" O ALA H4124 " (cutoff:3.500A) Processing helix chain 'H' and resid 4131 through 4146 Processing helix chain 'H' and resid 4152 through 4154 No H-bonds generated for 'chain 'H' and resid 4152 through 4154' Processing helix chain 'H' and resid 4155 through 4170 removed outlier: 3.696A pdb=" N LEU H4161 " --> pdb=" O ASN H4157 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE H4165 " --> pdb=" O LEU H4161 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU H4167 " --> pdb=" O GLU H4163 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR H4168 " --> pdb=" O SER H4164 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE H4169 " --> pdb=" O ILE H4165 " (cutoff:3.500A) Processing helix chain 'H' and resid 4193 through 4201 removed outlier: 3.509A pdb=" N GLU H4201 " --> pdb=" O ARG H4197 " (cutoff:3.500A) Processing helix chain 'H' and resid 4202 through 4218 Processing helix chain 'H' and resid 4222 through 4241 Processing helix chain 'H' and resid 4316 through 4331 Processing helix chain 'H' and resid 4544 through 4556 Processing helix chain 'H' and resid 4556 through 4577 removed outlier: 3.574A pdb=" N PHE H4577 " --> pdb=" O PHE H4573 " (cutoff:3.500A) Processing helix chain 'H' and resid 4636 through 4681 removed outlier: 4.369A pdb=" N ARG H4642 " --> pdb=" O GLU H4638 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS H4643 " --> pdb=" O PRO H4639 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL H4664 " --> pdb=" O ASN H4660 " (cutoff:3.500A) Proline residue: H4665 - end of helix Processing helix chain 'H' and resid 4694 through 4701 Processing helix chain 'H' and resid 4702 through 4706 removed outlier: 3.762A pdb=" N ASN H4705 " --> pdb=" O LEU H4702 " (cutoff:3.500A) Processing helix chain 'H' and resid 4708 through 4712 removed outlier: 4.166A pdb=" N ASN H4712 " --> pdb=" O PHE H4709 " (cutoff:3.500A) Processing helix chain 'H' and resid 4717 through 4724 Processing helix chain 'H' and resid 4732 through 4737 removed outlier: 3.704A pdb=" N ALA H4736 " --> pdb=" O ARG H4732 " (cutoff:3.500A) Processing helix chain 'H' and resid 4764 through 4768 Processing helix chain 'H' and resid 4770 through 4783 Processing helix chain 'H' and resid 4784 through 4803 Processing helix chain 'H' and resid 4807 through 4817 Processing helix chain 'H' and resid 4818 through 4829 Processing helix chain 'H' and resid 4831 through 4857 Processing helix chain 'H' and resid 4876 through 4889 Processing helix chain 'H' and resid 4894 through 4898 removed outlier: 3.545A pdb=" N ASP H4897 " --> pdb=" O GLY H4894 " (cutoff:3.500A) Processing helix chain 'H' and resid 4907 through 4925 removed outlier: 3.567A pdb=" N ARG H4911 " --> pdb=" O TYR H4907 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE H4925 " --> pdb=" O PHE H4921 " (cutoff:3.500A) Processing helix chain 'H' and resid 4927 through 4955 removed outlier: 4.374A pdb=" N GLN H4931 " --> pdb=" O LEU H4927 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU H4953 " --> pdb=" O ARG H4949 " (cutoff:3.500A) Processing helix chain 'H' and resid 4963 through 4969 Processing helix chain 'H' and resid 4972 through 4996 removed outlier: 3.701A pdb=" N HIS H4976 " --> pdb=" O ARG H4972 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS H4981 " --> pdb=" O THR H4977 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR H4986 " --> pdb=" O ASN H4982 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N MET H4987 " --> pdb=" O LEU H4983 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE H4988 " --> pdb=" O ALA H4984 " (cutoff:3.500A) Processing helix chain 'H' and resid 5002 through 5014 removed outlier: 3.678A pdb=" N MET H5011 " --> pdb=" O TYR H5007 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU H5014 " --> pdb=" O LYS H5010 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 21 Processing helix chain 'I' and resid 29 through 40 Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 65 through 90 Processing helix chain 'I' and resid 102 through 113 Processing helix chain 'I' and resid 118 through 127 removed outlier: 3.674A pdb=" N ASP I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 148 Processing helix chain 'J' and resid 56 through 66 Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.768A pdb=" N ILE K 64 " --> pdb=" O ASP K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 84 Processing helix chain 'K' and resid 255 through 257 No H-bonds generated for 'chain 'K' and resid 255 through 257' Processing helix chain 'K' and resid 394 through 421 removed outlier: 3.676A pdb=" N SER K 398 " --> pdb=" O GLN K 394 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE K 421 " --> pdb=" O GLY K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 452 Processing helix chain 'K' and resid 460 through 481 Processing helix chain 'K' and resid 482 through 496 removed outlier: 3.861A pdb=" N LEU K 486 " --> pdb=" O GLY K 482 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL K 496 " --> pdb=" O ASP K 492 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 508 Processing helix chain 'K' and resid 512 through 531 removed outlier: 4.369A pdb=" N LYS K 516 " --> pdb=" O ALA K 512 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU K 517 " --> pdb=" O GLU K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 533 through 541 removed outlier: 3.664A pdb=" N CYS K 537 " --> pdb=" O ASN K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 543 through 552 removed outlier: 4.244A pdb=" N LEU K 547 " --> pdb=" O ASN K 543 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP K 552 " --> pdb=" O VAL K 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 556 through 571 removed outlier: 3.801A pdb=" N ILE K 560 " --> pdb=" O ALA K 556 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER K 571 " --> pdb=" O VAL K 567 " (cutoff:3.500A) Processing helix chain 'K' and resid 571 through 577 removed outlier: 4.288A pdb=" N LEU K 575 " --> pdb=" O SER K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 579 through 594 removed outlier: 3.529A pdb=" N ILE K 583 " --> pdb=" O GLN K 579 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY K 594 " --> pdb=" O LEU K 590 " (cutoff:3.500A) Processing helix chain 'K' and resid 596 through 606 removed outlier: 4.284A pdb=" N LEU K 600 " --> pdb=" O ASN K 596 " (cutoff:3.500A) Processing helix chain 'K' and resid 614 through 626 Processing helix chain 'K' and resid 812 through 815 removed outlier: 3.857A pdb=" N VAL K 815 " --> pdb=" O HIS K 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 812 through 815' Processing helix chain 'K' and resid 871 through 889 removed outlier: 3.528A pdb=" N ALA K 875 " --> pdb=" O ARG K 871 " (cutoff:3.500A) Processing helix chain 'K' and resid 914 through 936 Processing helix chain 'K' and resid 943 through 949 removed outlier: 4.115A pdb=" N GLU K 947 " --> pdb=" O ASP K 943 " (cutoff:3.500A) Processing helix chain 'K' and resid 955 through 960 Processing helix chain 'K' and resid 978 through 1004 Processing helix chain 'K' and resid 1018 through 1022 removed outlier: 3.991A pdb=" N VAL K1022 " --> pdb=" O PRO K1019 " (cutoff:3.500A) Processing helix chain 'K' and resid 1028 through 1050 removed outlier: 3.596A pdb=" N LYS K1032 " --> pdb=" O ASP K1028 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG K1033 " --> pdb=" O GLU K1029 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER K1034 " --> pdb=" O ALA K1030 " (cutoff:3.500A) Processing helix chain 'K' and resid 1444 through 1446 No H-bonds generated for 'chain 'K' and resid 1444 through 1446' Processing helix chain 'K' and resid 1465 through 1469 Processing helix chain 'K' and resid 1574 through 1580 removed outlier: 3.846A pdb=" N ALA K1578 " --> pdb=" O PRO K1574 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET K1579 " --> pdb=" O LEU K1575 " (cutoff:3.500A) Processing helix chain 'K' and resid 1650 through 1654 removed outlier: 3.657A pdb=" N SER K1654 " --> pdb=" O ILE K1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1650 through 1654' Processing helix chain 'K' and resid 1656 through 1674 removed outlier: 3.754A pdb=" N GLN K1660 " --> pdb=" O ARG K1656 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS K1674 " --> pdb=" O TYR K1670 " (cutoff:3.500A) Processing helix chain 'K' and resid 1678 through 1689 removed outlier: 3.642A pdb=" N ALA K1684 " --> pdb=" O ARG K1680 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER K1687 " --> pdb=" O HIS K1683 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS K1688 " --> pdb=" O ALA K1684 " (cutoff:3.500A) Processing helix chain 'K' and resid 1690 through 1699 removed outlier: 3.894A pdb=" N LEU K1694 " --> pdb=" O ASP K1690 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU K1695 " --> pdb=" O GLN K1691 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU K1699 " --> pdb=" O LEU K1695 " (cutoff:3.500A) Processing helix chain 'K' and resid 1704 through 1719 removed outlier: 4.062A pdb=" N HIS K1719 " --> pdb=" O LEU K1715 " (cutoff:3.500A) Processing helix chain 'K' and resid 1720 through 1731 Processing helix chain 'K' and resid 1804 through 1826 Processing helix chain 'K' and resid 1830 through 1834 removed outlier: 4.070A pdb=" N SER K1834 " --> pdb=" O VAL K1831 " (cutoff:3.500A) Processing helix chain 'K' and resid 1839 through 1853 Processing helix chain 'K' and resid 1856 through 1868 Processing helix chain 'K' and resid 1933 through 1982 removed outlier: 3.844A pdb=" N ASP K1968 " --> pdb=" O GLU K1964 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS K1969 " --> pdb=" O ARG K1965 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN K1974 " --> pdb=" O LEU K1970 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY K1979 " --> pdb=" O ARG K1975 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE K1980 " --> pdb=" O ASP K1976 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET K1982 " --> pdb=" O TYR K1978 " (cutoff:3.500A) Processing helix chain 'K' and resid 1988 through 2001 removed outlier: 5.124A pdb=" N GLU K1998 " --> pdb=" O ARG K1994 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N PHE K1999 " --> pdb=" O ARG K1995 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG K2000 " --> pdb=" O THR K1996 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER K2001 " --> pdb=" O ARG K1997 " (cutoff:3.500A) Processing helix chain 'K' and resid 2002 through 2010 Processing helix chain 'K' and resid 2028 through 2044 removed outlier: 3.931A pdb=" N LEU K2032 " --> pdb=" O ILE K2028 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY K2044 " --> pdb=" O LEU K2040 " (cutoff:3.500A) Processing helix chain 'K' and resid 2094 through 2110 removed outlier: 3.890A pdb=" N ASP K2110 " --> pdb=" O TRP K2106 " (cutoff:3.500A) Processing helix chain 'K' and resid 2114 through 2130 removed outlier: 3.513A pdb=" N VAL K2118 " --> pdb=" O SER K2114 " (cutoff:3.500A) Processing helix chain 'K' and resid 2130 through 2139 removed outlier: 3.611A pdb=" N GLU K2134 " --> pdb=" O ASP K2130 " (cutoff:3.500A) Processing helix chain 'K' and resid 2140 through 2142 No H-bonds generated for 'chain 'K' and resid 2140 through 2142' Processing helix chain 'K' and resid 2146 through 2148 No H-bonds generated for 'chain 'K' and resid 2146 through 2148' Processing helix chain 'K' and resid 2149 through 2169 removed