Starting phenix.real_space_refine on Sun Mar 10 14:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w39_32274/03_2024/7w39_32274_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w39_32274/03_2024/7w39_32274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w39_32274/03_2024/7w39_32274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w39_32274/03_2024/7w39_32274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w39_32274/03_2024/7w39_32274_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w39_32274/03_2024/7w39_32274_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 16 5.49 5 Mg 5 5.21 5 S 616 5.16 5 C 67282 2.51 5 N 18304 2.21 5 O 20218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 106442 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3096 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 23, 'TRANS': 370} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3018 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 364} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2864 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3039 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3097 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 19, 'TRANS': 369} Chain: "F" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3251 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1889 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 1958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1981 Chain: "J" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1880 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1777 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1866 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "O" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1649 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1587 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1588 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1683 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6334 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 30, 'TRANS': 781} Chain breaks: 2 Chain: "V" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3612 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 15, 'TRANS': 428} Chain: "W" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3635 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 437} Chain: "X" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3009 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 369} Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "f" Number of atoms: 6866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6866 Classifications: {'peptide': 889} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 854} Chain: "g" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1880 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "h" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1861 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1782 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1861 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "m" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "n" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1510 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "p" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1588 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "s" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "t" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "u" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "v" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 53 Classifications: {'peptide': 10} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "x" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 588 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N ALA K 120 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA K 120 " occ=0.50 residue: pdb=" N LYS P 17 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS P 17 " occ=0.50 residue: pdb=" N ALA X 359 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.50 residue: pdb=" N GLN X 380 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.50 residue: pdb=" N GLY Z 30 " occ=0.38 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.38 residue: pdb=" N ILE b 90 " occ=0.46 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.46 residue: pdb=" N SER b 115 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.70 residue: pdb=" N ILE b 140 " occ=0.39 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.39 residue: pdb=" N VAL b 173 " occ=0.89 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.89 residue: pdb=" N GLY b 191 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.50 residue: pdb=" N ILE d 63 " occ=0.78 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.78 residue: pdb=" N SER d 70 " occ=0.95 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.95 ... (remaining 9 not shown) Time building chain proxies: 40.42, per 1000 atoms: 0.38 Number of scatterers: 106442 At special positions: 0 Unit cell: (347.98, 219.885, 221.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 616 16.00 P 16 15.00 Mg 5 11.99 O 20218 8.00 N 18304 7.00 C 67282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 270 " distance=2.03 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: 27.36 Conformation dependent library (CDL) restraints added in 14.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25306 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 500 helices and 84 sheets defined 55.5% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 46.11 Creating SS restraints... Processing helix chain 'A' and resid 41 through 64 removed outlier: 5.021A pdb=" N GLY A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.162A pdb=" N TRP A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.738A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 130 through 135 removed outlier: 4.757A pdb=" N ILE A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU A 135 " --> pdb=" O PRO A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.933A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.295A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.783A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 205 removed outlier: 5.029A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.995A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 246' Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.659A pdb=" N THR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.115A pdb=" N ILE A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 307 removed outlier: 3.974A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 360 removed outlier: 