outlier: 3.736A pdb=" N ILE K2168 " --> pdb=" O ARG K2164 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL K2169 " --> pdb=" O SER K2165 " (cutoff:3.500A) Processing helix chain 'K' and resid 2172 through 2188 removed outlier: 3.707A pdb=" N ASN K2188 " --> pdb=" O GLY K2184 " (cutoff:3.500A) Processing helix chain 'K' and resid 2190 through 2195 Processing helix chain 'K' and resid 2195 through 2202 removed outlier: 3.573A pdb=" N LEU K2202 " --> pdb=" O LEU K2198 " (cutoff:3.500A) Processing helix chain 'K' and resid 2203 through 2217 Processing helix chain 'K' and resid 2226 through 2244 removed outlier: 4.127A pdb=" N SER K2244 " --> pdb=" O PHE K2240 " (cutoff:3.500A) Processing helix chain 'K' and resid 2244 through 2254 Processing helix chain 'K' and resid 2254 through 2263 Processing helix chain 'K' and resid 2272 through 2282 removed outlier: 4.178A pdb=" N VAL K2276 " --> pdb=" O THR K2272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA K2277 " --> pdb=" O PRO K2273 " (cutoff:3.500A) Processing helix chain 'K' and resid 2284 through 2290 Processing helix chain 'K' and resid 2292 through 2309 Processing helix chain 'K' and resid 2313 through 2318 Processing helix chain 'K' and resid 2325 through 2339 removed outlier: 3.572A pdb=" N ALA K2339 " --> pdb=" O PHE K2335 " (cutoff:3.500A) Processing helix chain 'K' and resid 2347 through 2355 Processing helix chain 'K' and resid 2355 through 2360 Processing helix chain 'K' and resid 2378 through 2384 Processing helix chain 'K' and resid 2425 through 2437 removed outlier: 3.533A pdb=" N LEU K2434 " --> pdb=" O LEU K2430 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N CYS K2437 " --> pdb=" O LEU K2433 " (cutoff:3.500A) Processing helix chain 'K' and resid 2448 through 2455 removed outlier: 3.653A pdb=" N LEU K2452 " --> pdb=" O LYS K2448 " (cutoff:3.500A) Processing helix chain 'K' and resid 2455 through 2461 removed outlier: 3.839A pdb=" N LEU K2461 " --> pdb=" O ILE K2457 " (cutoff:3.500A) Processing helix chain 'K' and resid 2498 through 2509 removed outlier: 3.928A pdb=" N ASP K2508 " --> pdb=" O VAL K2504 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG K2509 " --> pdb=" O LEU K2505 " (cutoff:3.500A) Processing helix chain 'K' and resid 2549 through 2567 removed outlier: 3.712A pdb=" N CYS K2556 " --> pdb=" O ASN K2552 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU K2557 " --> pdb=" O ARG K2553 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU K2560 " --> pdb=" O CYS K2556 " (cutoff:3.500A) Proline residue: K2561 - end of helix Processing helix chain 'K' and resid 2580 through 2593 Processing helix chain 'K' and resid 2597 through 2613 removed outlier: 3.516A pdb=" N ARG K2613 " --> pdb=" O MET K2609 " (cutoff:3.500A) Processing helix chain 'K' and resid 2619 through 2629 Processing helix chain 'K' and resid 2642 through 2653 Processing helix chain 'K' and resid 2665 through 2682 Processing helix chain 'K' and resid 2689 through 2700 removed outlier: 3.503A pdb=" N UNK K2700 " --> pdb=" O UNK K2696 " (cutoff:3.500A) Processing helix chain 'K' and resid 2957 through 2978 Processing helix chain 'K' and resid 3000 through 3018 Processing helix chain 'K' and resid 3033 through 3046 Processing helix chain 'K' and resid 3052 through 3062 Processing helix chain 'K' and resid 3147 through 3166 Processing helix chain 'K' and resid 3181 through 3193 Processing helix chain 'K' and resid 3203 through 3216 Processing helix chain 'K' and resid 3226 through 3238 Processing helix chain 'K' and resid 3279 through 3288 Processing helix chain 'K' and resid 3293 through 3308 Processing helix chain 'K' and resid 3321 through 3335 Processing helix chain 'K' and resid 3347 through 3358 Processing helix chain 'K' and resid 3366 through 3384 Processing helix chain 'K' and resid 3399 through 3418 Proline residue: K3411 - end of helix Processing helix chain 'K' and resid 3420 through 3425 Processing helix chain 'K' and resid 3431 through 3449 Processing helix chain 'K' and resid 3449 through 3461 Processing helix chain 'K' and resid 3510 through 3526 Processing helix chain 'K' and resid 3535 through 3544 Processing helix chain 'K' and resid 3549 through 3555 Processing helix chain 'K' and resid 3566 through 3574 Processing helix chain 'K' and resid 3587 through 3603 Processing helix chain 'K' and resid 3629 through 3634 Processing helix chain 'K' and resid 3636 through 3640 removed outlier: 4.424A pdb=" N ASN K3639 " --> pdb=" O PRO K3636 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU K3640 " --> pdb=" O LEU K3637 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 3636 through 3640' Processing helix chain 'K' and resid 3643 through 3661 removed outlier: 3.901A pdb=" N ILE K3658 " --> pdb=" O LYS K3654 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU K3659 " --> pdb=" O ALA K3655 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR K3660 " --> pdb=" O ALA K3656 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU K3661 " --> pdb=" O TRP K3657 " (cutoff:3.500A) Processing helix chain 'K' and resid 3664 through 3676 removed outlier: 3.700A pdb=" N ARG K3668 " --> pdb=" O SER K3664 " (cutoff:3.500A) Processing helix chain 'K' and resid 3692 through 3707 removed outlier: 3.599A pdb=" N THR K3704 " --> pdb=" O HIS K3700 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA K3705 " --> pdb=" O PHE K3701 " (cutoff:3.500A) Processing helix chain 'K' and resid 3715 through 3730 Processing helix chain 'K' and resid 3748 through 3767 Processing helix chain 'K' and resid 3769 through 3782 removed outlier: 3.962A pdb=" N MET K3773 " --> pdb=" O GLY K3769 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N MET K3777 " --> pdb=" O MET K3773 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE K3778 " --> pdb=" O VAL K3774 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS K3782 " --> pdb=" O ILE K3778 " (cutoff:3.500A) Processing helix chain 'K' and resid 3786 through 3800 removed outlier: 4.064A pdb=" N SER K3798 " --> pdb=" O LYS K3794 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K3799 " --> pdb=" O LEU K3795 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU K3800 " --> pdb=" O GLY K3796 " (cutoff:3.500A) Processing helix chain 'K' and resid 3804 through 3819 removed outlier: 4.205A pdb=" N GLN K3808 " --> pdb=" O ASN K3804 " (cutoff:3.500A) Processing helix chain 'K' and resid 3822 through 3833 removed outlier: 3.941A pdb=" N SER K3826 " --> pdb=" O GLY K3822 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE K3827 " --> pdb=" O PHE K3823 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR K3833 " --> pdb=" O ALA K3829 " (cutoff:3.500A) Processing helix chain 'K' and resid 3838 through 3850 Processing helix chain 'K' and resid 3872 through 3887 removed outlier: 3.772A pdb=" N CYS K3887 " --> pdb=" O LEU K3883 " (cutoff:3.500A) Processing helix chain 'K' and resid 3892 through 3900 removed outlier: 3.541A pdb=" N TYR K3897 " --> pdb=" O ASP K3893 " (cutoff:3.500A) Processing helix chain 'K' and resid 3909 through 3932 Processing helix chain 'K' and resid 3942 through 3963 removed outlier: 4.314A pdb=" N LYS K3948 " --> pdb=" O ARG K3944 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA K3949 " --> pdb=" O ASN K3945 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET K3950 " --> pdb=" O PHE K3946 " (cutoff:3.500A) Processing helix chain 'K' and resid 3969 through 3977 Processing helix chain 'K' and resid 3983 through 3999 Processing helix chain 'K' and resid 4009 through 4025 removed outlier: 3.678A pdb=" N LEU K4025 " --> pdb=" O MET K4021 " (cutoff:3.500A) Processing helix chain 'K' and resid 4034 through 4046 removed outlier: 3.811A pdb=" N GLN K4038 " --> pdb=" O MET K4034 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP K4041 " --> pdb=" O ARG K4037 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL K4044 " --> pdb=" O VAL K4040 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU K4045 " --> pdb=" O ASP K4041 " (cutoff:3.500A) Processing helix chain 'K' and resid 4046 through 4066 removed outlier: 3.533A pdb=" N ILE K4053 " --> pdb=" O ASN K4049 " (cutoff:3.500A) Processing helix chain 'K' and resid 4069 through 4078 Processing helix chain 'K' and resid 4084 through 4090 removed outlier: 3.812A pdb=" N PHE K4088 " --> pdb=" O SER K4084 " (cutoff:3.500A) Processing helix chain 'K' and resid 4123 through 4128 removed outlier: 4.259A pdb=" N GLN K4128 " --> pdb=" O ALA K4124 " (cutoff:3.500A) Processing helix chain 'K' and resid 4131 through 4146 Processing helix chain 'K' and resid 4152 through 4154 No H-bonds generated for 'chain 'K' and resid 4152 through 4154' Processing helix chain 'K' and resid 4155 through 4170 removed outlier: 3.696A pdb=" N LEU K4161 " --> pdb=" O ASN K4157 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE K4165 " --> pdb=" O LEU K4161 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU K4167 " --> pdb=" O GLU K4163 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR K4168 " --> pdb=" O SER K4164 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE K4169 " --> pdb=" O ILE K4165 " (cutoff:3.500A) Processing helix chain 'K' and resid 4193 through 4201 removed outlier: 3.508A pdb=" N GLU K4201 " --> pdb=" O ARG K4197 " (cutoff:3.500A) Processing helix chain 'K' and resid 4202 through 4218 Processing helix chain 'K' and resid 4222 through 4241 Processing helix chain 'K' and resid 4316 through 4331 Processing helix chain 'K' and resid 4544 through 4556 Processing helix chain 'K' and resid 4556 through 4577 removed outlier: 3.574A pdb=" N PHE K4577 " --> pdb=" O PHE K4573 " (cutoff:3.500A) Processing helix chain 'K' and resid 4636 through 4681 removed outlier: 4.370A pdb=" N ARG K4642 " --> pdb=" O GLU K4638 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS K4643 " --> pdb=" O PRO K4639 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL K4664 " --> pdb=" O ASN K4660 " (cutoff:3.500A) Proline residue: K4665 - end of helix Processing helix chain 'K' and resid 4694 through 4701 Processing helix chain 'K' and resid 4702 through 4706 removed outlier: 3.763A pdb=" N ASN K4705 " --> pdb=" O LEU K4702 " (cutoff:3.500A) Processing helix chain 'K' and resid 4708 through 4712 removed outlier: 4.166A pdb=" N ASN K4712 " --> pdb=" O PHE K4709 " (cutoff:3.500A) Processing helix chain 'K' and resid 4717 through 4724 Processing helix chain 'K' and resid 4732 through 4737 removed outlier: 3.705A pdb=" N ALA K4736 " --> pdb=" O ARG K4732 " (cutoff:3.500A) Processing helix chain 'K' and resid 4764 through 4768 Processing helix chain 'K' and resid 4770 through 4783 Processing helix chain 'K' and resid 4784 through 4803 Processing helix chain 'K' and resid 4807 through 4817 Processing helix chain 'K' and resid 4818 through 4829 Processing helix chain 'K' and resid 4831 through 4857 Processing helix chain 'K' and resid 4876 through 4889 Processing helix chain 'K' and resid 4894 through 4898 removed outlier: 3.545A pdb=" N ASP K4897 " --> pdb=" O GLY K4894 " (cutoff:3.500A) Processing helix chain 'K' and resid 4907 through 4925 removed outlier: 3.567A pdb=" N ARG K4911 " --> pdb=" O TYR K4907 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE K4925 " --> pdb=" O PHE K4921 " (cutoff:3.500A) Processing helix chain 'K' and resid 4927 through 4955 removed outlier: 4.374A