5.577A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.116A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.795A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.935A pdb=" N TYR A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.505A pdb=" N LYS A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 423 " --> pdb=" O TYR A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 86 removed outlier: 5.060A pdb=" N LYS B 86 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 removed outlier: 5.104A pdb=" N ARG B 96 " --> pdb=" O GLN B 92 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.800A pdb=" N THR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.276A pdb=" N ILE B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 188' Processing helix chain 'B' and resid 190 through 201 removed outlier: 6.396A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 208 through 215 removed outlier: 5.177A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.073A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.721A pdb=" N HIS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 4.773A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 318 removed outlier: 3.876A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.701A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 4.256A pdb=" N LYS B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.470A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 removed outlier: 3.650A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 426 removed outlier: 3.919A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 423 " --> pdb=" O PHE B 419 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 65 removed outlier: 4.365A pdb=" N LEU C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 removed outlier: 4.535A pdb=" N THR C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 142 removed outlier: 4.383A pdb=" N LEU C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.925A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 179 removed outlier: 4.063A pdb=" N GLU C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 217 through 225 removed outlier: 4.063A pdb=" N GLN C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 removed outlier: 4.500A pdb=" N VAL C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 283 removed outlier: 3.633A pdb=" N ARG C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLY C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.960A pdb=" N ILE C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 3.796A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY C 367 " --> pdb=" O CYS C 363 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 397 removed outlier: 5.049A pdb=" N LYS C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 79 removed outlier: 3.647A pdb=" N VAL D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 4.352A pdb=" N LEU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 125' Processing helix chain 'D' and resid 163 through 168 removed outlier: 4.949A pdb=" N GLY D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.132A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 195 Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.865A pdb=" N VAL D 250 " --> pdb=" O MET D 246 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 251 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 299 removed outlier: 6.104A pdb=" N ARG D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 removed outlier: 4.562A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 323' Processing helix chain 'D' and resid 338 through 353 removed outlier: 3.592A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 4.712A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 390 removed outlier: 4.206A pdb=" N ILE D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN D 376 " --> pdb=" O GLY D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 removed outlier: 4.417A pdb=" N LYS D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 237 removed outlier: 3.968A pdb=" N PHE D 235 " --> pdb=" O GLY D 232 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 236 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLN D 237 " --> pdb=" O GLU D 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 52 removed outlier: 4.508A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR E 12 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.979A pdb=" N LEU E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 93' Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.872A pdb=" N HIS E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 125 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.650A pdb=" N ILE E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 131 through 136' Processing helix chain 'E' and resid 138 through 155 removed outlier: 3.969A pdb=" N VAL E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 163 Processing helix chain 'E' and resid 179 through 192 removed outlier: 3.870A pdb=" N GLN E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 6.965A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'E' and resid 209 through 226 removed outlier: 3.539A pdb=" N ILE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.732A pdb=" N ILE E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 266 removed outlier: 3.856A pdb=" N GLU E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.686A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 removed outlier: 3.913A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP E 336 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 removed outlier: 4.346A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG E 344 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 380 removed outlier: 3.898A pdb=" N ASP E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS E 378 " --> pdb=" O VAL E 374 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 36 removed outlier: 4.007A pdb=" N GLU F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N MET F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 84 removed outlier: 3.764A pdb=" N LEU F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 4.204A pdb=" N LEU F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 169 through 177 removed outlier: 5.764A pdb=" N VAL F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.453A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY F 189 " --> pdb=" O TYR F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'F' and resid 191 through 208 removed outlier: 4.589A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 removed outlier: 3.819A pdb=" N LEU F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 removed outlier: 3.731A pdb=" N LEU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 4.125A pdb=" N