pdb=" N GLN K4931 " --> pdb=" O LEU K4927 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU K4953 " --> pdb=" O ARG K4949 " (cutoff:3.500A) Processing helix chain 'K' and resid 4963 through 4969 removed outlier: 3.500A pdb=" N THR K4969 " --> pdb=" O TYR K4965 " (cutoff:3.500A) Processing helix chain 'K' and resid 4972 through 4996 removed outlier: 3.701A pdb=" N HIS K4976 " --> pdb=" O ARG K4972 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS K4981 " --> pdb=" O THR K4977 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR K4986 " --> pdb=" O ASN K4982 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N MET K4987 " --> pdb=" O LEU K4983 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE K4988 " --> pdb=" O ALA K4984 " (cutoff:3.500A) Processing helix chain 'K' and resid 5002 through 5014 removed outlier: 3.678A pdb=" N MET K5011 " --> pdb=" O TYR K5007 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU K5014 " --> pdb=" O LYS K5010 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 21 Processing helix chain 'L' and resid 29 through 40 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 65 through 90 Processing helix chain 'L' and resid 102 through 113 Processing helix chain 'L' and resid 118 through 127 removed outlier: 3.674A pdb=" N ASP L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 4.082A pdb=" N GLU A 3 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 75 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 5 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 73 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR A 27 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 removed outlier: 4.092A pdb=" N CYS A 22 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.743A pdb=" N VAL B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 26 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 21 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN B 203 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.867A pdb=" N ILE B 170 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.810A pdb=" N SER B 183 " --> pdb=" O GLN B 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN B 190 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.772A pdb=" N ARG B 261 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.679A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 359 removed outlier: 3.653A pdb=" N THR B 358 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AB3, first strand: chain 'B' and resid 634 through 639 removed outlier: 4.149A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B1640 " --> pdb=" O GLN B 634 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 636 " --> pdb=" O ALA B1638 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B1638 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 682 through 687 removed outlier: 3.523A pdb=" N PHE B 783 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 642 " --> pdb=" O PHE B 783 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 824 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 743 through 749 removed outlier: 3.776A pdb=" N ALA B 809 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 743 through 749 removed outlier: 3.539A pdb=" N ARG B 790 " --> pdb=" O MET B 667 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 789 " --> pdb=" O VAL B1628 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B1629 " --> pdb=" O GLU B1616 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B1616 " --> pdb=" O GLN B1629 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 717 removed outlier: 4.225A pdb=" N GLY B 715 " --> pdb=" O TRP B 722 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 717 " --> pdb=" O HIS B 720 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS B 720 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 767 through 769 removed outlier: 3.502A pdb=" N THR B1475 " --> pdb=" O VAL B 767 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 830 through 831 removed outlier: 3.548A pdb=" N HIS B1201 " --> pdb=" O GLU B1093 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B1203 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B1091 " --> pdb=" O ASN B1203 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP B1088 " --> pdb=" O ILE B1153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 830 through 831 removed outlier: 3.548A pdb=" N HIS B1201 " --> pdb=" O GLU B1093 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B1203 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B1091 " --> pdb=" O ASN B1203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1121 through 1124 removed outlier: 3.547A pdb=" N LEU B1194 " --> pdb=" O ARG B1073 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG B1073 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1131 through 1132 removed outlier: 3.899A pdb=" N GLU B1137 " --> pdb=" O ARG B1131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1244 through 1246 removed outlier: 3.551A pdb=" N GLN B1244 " --> pdb=" O MET B1601 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B1601 " --> pdb=" O GLN B1244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1255 through 1257 removed outlier: 3.760A pdb=" N THR B1273 " --> pdb=" O GLU B1256 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B1272 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B1565 " --> pdb=" O SER B1436 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B1436 " --> pdb=" O GLU B1565 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B1528 " --> pdb=" O LEU B1519 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B1534 " --> pdb=" O ALA B1531 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1448 through 1453 Processing sheet with id=AC7, first strand: chain 'B' and resid 1736 through 1737 removed outlier: 7.204A pdb=" N VAL B1736 " --> pdb=" O ILE B2145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 1778 through 1779 Processing sheet with id=AC9, first strand: chain 'D' and resid 3 through 5 removed outlier: 4.082A pdb=" N GLU D 3 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 75 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 5 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 73 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR D 27 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 21 through 23 removed outlier: 4.091A pdb=" N CYS D 22 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 31 through 36 removed outlier: 3.744A pdb=" N VAL E 28 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 26 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL E 21 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN E 203 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.866A pdb=" N ILE E 170 " --> pdb=" O HIS E 151 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 117 through 120 Processing sheet with id=AD5, first strand: chain 'E' and resid 179 through 183 removed outlier: 3.810A pdb=" N SER E 183 " --> pdb=" O GLN E 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN E 190 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 281 through 283 removed outlier: 3.772A pdb=" N ARG E 261 " --> pdb=" O ARG E 283 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 290 through 292 removed outlier: 3.679A pdb=" N VAL E 300 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 314 through 317 Processing sheet with id=AD9, first strand: chain 'E' and resid 356 through 359 removed outlier: 3.653A pdb=" N THR E 358 " --> pdb=" O ILE E 377 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 608 through 609 Processing sheet with id=AE2, first strand: chain 'E' and resid 634 through 639 removed outlier: 4.148A pdb=" N GLN E 634 " --> pdb=" O HIS E1640 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E1640 " --> pdb=" O GLN E 634 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN E 636 " --> pdb=" O ALA E1638 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA E1638 " --> pdb=" O ASN E 636 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 682 through 687 removed outlier: 3.524A pdb=" N PHE E 783 " --> pdb=" O THR E 642 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR E 642 " --> pdb=" O PHE E 783 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 824 " --> pdb=" O ARG E 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 743 through 749 removed outlier: 3.774A pdb=" N ALA E 809 " --> pdb=" O LYS E 661 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 743 through 749 removed outlier: 3.539A pdb=" N ARG E 790 " --> pdb=" O MET E 667 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 789 " --> pdb=" O VAL E1628 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN E1629 " --> pdb=" O GLU E1616 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU E1616 " --> pdb=" O GLN E1629 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 715 through 717 removed outlier: 4.223A pdb=" N GLY E 715 " --> pdb=" O TRP E 722 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP E 717 " --> pdb=" O HIS E 720 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS E 720 " --> pdb=" O ASP E 717 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 767 through 769 removed outlier: 3.502A pdb=" N THR E1475 " --> pdb=" O VAL E 767 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 830 through 831 removed outlier: 3.548A pdb=" N HIS E1201 " --> pdb=" O GLU E1093 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN E1203 " --> pdb=" O GLU E1091 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU E1091 " --> pdb=" O ASN E1203 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP E1088 " --> pdb=" O ILE E1153 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 830 through 831 removed outlier: 3.548A pdb=" N HIS E1201 " --> pdb=" O GLU E1093 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN E1203 " --> pdb=" O GLU E1091 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU E1091 " --> pdb=" O ASN E1203 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 1121 through 1124 removed outlier: 3.547A pdb=" N LEU E1194 " --> pdb=" O ARG E1073 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG E1073 " --> pdb=" O LEU E1194 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE E1074 " --> pdb=" O SER E1239 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 1131 through 1132 removed outlier: 3.899A pdb=" N GLU E1137 " --> pdb=" O ARG E1131 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 1244 through 1246 removed outlier: 3.552A pdb=" N GLN E1244 " --> pdb=" O MET E1601 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET E1601 " --> pdb=" O GLN E1244 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 1255 through 1257 removed outlier: 3.760A pdb=" N THR E1273 " --> pdb=" O GLU E1256 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E1272 " --> pdb=" O ILE E1562 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE E1562 " --> pdb=" O LEU E1272 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU E1565 " --> pdb=" O SER E1436 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER E1436 " --> pdb=" O GLU E1565 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR E1528 " --> pdb=" O LEU E1519 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E1534 " --> pdb=" O ALA E1531 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 1448 through 1453 