LEU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 257' Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.481A pdb=" N ALA F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 293 removed outlier: 3.902A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 318 removed outlier: 5.259A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 4.913A pdb=" N LEU F 338 " --> pdb=" O ARG F 334 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 358 through 371 removed outlier: 6.096A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 4.698A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 removed outlier: 3.814A pdb=" N CYS F 400 " --> pdb=" O CYS F 396 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.655A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.205A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 67' Processing helix chain 'G' and resid 83 through 105 Processing helix chain 'G' and resid 110 through 129 removed outlier: 4.058A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 4.189A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.758A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.739A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.683A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 67' Processing helix chain 'g' and resid 83 through 105 Processing helix chain 'g' and resid 110 through 129 removed outlier: 4.043A pdb=" N VAL g 124 " --> pdb=" O ASP g 120 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR g 126 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 3.974A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 3.706A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 231 through 245 removed outlier: 4.459A pdb=" N GLU g 244 " --> pdb=" O VAL g 240 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG g 245 " --> pdb=" O ALA g 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.761A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 63 removed outlier: 4.667A pdb=" N VAL H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N HIS H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 63' Processing helix chain 'H' and resid 79 through 102 Processing helix chain 'H' and resid 106 through 124 Processing helix chain 'H' and resid 166 through 178 removed outlier: 3.847A pdb=" N GLY H 170 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.089A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 removed outlier: 4.331A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 209' Processing helix chain 'H' and resid 222 through 233 removed outlier: 5.274A pdb=" N ALA H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE H 233 " --> pdb=" O TYR H 229 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.694A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 4.683A pdb=" N VAL h 62 " --> pdb=" O ASP h 58 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS h 63 " --> pdb=" O GLU h 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 58 through 63' Processing helix chain 'h' and resid 79 through 102 Processing helix chain 'h' and resid 106 through 124 removed outlier: 3.805A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER h 124 " --> pdb=" O GLU h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 4.116A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 209 removed outlier: 4.315A pdb=" N ILE h 208 " --> pdb=" O THR h 204 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU h 209 " --> pdb=" O GLU h 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 204 through 209' Processing helix chain 'h' and resid 222 through 233 Processing helix chain 'I' and resid 2 through 7 removed outlier: 3.661A pdb=" N ASP I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 7' Processing helix chain 'I' and resid 18 through 32 removed outlier: 3.812A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 removed outlier: 3.787A pdb=" N ILE I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.568A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 207 through 212 removed outlier: 3.955A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 229 through 251 Processing helix chain 'i' and resid 2 through 7 removed outlier: 4.346A pdb=" N ASP i 6 " --> pdb=" O SER i 2 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER i 7 " --> pdb=" O ARG i 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 2 through 7' Processing helix chain 'i' and resid 18 through 32 removed outlier: 3.983A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLY i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.666A pdb=" N ILE i 117 " --> pdb=" O ALA i 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE i 124 " --> pdb=" O ALA i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 Processing helix chain 'i' and resid 185 through 201 Processing helix chain 'i' and resid 207 through 212 removed outlier: 4.306A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU i 212 " --> pdb=" O ALA i 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 207 through 212' Processing helix chain 'i' and resid 229 through 251 Processing helix chain 'J' and resid 16 through 29 removed outlier: 3.585A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 4.425A pdb=" N VAL J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG J 60 " --> pdb=" O GLU J 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 55 through 60' Processing helix chain 'J' and resid 76 through 99 Processing helix chain 'J' and resid 103 through 121 Processing helix chain 'J' and resid 164 through 176 Processing helix chain 'J' and resid 177 through 182 removed outlier: 3.591A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 177 through 182' Processing helix chain 'J' and resid 183 through 199 removed outlier: 4.137A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 removed outlier: 4.607A pdb=" N GLU J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 29 removed outlier: 3.639A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.382A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG j 60 " --> pdb=" O GLU j 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 55 through 60' Processing helix chain 'j' and resid 76 through 99 Processing helix chain 'j' and resid 103 through 121 removed outlier: 3.706A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 3.675A pdb=" N VAL j 168 " --> pdb=" O GLY j 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 182 Processing helix chain 'j' and resid 183 through 199 removed outlier: 3.802A pdb=" N GLU j 197 " --> pdb=" O LYS j 193 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 240 Processing helix chain 'K' and resid 21 through 34 removed outlier: 4.022A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.270A pdb=" N ILE K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 65' Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.973A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 121 removed outlier: 4.111A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.945A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 230 through 241 removed outlier: 4.229A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 34 removed outlier: 4.023A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 65 removed outlier: 4.171A pdb=" N ILE k 64 " --> pdb=" O GLU k 60 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU k 65 " --> pdb=" O PRO k 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 60 through 65' Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.767A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 3.972A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.686A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 Processing helix chain 'k' and resid 230 through 241 removed outlier: 3.842A pdb=" N GLU k 236 " --> pdb=" O GLU k 232 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL k 237 " --> pdb=" O GLU k 233 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.771A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 122 removed outlier: 4.341A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 164 through 180 removed outlier: 4.514A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 3.687A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 225 through 236 removed outlier: 4.317A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 3.950A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.593A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS l 30 " --> pdb=" O MET l 26 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 Processing helix chain 'l' and resid 104 through 122 removed outlier: 4.050A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix removed outlier: 3.940A pdb=" N ARG l 122 " --> pdb=" O ILE l 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 164 through 180 removed outlier: 4.579A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 3.799A pdb=" N GLU l 197 " --> pdb=" O ARG l 193 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU l 199 " --> pdb=" O LEU l 195 " (cutoff:3.500A) Proline residue: l 200 - end of helix Processing helix chain 'l' and resid 225 through 236 removed outlier: 4.401A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 6.042A pdb=" N GLY l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU l 236 " --> pdb=" O PHE l 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.792A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 107 through 124 removed outlier: 4.082A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 4.298A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 185 removed outlier: 4.081A pdb=" N MET M 184 " --> pdb=" O GLN M 180 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR M 185 " --> pdb=" O MET M 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 180 through 185' Processing helix chain 'M' and resid 186 through 201 removed outlier: 3.954A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 Processing helix chain 'm' and resid 20 through 33 removed outlier: 3.612A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 102 Processing helix chain 'm' and resid 107 through 124 removed outlier: 4.028A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 4.131A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 180 through 185 removed outlier: 3.962A pdb=" N MET m 184 " --> pdb=" O GLN m 180 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N THR m 185 " --> pdb=" O MET m 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 180 through 185' Processing helix chain 'm' and resid 186 through 201 removed outlier: 3.870A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 91 Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.036A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'n' and resid 48 through 71 Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.502A pdb=" N ARG n 91 " --> pdb=" O CYS n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.701A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.877A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.869A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.554A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG o 89 " --> pdb=" O GLN o 85 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.795A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 Processing helix chain 'P' and resid 2 through 8 removed outlier: 4.572A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY P 8 " --> pdb=" O MET P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 79 Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.345A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 3.977A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 4.234A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 3.532A pdb=" N TYR p 6 " --> pdb=" O SER p 2 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY p 8 " --> pdb=" O MET p 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 2 through 8' Processing helix chain 'p' and resid 56 through 79 Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.240A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 3.804A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.134A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 72 removed outlier: 6.721A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 93 removed outlier: 3.668A pdb=" N CYS Q 91 " --> pdb=" O ASN Q 87 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.625A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 170 Processing helix chain 'q' and resid 50 through 72 removed outlier: 6.718A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 93 removed outlier: 4.273A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.551A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 170 Processing helix chain 'R' and resid 48 through 71 Processing helix chain 'R' and resid 75 through 91 removed outlier: 3.890A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.680A pdb=" N VAL R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 201 removed outlier: 3.880A pdb=" N GLY R 201 " --> pdb=" O GLU R 197 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 71 Processing helix chain 'r' and resid 75 through 91 removed outlier: 3.854A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.726A pdb=" N VAL r 138 " --> pdb=" O TYR r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 Processing helix chain 'r' and resid 191 through 201 Processing helix chain 'S' and resid 57 through 79 Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.905A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 