Processing sheet with id=AF6, first strand: chain 'E' and resid 1736 through 1737 removed outlier: 7.204A pdb=" N VAL E1736 " --> pdb=" O ILE E2145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'E' and resid 1778 through 1779 Processing sheet with id=AF8, first strand: chain 'G' and resid 3 through 5 removed outlier: 4.082A pdb=" N GLU G 3 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR G 75 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G 5 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS G 73 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR G 27 " --> pdb=" O ASP G 100 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 21 through 23 removed outlier: 4.090A pdb=" N CYS G 22 " --> pdb=" O PHE G 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 31 through 36 removed outlier: 3.743A pdb=" N VAL H 28 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 26 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL H 21 " --> pdb=" O ASN H 203 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN H 203 " --> pdb=" O VAL H 21 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 67 through 69 removed outlier: 3.866A pdb=" N ILE H 170 " --> pdb=" O HIS H 151 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 117 through 120 Processing sheet with id=AG4, first strand: chain 'H' and resid 179 through 183 removed outlier: 3.811A pdb=" N SER H 183 " --> pdb=" O GLN H 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN H 190 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 281 through 283 removed outlier: 3.772A pdb=" N ARG H 261 " --> pdb=" O ARG H 283 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 290 through 292 removed outlier: 3.680A pdb=" N VAL H 300 " --> pdb=" O ALA H 292 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 314 through 317 Processing sheet with id=AG8, first strand: chain 'H' and resid 356 through 359 removed outlier: 3.653A pdb=" N THR H 358 " --> pdb=" O ILE H 377 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 608 through 609 Processing sheet with id=AH1, first strand: chain 'H' and resid 634 through 639 removed outlier: 4.147A pdb=" N GLN H 634 " --> pdb=" O HIS H1640 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS H1640 " --> pdb=" O GLN H 634 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN H 636 " --> pdb=" O ALA H1638 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA H1638 " --> pdb=" O ASN H 636 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 682 through 687 removed outlier: 3.523A pdb=" N PHE H 783 " --> pdb=" O THR H 642 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR H 642 " --> pdb=" O PHE H 783 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU H 824 " --> pdb=" O ARG H 645 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 743 through 749 removed outlier: 3.774A pdb=" N ALA H 809 " --> pdb=" O LYS H 661 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 743 through 749 removed outlier: 3.539A pdb=" N ARG H 790 " --> pdb=" O MET H 667 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL H 789 " --> pdb=" O VAL H1628 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN H1629 " --> pdb=" O GLU H1616 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU H1616 " --> pdb=" O GLN H1629 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 715 through 717 removed outlier: 4.224A pdb=" N GLY H 715 " --> pdb=" O TRP H 722 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP H 717 " --> pdb=" O HIS H 720 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS H 720 " --> pdb=" O ASP H 717 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 767 through 769 removed outlier: 3.502A pdb=" N THR H1475 " --> pdb=" O VAL H 767 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 830 through 831 removed outlier: 3.548A pdb=" N HIS H1201 " --> pdb=" O GLU H1093 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN H1203 " --> pdb=" O GLU H1091 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU H1091 " --> pdb=" O ASN H1203 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP H1088 " --> pdb=" O ILE H1153 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 830 through 831 removed outlier: 3.548A pdb=" N HIS H1201 " --> pdb=" O GLU H1093 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN H1203 " --> pdb=" O GLU H1091 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU H1091 " --> pdb=" O ASN H1203 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 1121 through 1124 removed outlier: 3.547A pdb=" N LEU H1194 " --> pdb=" O ARG H1073 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG H1073 " --> pdb=" O LEU H1194 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE H1074 " --> pdb=" O SER H1239 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 1131 through 1132 removed outlier: 3.898A pdb=" N GLU H1137 " --> pdb=" O ARG H1131 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 1244 through 1246 removed outlier: 3.552A pdb=" N GLN H1244 " --> pdb=" O MET H1601 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET H1601 " --> pdb=" O GLN H1244 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 1255 through 1257 removed outlier: 3.761A pdb=" N THR H1273 " --> pdb=" O GLU H1256 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H1272 " --> pdb=" O ILE H1562 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE H1562 " --> pdb=" O LEU H1272 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU H1565 " --> pdb=" O SER H1436 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER H1436 " --> pdb=" O GLU H1565 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR H1528 " --> pdb=" O LEU H1519 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS H1534 " --> pdb=" O ALA H1531 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 1448 through 1453 Processing sheet with id=AI5, first strand: chain 'H' and resid 1736 through 1737 removed outlier: 7.204A pdb=" N VAL H1736 " --> pdb=" O ILE H2145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'H' and resid 1778 through 1779 Processing sheet with id=AI7, first strand: chain 'J' and resid 3 through 5 removed outlier: 4.082A pdb=" N GLU J 3 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR J 75 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU J 5 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS J 73 " --> pdb=" O GLU J 5 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J 27 " --> pdb=" O ASP J 100 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 21 through 23 removed outlier: 4.091A pdb=" N CYS J 22 " --> pdb=" O PHE J 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 31 through 36 removed outlier: 3.743A pdb=" N VAL K 28 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA K 26 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL K 21 " --> pdb=" O ASN K 203 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN K 203 " --> pdb=" O VAL K 21 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 67 through 69 removed outlier: 3.866A pdb=" N ILE K 170 " --> pdb=" O HIS K 151 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 117 through 120 Processing sheet with id=AJ3, first strand: chain 'K' and resid 179 through 183 removed outlier: 3.810A pdb=" N SER K 183 " --> pdb=" O GLN K 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN K 190 " --> pdb=" O SER K 183 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 281 through 283 removed outlier: 3.772A pdb=" N ARG K 261 " --> pdb=" O ARG K 283 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'K' and resid 290 through 292 removed outlier: 3.681A pdb=" N VAL K 300 " --> pdb=" O ALA K 292 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'K' and resid 314 through 317 Processing sheet with id=AJ7, first strand: chain 'K' and resid 356 through 359 removed outlier: 3.653A pdb=" N THR K 358 " --> pdb=" O ILE K 377 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'K' and resid 608 through 609 Processing sheet with id=AJ9, first strand: chain 'K' and resid 634 through 639 removed outlier: 4.147A pdb=" N GLN K 634 " --> pdb=" O HIS K1640 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS K1640 " --> pdb=" O GLN K 634 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN K 636 " --> pdb=" O ALA K1638 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA K1638 " --> pdb=" O ASN K 636 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'K' and resid 682 through 687 removed outlier: 3.524A pdb=" N PHE K 783 " --> pdb=" O THR K 642 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR K 642 " --> pdb=" O PHE K 783 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU K 824 " --> pdb=" O ARG K 645 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'K' and resid 743 through 749 removed outlier: 3.777A pdb=" N ALA K 809 " --> pdb=" O LYS K 661 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'K' and resid 743 through 749 removed outlier: 3.539A pdb=" N ARG K 790 " --> pdb=" O MET K 667 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL K 789 " --> pdb=" O VAL K1628 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN K1629 " --> pdb=" O GLU K1616 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU K1616 " --> pdb=" O GLN K1629 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'K' and resid 715 through 717 removed outlier: 4.223A pdb=" N GLY K 715 " --> pdb=" O TRP K 722 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP K 717 " --> pdb=" O HIS K 720 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS K 720 " --> pdb=" O ASP K 717 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'K' and resid 767 through 769 removed outlier: 3.502A pdb=" N THR K1475 " --> pdb=" O VAL K 767 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'K' and resid 830 through 831 removed outlier: 3.549A pdb=" N HIS K1201 " --> pdb=" O GLU K1093 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN K1203 " --> pdb=" O GLU K1091 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU K1091 " --> pdb=" O ASN K1203 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP K1088 " --> pdb=" O ILE K1153 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'K' and resid 830 through 831 removed outlier: 3.549A pdb=" N HIS K1201 " --> pdb=" O GLU K1093 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN K1203 " --> pdb=" O GLU K1091 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU K1091 " --> pdb=" O ASN K1203 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'K' and resid 1121 through 1124 removed outlier: 3.548A pdb=" N LEU K1194 " --> pdb=" O ARG K1073 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG K1073 " --> pdb=" O LEU K1194 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE K1074 " --> pdb=" O SER K1239 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'K' and resid 1131 through 1132 removed outlier: 3.899A pdb=" N GLU K1137 " --> pdb=" O ARG K1131 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'K' and resid 1244 through 1246 removed outlier: 3.552A pdb=" N GLN K1244 " --> pdb=" O MET K1601 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET K1601 " --> pdb=" O GLN K1244 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'K' and resid 1255 through 1257 removed outlier: 3.761A pdb=" N THR K1273 " --> pdb=" O GLU K1256 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K1272 " --> pdb=" O ILE K1562 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE K1562 " --> pdb=" O LEU K1272 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU K1565 " --> pdb=" O SER K1436 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER K1436 " --> pdb=" O GLU K1565 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR K1528 " --> pdb=" O LEU K1519 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS K1534 " --> pdb=" O ALA K1531 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'K' and resid 1448 through 1453 Processing sheet with id=AL4, first strand: chain 'K' and resid 1736 through 1737 removed outlier: 7.204A pdb=" N VAL K1736 " --> pdb=" O ILE K2145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'K' and resid 1778 through 1779 6090 hydrogen bonds defined for protein. 