Processing helix chain 's' and resid 57 through 79 Processing helix chain 's' and resid 84 through 100 removed outlier: 3.906A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 removed outlier: 3.720A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 3.987A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.694A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 158 removed outlier: 4.358A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.577A pdb=" N LYS T 156 " --> pdb=" O GLU T 152 " (cutoff:3.500A) Proline residue: T 158 - end of helix Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 215 removed outlier: 4.673A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 209 through 215' Processing helix chain 't' and resid 56 through 78 removed outlier: 3.953A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.745A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 158 removed outlier: 4.460A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix Proline residue: t 158 - end of helix Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 4.676A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'U' and resid 7 through 14 removed outlier: 3.631A pdb=" N ASP U 13 " --> pdb=" O ILE U 9 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU U 14 " --> pdb=" O SER U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 31 removed outlier: 4.364A pdb=" N PHE U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 42 removed outlier: 3.961A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 52 removed outlier: 5.559A pdb=" N GLU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 removed outlier: 3.654A pdb=" N ALA U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.885A pdb=" N GLY U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 92 removed outlier: 4.054A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP U 92 " --> pdb=" O PHE U 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 119 removed outlier: 4.711A pdb=" N THR U 99 " --> pdb=" O GLU U 95 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE U 100 " --> pdb=" O TYR U 96 " (cutoff:3.500A) Proline residue: U 119 - end of helix Processing helix chain 'U' and resid 127 through 145 removed outlier: 4.286A pdb=" N ILE U 133 " --> pdb=" O ARG U 129 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS U 136 " --> pdb=" O GLY U 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 3.726A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 3.797A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 186 removed outlier: 3.799A pdb=" N SER U 180 " --> pdb=" O MET U 176 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU U 181 " --> pdb=" O LEU U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 208 removed outlier: 3.552A pdb=" N ARG U 194 " --> pdb=" O ASN U 190 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 4.318A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 4.018A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER U 230 " --> pdb=" O PRO U 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 256 removed outlier: 3.944A pdb=" N ALA U 245 " --> pdb=" O ASN U 241 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR U 246 " --> pdb=" O LEU U 242 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE U 248 " --> pdb=" O MET U 244 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N CYS U 249 " --> pdb=" O ALA U 245 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU U 252 " --> pdb=" O ILE U 248 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 270 removed outlier: 3.680A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN U 267 " --> pdb=" O SER U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 329 removed outlier: 3.928A pdb=" N MET U 325 " --> pdb=" O GLN U 321 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE U 326 " --> pdb=" O THR U 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 331 through 346 removed outlier: 4.274A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 358 removed outlier: 4.130A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP U 358 " --> pdb=" O LYS U 354 " (cutoff:3.500A) Processing helix chain 'U' and resid 363 through 378 removed outlier: 5.494A pdb=" N THR U 367 " --> pdb=" O SER U 363 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 390 removed outlier: 4.450A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU U 390 " --> pdb=" O LEU U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 391 through 396 removed outlier: 4.500A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 413 removed outlier: 5.215A pdb=" N LYS U 401 " --> pdb=" O THR U 397 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 424 removed outlier: 4.796A pdb=" N MET U 423 " --> pdb=" O ALA U 419 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA U 424 " --> pdb=" O LEU U 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 419 through 424' Processing helix chain 'U' and resid 427 through 432 removed outlier: 4.043A pdb=" N THR U 431 " --> pdb=" O LEU U 427 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER U 432 " --> pdb=" O PRO U 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 427 through 432' Processing helix chain 'U' and resid 435 through 451 removed outlier: 4.409A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY U 442 " --> pdb=" O GLN U 438 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR U 444 " --> pdb=" O GLY U 440 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 4.214A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN U 467 " --> pdb=" O ASN U 463 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 486 removed outlier: 4.026A pdb=" N ARG U 474 " --> pdb=" O ASN U 470 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS U 475 " --> pdb=" O ASP U 471 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 3.815A pdb=" N TYR U 494 " --> pdb=" O ARG U 490 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 521 removed outlier: 4.336A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 3.905A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 557 removed outlier: 4.340A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 573 removed outlier: 3.751A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.795A pdb=" N TYR U 590 " --> pdb=" O VAL U 586 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 removed outlier: 4.147A pdb=" N ARG U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 627 removed outlier: 4.296A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 643 removed outlier: 4.385A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 4.049A pdb=" N SER U 638 " --> pdb=" O PRO U 634 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 