17850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 76.86 Time building geometry restraints manager: 33.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 33701 1.34 - 1.46: 23983 1.46 - 1.58: 43476 1.58 - 1.70: 4 1.70 - 1.82: 800 Bond restraints: 101964 Sorted by residual: bond pdb=" CB PRO H2362 " pdb=" CG PRO H2362 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.10e+00 bond pdb=" CB PRO E2362 " pdb=" CG PRO E2362 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.03e+00 bond pdb=" CB PRO B2362 " pdb=" CG PRO B2362 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.01e+00 bond pdb=" CB PRO K2362 " pdb=" CG PRO K2362 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.89e+00 bond pdb=" CB PRO K 694 " pdb=" CG PRO K 694 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.74e+00 ... (remaining 101959 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.44: 1946 105.44 - 112.62: 55120 112.62 - 119.81: 28556 119.81 - 126.99: 52906 126.99 - 134.17: 1092 Bond angle restraints: 139620 Sorted by residual: angle pdb=" CA PRO K2362 " pdb=" N PRO K2362 " pdb=" CD PRO K2362 " ideal model delta sigma weight residual 112.00 103.49 8.51 1.40e+00 5.10e-01 3.69e+01 angle pdb=" CA PRO B2362 " pdb=" N PRO B2362 " pdb=" CD PRO B2362 " ideal model delta sigma weight residual 112.00 103.52 8.48 1.40e+00 5.10e-01 3.67e+01 angle pdb=" CA PRO H2362 " pdb=" N PRO H2362 " pdb=" CD PRO H2362 " ideal model delta sigma weight residual 112.00 103.53 8.47 1.40e+00 5.10e-01 3.66e+01 angle pdb=" CA PRO E2362 " pdb=" N PRO E2362 " pdb=" CD PRO E2362 " ideal model delta sigma weight residual 112.00 103.53 8.47 1.40e+00 5.10e-01 3.66e+01 angle pdb=" CA PRO E 694 " pdb=" N PRO E 694 " pdb=" CD PRO E 694 " ideal model delta sigma weight residual 112.00 103.98 8.02 1.40e+00 5.10e-01 3.28e+01 ... (remaining 139615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 56670 17.95 - 35.90: 2201 35.90 - 53.84: 393 53.84 - 71.79: 52 71.79 - 89.74: 12 Dihedral angle restraints: 59328 sinusoidal: 15792 harmonic: 43536 Sorted by residual: dihedral pdb=" CA HIS H 736 " pdb=" C HIS H 736 " pdb=" N LEU H 737 " pdb=" CA LEU H 737 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA HIS E 736 " pdb=" C HIS E 736 " pdb=" N LEU E 737 " pdb=" CA LEU E 737 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA HIS B 736 " pdb=" C HIS B 736 " pdb=" N LEU B 737 " pdb=" CA LEU B 737 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 59325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 12404 0.032 - 0.064: 3362 0.064 - 0.096: 917 0.096 - 0.128: 358 0.128 - 0.160: 19 Chirality restraints: 17060 Sorted by residual: chirality pdb=" CB ILE C 28 " pdb=" CA ILE C 28 " pdb=" CG1 ILE C 28 " pdb=" CG2 ILE C 28 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CB ILE F 28 " pdb=" CA ILE F 28 " pdb=" CG1 ILE F 28 " pdb=" CG2 ILE F 28 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CB ILE L 28 " pdb=" CA ILE L 28 " pdb=" CG1 ILE L 28 " pdb=" CG2 ILE L 28 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 17057 not shown) Planarity restraints: 18140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 693 " 0.094 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO E 694 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO E 694 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO E 694 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 693 " 0.093 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO B 694 " -0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 693 " 0.093 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO K 694 " -0.237 5.00e-02 4.00e+02 pdb=" CA PRO K 694 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO K 694 " 0.072 5.00e-02 4.00e+02 ... (remaining 18137 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 15553 2.76 - 3.30: 97972 3.30 - 3.83: 162335 3.83 - 4.37: 156551 4.37 - 4.90: 285864 Nonbonded interactions: 718275 Sorted by model distance: nonbonded pdb=" O PHE H2122 " pdb=" OH TYR H3721 " model vdw 2.228 2.440 nonbonded pdb=" O PHE E2122 " pdb=" OH TYR E3721 " model vdw 2.228 2.440 nonbonded pdb=" O PHE K2122 " pdb=" OH TYR K3721 " model vdw 2.229 2.440 nonbonded pdb=" O PHE B2122 " pdb=" OH TYR B3721 " model vdw 2.229 2.440 nonbonded pdb=" OE2 GLU E2210 " pdb=" ND2 ASN E2214 " model vdw 2.231 2.520 ... (remaining 718270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.680 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: 0.070 Extract box with map and model: 24.950 Check model and map are aligned: 1.210 Set scattering table: 0.690 Process input model: 244.830 Find NCS groups from input model: 5.750 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 287.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 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 : 0.002 0.123 101964 Z= 0.148 Angle : 0.529 9.178 139620 Z= 0.298 Chirality : 0.035 0.160 17060 Planarity : 0.004 0.137 18140 Dihedral : 10.402 89.738 30944 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.07), residues: 13324 helix: 2.17 (0.07), residues: 6476 sheet: -0.24 (0.15), residues: 1108 loop : -1.03 (0.08), residues: 5740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 686 HIS 0.012 0.001 HIS B 502 PHE 0.029 0.001 PHE H4566 TYR 0.030 0.001 TYR K2239 ARG 0.018 0.001 ARG H 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26648 Ramachandran restraints generated. 13324 Oldfield, 0 Emsley, 13324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26648 Ramachandran restraints generated. 13324 Oldfield, 0 Emsley, 13324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.062 Fit side-chains REVERT: A 27 THR cc_start: 0.7579 (m) cc_final: 0.6421 (t) REVERT: A 34 LYS cc_start: 0.8299 (mttp) cc_final: 0.7906 (ptmt) REVERT: A 37 ASP cc_start: 0.8008 (t0) cc_final: 0.7542 (t0) REVERT: A 42 ARG cc_start: 0.6715 (ptt90) cc_final: 0.6496 (mmt180) REVERT: A 70 GLN cc_start: 0.8407 (tt0) cc_final: 0.7664 (tp-100) REVERT: A 75 THR cc_start: 0.9371 (m) cc_final: 0.9006 (t) REVERT: A 94 ASN cc_start: 0.7762 (t0) cc_final: 0.7254 (t0) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0935 time to fit residues: 2.8783 Evaluate side-chains 20 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.060 Evaluate side-chains 687 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 1.861 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: B 164 ARG cc_start: 0.8268 (mmt90) cc_final: 0.7865 (mtp85) REVERT: B 253 CYS cc_start: 0.8434 (p) cc_final: 0.7975 (t) REVERT: B 464 LYS cc_start: 0.9073 (tttt) cc_final: 0.8733 (tttp) REVERT: B 471 LEU cc_start: 0.8946 (tp) cc_final: 0.8391 (tp) REVERT: B 472 ARG cc_start: 0.8318 (mmt-90) cc_final: 0.8048 (mmm-85) REVERT: B 488 LEU cc_start: 0.9409 (mm) cc_final: 0.8921 (tp) REVERT: B 518 ILE cc_start: 0.9342 (tt) cc_final: 0.9079 (tp) REVERT: B 521 LEU cc_start: 0.9595 (mt) cc_final: 0.9292 (mp) REVERT: B 529 LEU cc_start: 0.9236 (mp) cc_final: 0.8587 (tt) REVERT: B 568 LEU cc_start: 0.9338 (mt) cc_final: 0.9010 (mt) REVERT: B 593 HIS cc_start: 0.7138 (m90) cc_final: 0.6856 (m90) REVERT: B 781 VAL cc_start: 0.8934 (t) cc_final: 0.8609 (p) REVERT: B 831 ARG cc_start: 0.7367 (ptp90) cc_final: 0.7115 (mpp80) REVERT: B 1074 ILE cc_start: 0.7785 (mt) cc_final: 0.7510 (tp) REVERT: B 1104 TRP cc_start: 0.8722 (m100) cc_final: 0.8333 (m100) REVERT: B 1158 ASN cc_start: 0.7671 (m110) cc_final: 0.7388 (m110) REVERT: B 1659 LEU cc_start: 0.8762 (mt) cc_final: 0.8493 (mm) REVERT: B 1660 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7502 (tm-30) REVERT: B 1670 TYR cc_start: 0.8394 (m-10) cc_final: 0.8141 (m-80) REVERT: B 1674 CYS cc_start: 0.8903 (p) cc_final: 0.8455 (p) REVERT: B 1731 LEU cc_start: 0.8668 (tp) cc_final: 0.8181 (tp) REVERT: B 1808 LEU cc_start: 0.8833 (tp) cc_final: 0.8515 (tp) REVERT: B 1839 PHE cc_start: 0.8818 (m-10) cc_final: 0.8591 (m-10) REVERT: B 1844 LYS cc_start: 0.8829 (tttm) cc_final: 0.8550 (tttp) REVERT: B 1945 GLU cc_start: 0.8501 (tt0) cc_final: 0.8056 (pt0) REVERT: B 1948 CYS cc_start: 0.8924 (t) cc_final: 0.8235 (t) REVERT: B 1949 ASP cc_start: 0.8874 (m-30) cc_final: 0.8382 (t70) REVERT: B 1952 LEU cc_start: 0.9061 (tp) cc_final: 0.8795 (tt) REVERT: B 1966 TYR cc_start: 0.8145 (t80) cc_final: 0.7902 (t80) REVERT: B 2011 LEU cc_start: 0.9172 (tp) cc_final: 0.8848 (mp) REVERT: B 2104 VAL cc_start: 0.9416 (t) cc_final: 0.9186 (p) REVERT: B 2122 PHE cc_start: 0.8553 (m-80) cc_final: 0.7997 (m-80) REVERT: B 2139 LEU cc_start: 0.9176 (mt) cc_final: 0.8745 (mt) REVERT: B 2179 MET cc_start: 0.8479 (tmm) cc_final: 0.8201 (tmm) REVERT: B 2209 MET cc_start: 0.8535 (mmm) cc_final: 0.8301 (mmp) REVERT: B 2212 MET cc_start: 0.8623 (ttt) cc_final: 0.7953 (tpp) REVERT: B 2229 MET cc_start: 0.8262 (tmm) cc_final: 0.7804 (tmm) REVERT: B 2236 PHE cc_start: 0.9214 (t80) cc_final: 0.8924 (t80) REVERT: B 2291 LEU cc_start: 0.9104 (tp) cc_final: 0.8703 (tt) REVERT: B 2338 PHE cc_start: 0.7334 (m-10) cc_final: 0.7084 (m-10) REVERT: B 3654 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8607 (ttmm) REVERT: B 3673 LEU cc_start: 0.8608 (tp) cc_final: 0.8060 (tp) REVERT: B 3727 LYS cc_start: 0.8439 (tptp) cc_final: 0.8172 (tmtt) REVERT: B 3759 LEU cc_start: 0.8944 (mt) cc_final: 0.8640 (mt) REVERT: B 3778 ILE cc_start: 0.9022 (mm) cc_final: 0.8615 (tp) REVERT: B 3810 LYS cc_start: 0.8746 (tptt) cc_final: 0.8535 (tppp) REVERT: B 3840 ASN cc_start: 0.8599 (p0) cc_final: 0.8240 (p0) REVERT: B 3878 ASP cc_start: 0.8075 (m-30) cc_final: 0.7483 (m-30) REVERT: B 3896 ASN cc_start: 0.8319 (t0) cc_final: 0.8000 (t0) REVERT: B 3930 TRP cc_start: 0.8512 (m100) cc_final: 0.8199 (t60) REVERT: B 3996 MET cc_start: 0.7532 (mmt) cc_final: 0.7301 (mmp) REVERT: B 4039 MET cc_start: 0.9025 (mmm) cc_final: 0.8025 (tpp) REVERT: B 4151 HIS cc_start: 0.8092 (p-80) cc_final: 0.7869 (p-80) REVERT: B 4208 SER cc_start: 0.9426 (m) cc_final: 0.9119 (t) REVERT: B 4211 GLN cc_start: 0.9293 (tm-30) cc_final: 0.9037 (tm-30) REVERT: B 4212 PHE cc_start: 0.8637 (t80) cc_final: 0.8408 (t80) REVERT: B 4226 MET cc_start: 0.8637 (tpt) cc_final: 0.8159 (tpt) REVERT: B 4802 TYR cc_start: 0.8483 (t80) cc_final: 0.8208 (t80) REVERT: B 4805 PHE cc_start: 0.7913 (m-10) cc_final: 0.7646 (m-10) REVERT: B 4842 LEU cc_start: 0.9238 (tp) cc_final: 0.8856 (tp) REVERT: B 4885 MET cc_start: 0.8342 (ttt) cc_final: 0.7956 (tmm) REVERT: B 4920 PHE cc_start: 0.8181 (t80) cc_final: 0.7821 (t80) REVERT: B 4952 MET cc_start: 0.8153 (tmm) cc_final: 0.7877 (tmm) REVERT: B 4993 LEU cc_start: 0.9312 (mp) cc_final: 0.8685 (mm) REVERT: B 5004 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8085 (mp10) REVERT: B 5009 TRP cc_start: 0.8136 (t-100) cc_final: 0.7456 (t-100) outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 0.2858 time to fit residues: 311.2589 Evaluate side-chains 523 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 523 time to evaluate : 1.833 Evaluate side-chains 28 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.064 Fit side-chains REVERT: C 8 GLU cc_start: 0.7940 (mp0) cc_final: 0.7577 (pm20) REVERT: C 9 GLN cc_start: 0.8774 (tt0) cc_final: 0.8262 (mt0) REVERT: C 12 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8679 (mt-10) REVERT: C 72 MET cc_start: 0.8738 (ppp) cc_final: 0.7822 (ppp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0911 time to fit residues: 2.8019 Evaluate side-chains 22 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1500 random chunks: chunk 1266 optimal weight: 6.9990 chunk 1136 optimal weight: 10.0000 chunk 630 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 766 optimal weight: 6.9990 chunk 607 optimal weight: 9.9990 chunk 1175 optimal weight: 3.9990 chunk 454 optimal weight: 0.8980 chunk 714 optimal weight: 5.9990 chunk 875 optimal weight: 0.4980 chunk 1362 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS D 105 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 GLN E 197 GLN E 379 HIS ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 ASN E 681 HIS ** E 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1274 HIS ** E1458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1590 GLN E1663 HIS E1693 GLN E2037 GLN E2177 ASN E3696 GLN E3958 ASN E4148 HIS ** E4572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4801 HIS E4804 ASN Total number of N/Q/H flips: 16 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 101964 Z= 0.324 Angle : 0.656 10.398 139620 Z= 0.351 Chirality : 0.039 0.363 17060 Planarity : 0.005 0.078 18140 Dihedral : 3.667 20.580 15564 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.27 % Allowed : 6.08 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.07), residues: 13324 helix: 1.90 (0.06), residues: 6576 sheet: -0.56 (0.15), residues: 1100 loop : -0.98 (0.08), residues: 5648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 722 HIS 0.007 0.002 HIS H 350 PHE 0.032 0.002 PHE E4806 TYR 0.031 0.002 TYR H4886 ARG 0.021 0.001 ARG B2137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26368 Ramachandran restraints generated. 13184 Oldfield, 0 Emsley, 13184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26368 Ramachandran restraints generated. 13184 Oldfield, 0 Emsley, 13184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.062 Fit side-chains REVERT: D 34 LYS cc_start: 0.8394 (mttp) cc_final: 0.8092 (ptmt) REVERT: D 37 ASP cc_start: 0.8053 (t0) cc_final: 0.7675 (t0) REVERT: D 42 ARG cc_start: 0.7205 (ptt90) cc_final: 0.6989 (mmt180) REVERT: D 70 GLN cc_start: 0.8033 (tt0) cc_final: 0.7257 (tp-100) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0895 time to fit residues: 2.3768 Evaluate side-chains 22 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.083 Evaluate side-chains 581 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 576 time to evaluate : 1.845 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: E 164 ARG cc_start: 0.8269 (mmt90) cc_final: 0.7882 (mtp85) REVERT: E 215 THR cc_start: 0.7647 (t) cc_final: 0.6667 (t) REVERT: E 253 CYS cc_start: 0.8831 (p) cc_final: 0.8119 (t) REVERT: E 269 TRP cc_start: 0.8169 (m-10) cc_final: 0.7800 (m-10) REVERT: E 303 ASP cc_start: 0.8425 (t0) cc_final: 0.8038 (t0) REVERT: E 334 MET cc_start: 0.7339 (mmp) cc_final: 0.6919 (mmp) REVERT: E 464 LYS cc_start: 0.9139 (tttt) cc_final: 0.8881 (ttmt) REVERT: E 471 LEU cc_start: 0.9007 (tp) cc_final: 0.8698 (tp) REVERT: E 472 ARG cc_start: 0.8930 (mmt-90) cc_final: 0.8141 (mmm-85) REVERT: E 475 GLN cc_start: 0.8787 (mt0) cc_final: 0.8442 (mt0) REVERT: E 488 LEU cc_start: 0.9482 (mm) cc_final: 0.9107 (tp) REVERT: E 493 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8149 (mtm-85) REVERT: E 521 LEU cc_start: 0.9624 (mt) cc_final: 0.9368 (mp) REVERT: E 534 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8044 (mtp-110) REVERT: E 590 LEU cc_start: 0.8818 (tp) cc_final: 0.8584 (tp) REVERT: E 593 HIS cc_start: 0.7551 (m90) cc_final: 0.7031 (m90) REVERT: E 615 CYS cc_start: 0.8594 (p) cc_final: 0.8370 (p) REVERT: E 667 MET cc_start: 0.6673 (pmm) cc_final: 0.6346 (pmm) REVERT: E 781 VAL cc_start: 0.9243 (t) cc_final: 0.8901 (p) REVERT: E 1104 TRP cc_start: 0.9087 (m100) cc_final: 0.8796 (m100) REVERT: E 1603 VAL cc_start: 0.9552 (t) cc_final: 0.9319 (p) REVERT: E 1659 LEU cc_start: 0.9063 (mt) cc_final: 0.8588 (mm) REVERT: E 1844 LYS cc_start: 0.9098 (tttm) cc_final: 0.8814 (ttmm) REVERT: E 1940 MET cc_start: 0.8633 (mmm) cc_final: 0.8427 (mmm) REVERT: E 1948 CYS cc_start: 0.8942 (t) cc_final: 0.8252 (t) REVERT: E 1949 ASP cc_start: 0.8985 (m-30) cc_final: 0.8434 (t0) REVERT: E 1952 LEU cc_start: 0.9155 (tp) cc_final: 0.8877 (tt) REVERT: E 2111 PHE cc_start: 0.7567 (t80) cc_final: 0.7121 (t80) REVERT: E 2122 PHE cc_start: 0.8753 (m-80) cc_final: 0.8217 (m-80) REVERT: E 2152 ASP cc_start: 0.9058 (m-30) cc_final: 0.8834 (m-30) REVERT: E 2179 MET cc_start: 0.8522 (tmm) cc_final: 0.7715 (tmm) REVERT: E 2209 MET cc_start: 0.8754 (mmm) cc_final: 0.8328 (mmp) REVERT: E 2291 LEU cc_start: 0.9078 (tp) cc_final: 0.8770 (tp) REVERT: E 2609 MET cc_start: 0.8211 (mtp) cc_final: 0.7763 (tpt) REVERT: E 3673 LEU cc_start: 0.8939 (tp) cc_final: 0.8671 (tp) REVERT: E 3717 LEU cc_start: 0.9304 (mm) cc_final: 0.9060 (mm) REVERT: E 3719 MET cc_start: 0.7761 (tmm) cc_final: 0.7436 (tmm) REVERT: E 3725 MET cc_start: 0.8445 (mtm) cc_final: 0.8244 (mtm) REVERT: E 3727 LYS cc_start: 0.8682 (tptp) cc_final: 0.8278 (ttpt) REVERT: E 3729 CYS cc_start: 0.8600 (t) cc_final: 0.8330 (t) REVERT: E 3748 PHE cc_start: 0.8837 (p90) cc_final: 0.8553 (p90) REVERT: E 3773 MET cc_start: 0.8188 (mmm) cc_final: 0.7671 (tpt) REVERT: E 3778 ILE cc_start: 0.9288 (mm) cc_final: 0.9078 (mm) REVERT: E 3794 LYS cc_start: 0.9264 (mptt) cc_final: 0.8999 (mmmt) REVERT: E 3840 ASN cc_start: 0.8775 (p0) cc_final: 0.8543 (p0) REVERT: E 3884 GLN cc_start: 0.8431 (tt0) cc_final: 0.7920 (tt0) REVERT: E 3930 TRP cc_start: 0.8770 (m100) cc_final: 0.8074 (t60) REVERT: E 3958 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8619 (t0) REVERT: E 3996 MET cc_start: 0.7798 (mmt) cc_final: 0.7573 (mmp) REVERT: E 4021 MET cc_start: 0.8475 (ptt) cc_final: 0.7507 (ppp) REVERT: E 4022 LEU cc_start: 0.9048 (mt) cc_final: 0.7832 (mt) REVERT: E 4039 MET cc_start: 0.9050 (mmm) cc_final: 0.8019 (tpp) REVERT: E 4208 SER cc_start: 0.9388 (m) cc_final: 0.9157 (t) REVERT: E 4211 GLN cc_start: 0.9419 (tm-30) cc_final: 0.9210 (tm-30) REVERT: E 4212 PHE cc_start: 0.8825 (t80) cc_final: 0.8619 (t80) REVERT: E 4226 MET cc_start: 0.8691 (tpt) cc_final: 0.8312 (tpt) REVERT: E 4552 TYR cc_start: 0.9205 (t80) cc_final: 0.8978 (t80) REVERT: E 4647 LEU cc_start: 0.9101 (mm) cc_final: 0.8314 (tt) REVERT: E 4842 LEU cc_start: 0.9296 (tp) cc_final: 0.8968 (tp) REVERT: E 4881 TYR cc_start: 0.9030 (t80) cc_final: 0.8504 (t80) REVERT: E 4885 MET cc_start: 0.8707 (ttt) cc_final: 0.8252 (mtt) REVERT: E 4920 PHE cc_start: 0.8515 (t80) cc_final: 0.8049 (t80) REVERT: E 4952 MET cc_start: 0.8430 (tmm) cc_final: 0.8052 (tmm) REVERT: E 4991 MET cc_start: 0.8810 (ptt) cc_final: 0.8331 (ptt) REVERT: E 5004 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8298 (mp10) REVERT: E 5011 MET cc_start: 0.8989 (mpp) cc_final: 0.8545 (tpt) outliers start: 5 outliers final: 0 residues processed: 578 average time/residue: 0.2657 time to fit residues: 248.2800 Evaluate side-chains 460 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 1.880 Evaluate side-chains 25 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: I 8 GLU cc_start: 0.8018 (mp0) cc_final: 0.7604 (pm20) REVERT: I 9 GLN cc_start: 0.8681 (tt0) cc_final: 0.8111 (pt0) REVERT: I 12 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8685 (mp0) REVERT: I 15 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8128 (tm-30) REVERT: I 19 LEU cc_start: 0.9061 (mt) cc_final: 0.8638 (mt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0861 time to fit residues: 2.3885 Evaluate side-chains 25 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1500 random chunks: chunk 757 optimal weight: 9.9990 chunk 422 optimal weight: 0.6980 chunk 1133 optimal weight: 2.9990 chunk 927 optimal weight: 0.8980 chunk 375 optimal weight: 9.9990 chunk 1364 optimal weight: 9.9990 chunk 1474 optimal weight: 0.6980 chunk 1215 optimal weight: 4.9990 chunk 1353 optimal weight: 10.0000 chunk 465 optimal weight: 0.0060 chunk 1094 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 218 HIS E 349 GLN E 383 HIS ** E 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1125 ASN ** E1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1460 HIS ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2042 HIS ** E2247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3955 GLN E4148 HIS E4572 ASN ** E4944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 101964 Z= 0.293 Angle : 0.809 20.350 139620 Z= 0.416 Chirality : 0.046 0.454 17060 Planarity : 0.007 0.069 18140 Dihedral : 4.048 21.385 15564 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.75 % Allowed : 5.70 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.07), residues: 13324 helix: 1.10 (0.06), residues: 6564 sheet: -0.52 (0.15), residues: 1144 loop : -1.21 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP B 147 HIS 0.038 0.005 HIS K1298 PHE 0.077 0.005 PHE B2240 TYR 0.104 0.006 TYR H1711 ARG 0.041 0.002 ARG H2000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26166 Ramachandran restraints generated. 13083 Oldfield, 0 Emsley, 13083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26166 Ramachandran restraints generated. 13083 Oldfield, 0 Emsley, 13083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.065 Fit side-chains REVERT: G 4 ILE cc_start: 0.9306 (tt) cc_final: 0.8850 (mm) REVERT: G 34 LYS cc_start: 0.8357 (mttp) cc_final: 0.7910 (ptmt) REVERT: G 37 ASP cc_start: 0.7735 (t0) cc_final: 0.7400 (t0) REVERT: G 42 ARG cc_start: 0.7422 (ptt90) cc_final: 0.7128 (mmt180) REVERT: G 70 GLN cc_start: 0.7893 (tt0) cc_final: 0.7280 (tp-100) REVERT: G 75 THR cc_start: 0.9514 (m) cc_final: 0.9226 (p) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0866 time to fit residues: 2.4891 Evaluate side-chains 25 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.066 Evaluate side-chains 569 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 556 time to evaluate : 1.865 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: E 25 ASN cc_start: 0.8714 (m-40) cc_final: 0.8179 (m-40) REVERT: E 100 THR cc_start: 0.8930 (m) cc_final: 0.8653 (m) REVERT: E 138 GLN cc_start: 0.7250 (pp30) cc_final: 0.6952 (pp30) REVERT: E 164 ARG cc_start: 0.8252 (mmt90) cc_final: 0.7909 (mtp85) REVERT: E 215 THR cc_start: 0.7563 (t) cc_final: 0.6646 (t) REVERT: E 253 CYS cc_start: 0.8828 (p) cc_final: 0.8123 (t) REVERT: E 269 TRP cc_start: 0.8096 (m-10) cc_final: 0.7761 (m-10) REVERT: E 283 ARG cc_start: 0.6048 (ttt90) cc_final: 0.5681 (ttt-90) REVERT: E 303 ASP cc_start: 0.8309 (t0) cc_final: 0.7871 (t70) REVERT: E 334 MET cc_start: 0.7391 (mmp) cc_final: 0.7171 (mmp) REVERT: E 413 HIS cc_start: 0.8394 (t70) cc_final: 0.8087 (t-90) REVERT: E 464 LYS cc_start: 0.9065 (tttt) cc_final: 0.8793 (tttp) REVERT: E 468 LEU cc_start: 0.9301 (mt) cc_final: 0.9023 (mt) REVERT: E 471 LEU cc_start: 0.8877 (tp) cc_final: 0.8612 (tp) REVERT: E 472 ARG cc_start: 0.8823 (mmt-90) cc_final: 0.8022 (mmm-85) REVERT: E 488 LEU cc_start: 0.9410 (mm) cc_final: 0.9060 (tp) REVERT: E 493 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7728 (mtm-85) REVERT: E 518 ILE cc_start: 0.9598 (pt) cc_final: 0.9313 (tp) REVERT: E 521 LEU cc_start: 0.9496 (mt) cc_final: 0.9252 (mp) REVERT: E 567 VAL cc_start: 0.9300 (p) cc_final: 0.9096 (p) REVERT: E 592 LYS cc_start: 0.9021 (ptmt) cc_final: 0.8080 (ptmt) REVERT: E 593 HIS cc_start: 0.7438 (m90) cc_final: 0.6848 (m90) REVERT: E 615 CYS cc_start: 0.8472 (p) cc_final: 0.8177 (p) REVERT: E 667 MET cc_start: 0.7300 (pmm) cc_final: 0.7067 (pmm) REVERT: E 781 VAL cc_start: 0.9183 (t) cc_final: 0.8733 (p) REVERT: E 1104 TRP cc_start: 0.9012 (m100) cc_final: 0.8758 (m100) REVERT: E 1603 VAL cc_start: 0.9455 (t) cc_final: 0.9237 (p) REVERT: E 1659 LEU cc_start: 0.9043 (mt) cc_final: 0.8807 (mm) REVERT: E 1674 CYS cc_start: 0.9082 (p) cc_final: 0.8771 (p) REVERT: E 1718 ILE cc_start: 0.9159 (mm) cc_final: 0.8920 (mm) REVERT: E 1844 LYS cc_start: 0.9072 (tttm) cc_final: 0.8666 (ttmm) REVERT: E 1940 MET cc_start: 0.8456 (mmm) cc_final: 0.8230 (mmm) REVERT: E 1948 CYS cc_start: 0.9000 (t) cc_final: 0.8575 (t) REVERT: E 2111 PHE cc_start: 0.7289 (t80) cc_final: 0.7003 (t80) REVERT: E 2122 PHE cc_start: 0.8721 (m-80) cc_final: 0.8141 (m-80) REVERT: E 2152 ASP cc_start: 0.8905 (m-30) cc_final: 0.8587 (m-30) REVERT: E 2186 ILE cc_start: 0.9254 (tt) cc_final: 0.8835 (tt) REVERT: E 2189 ASN cc_start: 0.8407 (m110) cc_final: 0.7533 (m110) REVERT: E 2209 MET cc_start: 0.8513 (mmm) cc_final: 0.8107 (mmp) REVERT: E 2212 MET cc_start: 0.8791 (ttt) cc_final: 0.8429 (ttt) REVERT: E 2237 LEU cc_start: 0.9275 (tp) cc_final: 0.8715 (tp) REVERT: E 2240 PHE cc_start: 0.9191 (t80) cc_final: 0.8764 (t80) REVERT: E 2291 LEU cc_start: 0.9056 (tp) cc_final: 0.8575 (tt) REVERT: E 2609 MET cc_start: 0.8082 (mtp) cc_final: 0.7641 (tpt) REVERT: E 3673 LEU cc_start: 0.8883 (tp) cc_final: 0.8609 (tp) REVERT: E 3717 LEU cc_start: 0.9180 (mm) cc_final: 0.8908 (mm) REVERT: E 3719 MET cc_start: 0.7666 (tmm) cc_final: 0.7250 (tmm) REVERT: E 3727 LYS cc_start: 0.8661 (tptp) cc_final: 0.8294 (tmtt) REVERT: E 3729 CYS cc_start: 0.8385 (t) cc_final: 0.8127 (t) REVERT: E 3748 PHE cc_start: 0.8746 (p90) cc_final: 0.8445 (p90) REVERT: E 3755 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8708 (mttt) REVERT: E 3773 MET cc_start: 0.8072 (mmm) cc_final: 0.7529 (tpt) REVERT: E 3782 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8639 (mmtm) REVERT: E 3794 LYS cc_start: 0.9212 (mptt) cc_final: 0.8979 (mmmt) REVERT: E 3810 LYS cc_start: 0.8848 (tppt) cc_final: 0.8310 (tppp) REVERT: E 3840 ASN cc_start: 0.8765 (p0) cc_final: 0.8479 (p0) REVERT: E 3853 MET cc_start: 0.7653 (ppp) cc_final: 0.7425 (ppp) REVERT: E 3884 GLN cc_start: 0.7929 (tt0) cc_final: 0.7436 (tt0) REVERT: E 3930 TRP cc_start: 0.8688 (m100) cc_final: 0.8049 (t60) REVERT: E 3996 MET cc_start: 0.7756 (mmt) cc_final: 0.7528 (mmp) REVERT: E 4021 MET cc_start: 0.8134 (ptt) cc_final: 0.7389 (ppp) REVERT: E 4022 LEU cc_start: 0.9098 (mt) cc_final: 0.7667 (mt) REVERT: E 4034 MET cc_start: 0.7542 (tmm) cc_final: 0.6965 (tmm) REVERT: E 4208 SER cc_start: 0.9398 (m) cc_final: 0.9181 (t) REVERT: E 4211 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9162 (tm-30) REVERT: E 4212 PHE cc_start: 0.8626 (t80) cc_final: 0.8405 (t80) REVERT: E 4226 MET cc_start: 0.8590 (tpt) cc_final: 0.8256 (tpt) REVERT: E 4552 TYR cc_start: 0.9172 (t80) cc_final: 0.8880 (t80) REVERT: E 4777 LYS cc_start: 0.9191 (pttt) cc_final: 0.8977 (pttt) REVERT: E 4842 LEU cc_start: 0.9219 (tp) cc_final: 0.8991 (tp) REVERT: E 4885 MET cc_start: 0.8670 (ttt) cc_final: 0.8467 (mmm) REVERT: E 4920 PHE cc_start: 0.8472 (t80) cc_final: 0.8031 (t80) REVERT: E 4952 MET cc_start: 0.8412 (tmm) cc_final: 0.7922 (tmm) REVERT: E 4991 MET cc_start: 0.8790 (ptt) cc_final: 0.8415 (ptt) REVERT: E 5004 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8268 (mp10) REVERT: E 5011 MET cc_start: 0.8870 (mpp) cc_final: 0.8418 (tpt) outliers start: 13 outliers final: 1 residues processed: 562 average time/residue: 0.2588 time to fit residues: 237.1616 Evaluate side-chains 467 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 466 time to evaluate : 1.881 Evaluate side-chains 27 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: I 8 GLU cc_start: 0.8009 (mp0) cc_final: 0.7571 (pm20) REVERT: I 9 GLN cc_start: 0.8847 (tt0) cc_final: 0.8071 (pt0) REVERT: I 12 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8683 (mp0) REVERT: I 15 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8081 (tm-30) REVERT: I 19 LEU cc_start: 0.9114 (mt) cc_final: 0.8562 (mt) REVERT: I 72 MET cc_start: 0.8428 (ppp) cc_final: 0.8107 (ppp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0920 time to fit residues: 2.7273 Evaluate side-chains 26 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1500 random chunks: chunk 1348 optimal weight: 1.9990 chunk 1025 optimal weight: 0.1980 chunk 708 optimal weight: 0.5980 chunk 151 optimal weight: 0.0070 chunk 651 optimal weight: 0.3980 chunk 916 optimal weight: 0.0970 chunk 1369 optimal weight: 10.0000 chunk 1449 optimal weight: 0.6980 chunk 715 optimal weight: 0.9980 chunk 1297 optimal weight: 0.5980 chunk 390 optimal weight: 0.2980 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 218 HIS ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 HIS ** E 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1158 ASN ** E1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E3955 GLN E3958 ASN ** E4038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4148 HIS ** E4572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4831 ASN ** E4944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4947 GLN E4981 HIS Total number of N/Q/H flips: 9 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 101964 Z= 0.290 Angle : 0.805 15.722 139620 Z= 0.413 Chirality : 0.047 0.516 17060 Planarity : 0.009 0.273 18140 Dihedral : 4.320 58.154 15564 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.21 % Allowed : 4.32 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.07), residues: 13324 helix: 0.89 (0.06), residues: 6564 sheet: -0.42 (0.16), residues: 1084 loop : -1.26 (0.08), residues: 5676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP E3981 HIS 0.065 0.006 HIS J 87 PHE 0.058 0.005 PHE B3987 TYR 0.058 0.006 TYR H 663 ARG 0.074 0.002 ARG K3979 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26166 Ramachandran restraints generated. 13083 Oldfield, 0 Emsley, 13083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26166 Ramachandran restraints generated. 13083 Oldfield, 0 Emsley, 13083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.062 Fit side-chains REVERT: G 34 LYS cc_start: 0.8393 (mttp) cc_final: 0.7863 (ptmt) REVERT: G 37 ASP cc_start: 0.7655 (t0) cc_final: 0.7341 (t0) REVERT: G 42 ARG cc_start: 0.7337 (ptt90) cc_final: 0.7033 (mmt180) REVERT: G 70 GLN cc_start: 0.7732 (tt0) cc_final: 0.7179 (tp-100) REVERT: G 75 THR cc_start: 0.9465 (m) cc_final: 0.9219 (p) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0848 time to fit residues: 2.5428 Evaluate side-chains 23 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.062 Evaluate side-chains 550 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 547 time to evaluate : 1.832 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: E 25 ASN cc_start: 0.8754 (m-40) cc_final: 0.7568 (m-40) REVERT: E 100 THR cc_start: 0.8983 (m) cc_final: 0.8737 (m) REVERT: E 138 GLN cc_start: 0.7364 (pp30) cc_final: 0.7036 (pp30) REVERT: E 164 ARG cc_start: 0.8209 (mmt90) cc_final: 0.7861 (mtp85) REVERT: E 215 THR cc_start: 0.7455 (t) cc_final: 0.6442 (t) REVERT: E 269 TRP cc_start: 0.8062 (m-10) cc_final: 0.7717 (m-10) REVERT: E 394 GLN cc_start: 0.7454 (pt0) cc_final: 0.7183 (mp10) REVERT: E 413 HIS cc_start: 0.8384 (t70) cc_final: 0.8120 (t70) REVERT: E 464 LYS cc_start: 0.9033 (tttt) cc_final: 0.8766 (tttp) REVERT: E 468 LEU cc_start: 0.9309 (mt) cc_final: 0.9024 (mt) REVERT: E 471 LEU cc_start: 0.8944 (tp) cc_final: 0.8636 (tp) REVERT: E 472 ARG cc_start: 0.8803 (mmt-90) cc_final: 0.7996 (mmm-85) REVERT: E 488 LEU cc_start: 0.9404 (mm) cc_final: 0.9081 (tp) REVERT: E 493 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.7753 (mtm-85) REVERT: E 518 ILE cc_start: 0.9587 (pt) cc_final: 0.9305 (tp) REVERT: E 521 LEU cc_start: 0.9474 (mt) cc_final: 0.9214 (mp) REVERT: E 577 ILE cc_start: 0.8914 (mm) cc_final: 0.8666 (tp) REVERT: E 592 LYS cc_start: 0.9045 (ptmt) cc_final: 0.8133 (ptmt) REVERT: E 593 HIS cc_start: 0.7419 (m90) cc_final: 0.6789 (m90) REVERT: E 615 CYS cc_start: 0.8432 (p) cc_final: 0.8134 (p) REVERT: E 781 VAL cc_start: 0.9203 (t) cc_final: 0.8742 (p) REVERT: E 816 LEU cc_start: 0.7238 (mm) cc_final: 0.6492 (pp) REVERT: E 831 ARG cc_start: 0.7247 (ptp90) cc_final: 0.6937 (mpp80) REVERT: E 839 LEU cc_start: 0.8835 (mt) cc_final: 0.8619 (mt) REVERT: E 1104 TRP cc_start: 0.9069 (m100) cc_final: 0.8849 (m100) REVERT: E 1674 CYS cc_start: 0.9096 (p) cc_final: 0.8719 (p) REVERT: E 1718 ILE cc_start: 0.9120 (mm) cc_final: 0.8897 (mm) REVERT: E 1844 LYS cc_start: 0.9007 (tttm) cc_final: 0.8658 (ttmm) REVERT: E 1948 CYS cc_start: 0.9039 (t) cc_final: 0.8595 (t) REVERT: E 2111 PHE cc_start: 0.7225 (t80) cc_final: 0.6855 (t80) REVERT: E 2122 PHE cc_start: 0.8750 (m-80) cc_final: 0.8130 (m-80) REVERT: E 2152 ASP cc_start: 0.8888 (m-30) cc_final: 0.8525 (m-30) REVERT: E 2186 ILE cc_start: 0.9212 (tt) cc_final: 0.8742 (tt) REVERT: E 2189 ASN cc_start: 0.8244 (m110) cc_final: 0.7425 (m110) REVERT: E 2209 MET cc_start: 0.8669 (mmm) cc_final: 0.8204 (mmp) REVERT: E 2212 MET cc_start: 0.8876 (ttt) cc_final: 0.8319 (tpp) REVERT: E 2240 PHE cc_start: 0.9145 (t80) cc_final: 0.8917 (t80) REVERT: E 2291 LEU cc_start: 0.9139 (tp) cc_final: 0.8565 (tt) REVERT: E 2609 MET cc_start: 0.8003 (mtp) cc_final: 0.7568 (tpt) REVERT: E 3673 LEU cc_start: 0.8893 (tp) cc_final: 0.8643 (tp) REVERT: E 3703 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.7812 (ttm-80) REVERT: E 3716 TYR cc_start: 0.7007 (t80) cc_final: 0.6797 (t80) REVERT: E 3717 LEU cc_start: 0.9228 (mm) cc_final: 0.8986 (mm) REVERT: E 3719 MET cc_start: 0.7731 (tmm) cc_final: 0.7219 (tmm) REVERT: E 3727 LYS cc_start: 0.8646 (tptp) cc_final: 0.8292 (tmtt) REVERT: E 3729 CYS cc_start: 0.8265 (t) cc_final: 0.8033 (t) REVERT: E 3748 PHE cc_start: 0.8746 (p90) cc_final: 0.8461 (p90) REVERT: E 3755 LYS cc_start: 0.9177 (mtmm) cc_final: 0.8727 (mttt) REVERT: E 3773 MET cc_start: 0.8030 (mmm) cc_final: 0.7397 (tpt) REVERT: E 3794 LYS cc_start: 0.9208 (mptt) cc_final: 0.8988 (mmmt) REVERT: E 3810 LYS cc_start: 0.8797 (tppt) cc_final: 0.8431 (tppp) REVERT: E 3840 ASN cc_start: 0.8752 (p0) cc_final: 0.8505 (p0) REVERT: E 3853 MET cc_start: 0.7760 (ppp) cc_final: 0.7551 (ppp) REVERT: E 3876 THR cc_start: 0.9304 (t) cc_final: 0.8942 (t) REVERT: E 3930 TRP cc_start: 0.8626 (m100) cc_final: 0.7998 (t60) REVERT: E 3958 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8722 (t0) REVERT: E 3996 MET cc_start: 0.7743 (mmt) cc_final: 0.7537 (mmp) REVERT: E 4021 MET cc_start: 0.8253 (ptt) cc_final: 0.7804 (ppp) REVERT: E 4022 LEU cc_start: 0.9046 (mt) cc_final: 0.8571 (mt) REVERT: E 4039 MET cc_start: 0.8899 (mmp) cc_final: 0.8655 (mmp) REVERT: E 4168 TYR cc_start: 0.8675 (t80) cc_final: 0.8281 (t80) REVERT: E 4208 SER cc_start: 0.9392 (m) cc_final: 0.9184 (t) REVERT: E 4212 PHE cc_start: 0.8614 (t80) cc_final: 0.8357 (t80) REVERT: E 4226 MET cc_start: 0.8568 (tpt) cc_final: 0.8249 (tpt) REVERT: E 4559 THR cc_start: 0.9051 (p) cc_final: 0.8721 (p) REVERT: E 4777 LYS cc_start: 0.9241 (pttt) cc_final: 0.8922 (pttt) REVERT: E 4842 LEU cc_start: 0.9176 (tp) cc_final: 0.8966 (tp) REVERT: E 4952 MET cc_start: 0.8397 (tmm) cc_final: 0.7925 (tmm) REVERT: E 5004 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8242 (mp10) REVERT: E 5011 MET cc_start: 0.8865 (mpp) cc_final: 0.8394 (tpt) outliers start: 3 outliers final: 1 residues processed: 548 average time/residue: 0.2588 time to fit residues: 230.8032 Evaluate side-chains 471 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 469 time to evaluate : 1.852 Evaluate side-chains 26 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.065 Fit side-chains REVERT: I 8 GLU cc_start: 0.8014 (mp0) cc_final: 0.7602 (pm20) REVERT: I 9 GLN cc_start: 0.8846 (tt0) cc_final: 0.8130 (pt0) REVERT: I 12 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8702 (mp0) REVERT: I 15 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8151 (tm-30) REVERT: I 19 LEU cc_start: 0.9106 (mt) cc_final: 0.8501 (mt) REVERT: I 73 MET cc_start: 0.8576 (tmm) cc_final: 0.8287 (tmm) REVERT: I 75 ARG cc_start: 0.7985 (ptt-90) cc_final: 0.7675 (pmt170) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0822 time to fit residues: 2.3948 Evaluate side-chains 26 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1500 random chunks: chunk 1207 optimal weight: 9.9990 chunk 823 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 1079 optimal weight: 1.9990 chunk 598 optimal weight: 0.0010 chunk 1237 optimal weight: 4.9990 chunk 1002 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 740 optimal weight: 10.0000 chunk 1301 optimal weight: 8.9990 chunk 365 optimal weight: 8.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN ** E 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1158 ASN ** E1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2552 ASN ** E3663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4038 GLN E4148 HIS ** E4572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 101964 Z= 0.347 Angle : 0.829 18.569 139620 Z= 0.424 Chirality : 0.053 1.479 17060 Planarity : 0.008 0.209 18140 Dihedral : 4.259 25.935 15564 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.21 % Allowed : 3.30 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.07), residues: 13324 helix: 0.77 (0.06), residues: 6564 sheet: -0.73 (0.15), residues: 1132 loop : -1.30 (0.08), residues: 5628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP E 147 HIS 0.041 0.005 HIS D 87 PHE 0.080 0.005 PHE B3987 TYR 0.114 0.006 TYR B 663 ARG 0.045 0.002 ARG B2000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26166 Ramachandran restraints generated. 13083 Oldfield, 0 Emsley, 13083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26166 Ramachandran restraints generated. 13083 Oldfield, 0 Emsley, 13083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.086 Fit side-chains REVERT: G 34 LYS cc_start: 0.8346 (mttp) cc_final: 0.7948 (ptmt) REVERT: G 37 ASP cc_start: 0.7696 (t0) cc_final: 0.7373 (t0) REVERT: G 42 ARG cc_start: 0.7349 (ptt90) cc_final: 0.7025 (mmt180) REVERT: G 70 GLN cc_start: 0.7790 (tt0) cc_final: 0.7108 (tp-100) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1019 time to fit residues: 2.7875 Evaluate side-chains 23 residues out of total 86 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.080 Evaluate side-chains 540 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 536 time to evaluate : 1.947 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: E 100 THR cc_start: 0.9018 (m) cc_final: 0.8745 (m) REVERT: E 138 GLN cc_start: 0.7463 (pp30) cc_final: 0.7220 (pp30) REVERT: E 164 ARG cc_start: 0.8244 (mmt90) cc_final: 0.7924 (mtp85) REVERT: E 192 ASP cc_start: 0.7121 (m-30) cc_final: 0.6791 (m-30) REVERT: E 215 THR cc_start: 0.7134 (OUTLIER) cc_final: 0.6559 (t) REVERT: E 269 TRP cc_start: 0.8096 (m-10) cc_final: 0.7780 (m-10) REVERT: E 334 MET cc_start: 0.7296 (mmp) cc_final: 0.6623 (mmp) REVERT: E 394 GLN cc_start: 0.7505 (pt0) cc_final: 0.7118 (mp10) REVERT: E 413 HIS cc_start: 0.8433 (t70) cc_final: 0.8142 (t-90) REVERT: E 464 LYS cc_start: 0.9061 (tttt) cc_final: 0.8798 (tttp) REVERT: E 468 LEU cc_start: 0.9353 (mt) cc_final: 0.9039 (mt) REVERT: E 471 LEU cc_start: 0.9002 (tp) cc_final: 0.8695 (tp) REVERT: E 472 ARG cc_start: 0.8861 (mmt-90) cc_final: 0.8068 (mmm-85) REVERT: E 488 LEU cc_start: 0.9370 (mm) cc_final: 0.9090 (tp) REVERT: E 493 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7784 (mtm-85) REVERT: E 518 ILE cc_start: 0.9606 (pt) cc_final: 0.9293 (tp) REVERT: E 521 LEU cc_start: 0.9487 (mt) cc_final: 0.9237 (mp) REVERT: E 592 LYS cc_start: 0.8975 (ptmt) cc_final: 0.8055 (ptmt) REVERT: E 593 HIS cc_start: 0.7333 (m170) cc_final: 0.6762 (m90) REVERT: E 781 VAL cc_start: 0.9194 (t) cc_final: 0.8740 (p) REVERT: E 816 LEU cc_start: 0.7567 (mm) cc_final: 0.6911 (pp) REVERT: E 831 ARG cc_start: 0.7278 (ptp90) cc_final: 0.6977 (mpp80) REVERT: E 1100 MET cc_start: 0.7769 (tpt) cc_final: 0.7189 (tpp) REVERT: E 1104 TRP cc_start: 0.9098 (m100) cc_final: 0.8847 (m100) REVERT: E 1636 MET cc_start: 0.8491 (ppp) cc_final: 0.7912 (ppp) REVERT: E 1718 ILE cc_start: 0.9137 (mm) cc_final: 0.8912 (mm) REVERT: E 1844 LYS cc_start: 0.9085 (tttm) cc_final: 0.8703 (ttmm) REVERT: E 1948 CYS cc_start: 0.9096 (t) cc_final: 0.8583 (t) REVERT: E 2111 PHE cc_start: 0.7239 (t80) cc_final: 0.6927 (t80) REVERT: E 2122 PHE cc_start: 0.8773 (m-80) cc_final: 0.8153 (m-80) REVERT: E 2152 ASP cc_start: 0.8905 (m-30) cc_final: 0.8559 (m-30) REVERT: E 2186 ILE cc_start: 0.9262 (tt) cc_final: 0.9030 (tt) REVERT: E 2187 MET cc_start: 0.8919 (mmt) cc_final: 0.8502 (mmp) REVERT: E 2189 ASN cc_start: 0.8175 (m110) cc_final: 0.7705 (m110) REVERT: E 2193 TYR cc_start: 0.8624 (m-80) cc_final: 0.8409 (m-80) REVERT: E 2209 MET cc_start: 0.8755 (mmm) cc_final: 0.8210 (mmp) REVERT: E 2212 MET cc_start: 0.8892 (ttt) cc_final: 0.8349 (tpp) REVERT: E 2237 LEU cc_start: 0.9246 (tp) cc_final: 0.9016 (tp) REVERT: E 2240 PHE cc_start: 0.9142 (t80) cc_final: 0.8926 (t80) REVERT: E 2291 LEU cc_start: 0.9151 (tp) cc_final: 0.8630 (tt) REVERT: E 2609 MET cc_start: 0.8074 (mtp) cc_final: 0.7632 (tpt) REVERT: E 3673 LEU cc_start: 0.8891 (tp) cc_final: 0.8675 (tp) REVERT: E 3703 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8012 (mtp-110) REVERT: E 3716 TYR cc_start: 0.7278 (t80) cc_final: 0.6929 (t80) REVERT: E 3719 MET cc_start: 0.7781 (tmm) cc_final: 0.7233 (tmm) REVERT: E 3727 LYS cc_start: 0.8673 (tptp) cc_final: 0.8327 (tmtt) REVERT: E 3729 CYS cc_start: 0.8379 (t) cc_final: 0.8020 (t) REVERT: E 3748 PHE cc_start: 0.8746 (p90) cc_final: 0.8485 (p90) REVERT: E 3755 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8771 (mttt) REVERT: E 3794 LYS cc_start: 0.9331 (mmtt) cc_final: 0.8988 (mmmt) REVERT: E 3800 LEU cc_start: 0.8819 (mm) cc_final: 0.8444 (mm) REVERT: E 3810 LYS cc_start: 0.8782 (tppt) cc_final: 0.8367 (tppp) REVERT: E 3840 ASN cc_start: 0.8822 (p0) cc_final: 0.8531 (p0) REVERT: E 3853 MET cc_start: 0.7871 (ppp) cc_final: 0.7521 (ppp) REVERT: E 3876 THR cc_start: 0.9287 (t) cc_final: 0.9052 (t) REVERT: E 3930 TRP cc_start: 0.8626 (m100) cc_final: 0.8001 (t60) REVERT: E 3955 GLN cc_start: 0.8771 (pp30) cc_final: 0.8519 (pp30) REVERT: E 4021 MET cc_start: 0.8288 (ptt) cc_final: 0.7690 (ppp) REVERT: E 4022 LEU cc_start: 0.9032 (mt) cc_final: 0.8683 (mt) REVERT: E 4034 MET cc_start: 0.7436 (tmm) cc_final: 0.7191 (tmm) REVERT: E 4039 MET cc_start: 0.8896 (mmp) cc_final: 0.8659 (mmp) REVERT: E 4212 PHE cc_start: 0.8624 (t80) cc_final: 0.8418 (t80) REVERT: E 4226 MET cc_start: 0.8561 (tpt) cc_final: 0.8252 (tpt) REVERT: E 4777 LYS cc_start: 0.9242 (pttt) cc_final: 0.8931 (pttt) REVERT: E 4842 LEU cc_start: 0.9282 (tp) cc_final: 0.8993 (tp) REVERT: E 4952 MET cc_start: 0.8383 (tmm) cc_final: 0.7925 (tmm) REVERT: E 5004 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8285 (mp10) REVERT: E 5009 TRP cc_start: 0.8306 (t-100) cc_final: 0.7470 (t-100) REVERT: E 5011 MET cc_start: 0.8891 (mpp) cc_final: 0.8408 (tpt) outliers start: 4 outliers final: 2 residues processed: 537 average time/residue: 0.2613 time to fit residues: 228.9364 Evaluate side-chains 469 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 466 time to evaluate : 1.918 Evaluate side-chains 26 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.065 Fit side-chains REVERT: I 8 GLU cc_start: 0.8026 (mp0) cc_final: 0.7614 (pm20) REVERT: I 9 GLN cc_start: 0.8870 (tt0) cc_final: 0.8144 (pt0) REVERT: I 12 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8632 (mp0) REVERT: I 15 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8029 (tm-30) REVERT: I 19 LEU cc_start: 0.9122 (mt) cc_final: 0.8730 (mt) REVERT: I 72 MET cc_start: 0.8373 (ppp) cc_final: 0.7489 (ppp) REVERT: I 75 ARG cc_start: 0.7983 (ptt-90) cc_final: 0.7668 (pmt170) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0825 time to fit residues: 2.3911 Evaluate side-chains 26 residues out of total 116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** 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 306, in __init__ self.caller(self.refine_xyz) 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 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.5679 > 50: distance: 0 - 1: 25.243 distance: 0 - 3: 10.217 distance: 3 - 4: 13.603 distance: 4 - 5: 13.525 distance: 4 - 7: 23.045 distance: 5 - 8: 7.187 distance: 8 - 9: 18.474 distance: 9 - 10: 6.837 distance: 9 - 12: 17.800 distance: 10 - 11: 34.673 distance: 10 - 13: 24.420 distance: 13 - 14: 26.040 distance: 14 - 15: 20.158 distance: 14 - 17: 18.376 distance: 15 - 16: 16.541 distance: 15 - 18: 14.543 distance: 18 - 19: 19.330 distance: 19 - 20: 41.398 distance: 19 - 22: 27.867 distance: 20 - 21: 45.585 distance: 20 - 23: 31.930 distance: 23 - 24: 31.580 distance: 24 - 25: 45.620 distance: 24 - 27: 43.343 distance: 25 - 26: 30.929 distance: 25 - 28: 34.900 distance: 28 - 29: 15.467 distance: 29 - 30: 11.953 distance: 29 - 32: 17.828 distance: 30 - 31: 25.328 distance: 30 - 33: 31.574 distance: 33 - 34: 13.825 distance: 34 - 35: 29.982 distance: 34 - 37: 17.585 distance: 35 - 36: 17.274 distance: 35 - 38: 18.996 distance: 38 - 39: 30.147 distance: 39 - 40: 10.640 distance: 39 - 42: 29.161 distance: 40 - 41: 34.866 distance: 40 - 43: 17.796 distance: 41 - 58: 38.577 distance: 43 - 44: 36.975 distance: 44 - 45: 26.437 distance: 44 - 47: 14.888 distance: 45 - 46: 35.917 distance: 45 - 48: 32.124 distance: 48 - 49: 14.197 distance: 49 - 50: 33.159 distance: 49 - 52: 44.587 distance: 50 - 51: 45.746 distance: 50 - 53: 21.084 distance: 53 - 54: 32.610 distance: 54 - 55: 33.105 distance: 54 - 57: 13.914 distance: 55 - 56: 30.104 distance: 55 - 58: 38.463 distance: 58 - 59: 34.061 distance: 59 - 60: 19.619 distance: 60 - 61: 7.303