removed outlier: 3.700A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 677 Proline residue: U 674 - end of helix removed outlier: 4.863A pdb=" N ASN U 677 " --> pdb=" O GLU U 673 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.826A pdb=" N MET U 695 " --> pdb=" O SER U 691 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 705 through 719 Processing helix chain 'U' and resid 723 through 739 removed outlier: 3.797A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA U 739 " --> pdb=" O GLY U 735 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 769 removed outlier: 4.152A pdb=" N THR U 767 " --> pdb=" O VAL U 763 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) Processing helix chain 'U' and resid 772 through 784 removed outlier: 4.179A pdb=" N SER U 776 " --> pdb=" O TRP U 772 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N HIS U 777 " --> pdb=" O PHE U 773 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR U 784 " --> pdb=" O SER U 780 " (cutoff:3.500A) Processing helix chain 'U' and resid 807 through 812 removed outlier: 4.130A pdb=" N PHE U 811 " --> pdb=" O LYS U 807 " (cutoff:3.500A) Processing helix chain 'U' and resid 885 through 890 removed outlier: 4.837A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 89 Processing helix chain 'V' and resid 91 through 106 Proline residue: V 102 - end of helix removed outlier: 4.773A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 122 removed outlier: 4.376A pdb=" N THR V 122 " --> pdb=" O GLN V 118 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.560A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix removed outlier: 5.156A pdb=" N GLU V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 158 Proline residue: V 158 - end of helix Processing helix chain 'V' and resid 160 through 179 Processing helix chain 'V' and resid 180 through 199 removed outlier: 3.516A pdb=" N ALA V 184 " --> pdb=" O ARG V 180 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 222 removed outlier: 3.991A pdb=" N ASP V 204 " --> pdb=" O ARG V 200 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.415A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 removed outlier: 3.844A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER V 262 " --> pdb=" O TYR V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 removed outlier: 3.692A pdb=" N LYS V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 3.650A pdb=" N LEU V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 316 removed outlier: 3.513A pdb=" N ALA V 305 " --> pdb=" O GLU V 301 " (cutoff:3.500A) Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 345 through 350 removed outlier: 3.735A pdb=" N ARG V 349 " --> pdb=" O ARG V 345 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN V 350 " --> pdb=" O LEU V 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 345 through 350' Processing helix chain 'V' and resid 353 through 370 Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 371 through 383 removed outlier: 3.641A pdb=" N PHE V 375 " --> pdb=" O ASN V 371 " (cutoff:3.500A) Processing helix chain 'V' and resid 384 through 390 Processing helix chain 'V' and resid 391 through 415 removed outlier: 3.909A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 3.719A pdb=" N LEU V 426 " --> pdb=" O ILE V 422 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN V 427 " --> pdb=" O ALA V 423 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 Processing helix chain 'V' and resid 465 through 494 removed outlier: 5.265A pdb=" N ARG V 470 " --> pdb=" O ILE V 466 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLU V 471 " --> pdb=" O TYR V 467 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 4.007A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 38 Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 39 through 58 Processing helix chain 'W' and resid 59 through 78 Processing helix chain 'W' and resid 79 through 93 removed outlier: 4.416A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 115 Processing helix chain 'W' and resid 118 through 132 removed outlier: 4.266A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG W 123 " --> pdb=" O PRO W 119 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET W 130 " --> pdb=" O ASP W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 156 removed outlier: 5.000A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU W 154 " --> pdb=" O ALA W 150 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN W 156 " --> pdb=" O ILE W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 176 removed outlier: 3.627A pdb=" N GLN W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY W 175 " --> pdb=" O VAL W 171 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 197 removed outlier: 4.088A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 213 removed outlier: 3.670A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS W 212 " --> pdb=" O LYS W 208 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE W 213 " --> pdb=" O ILE W 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 238 removed outlier: 4.622A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N MET W 230 " --> pdb=" O TYR W 226 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE W 231 " --> pdb=" O TYR W 227 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 258 removed outlier: 5.485A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix Processing helix chain 'W' and resid 259 through 278 removed outlier: 4.366A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 292 removed outlier: 5.223A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 310 removed outlier: 4.552A pdb=" N LYS W 303 " --> pdb=" O ILE W 299 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR W 310 " --> pdb=" O LEU W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 325 removed outlier: 3.744A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 344 through 370 removed outlier: 3.648A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 Processing helix chain 'W' and resid 385 through 400 Processing helix chain 'W' and resid 420 through 456 Processing helix chain 'W' and resid 293 through 298 removed outlier: 3.629A pdb=" N LEU W 296 " --> pdb=" O ASP W 293 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU W 297 " --> pdb=" O LYS W 294 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU W 298 " --> pdb=" O LYS W 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 293 through 298' Processing helix chain 'X' and resid 43 through 61 removed outlier: 4.478A pdb=" N LEU X 51 " --> pdb=" O GLU X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 77 removed outlier: 4.095A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) Proline residue: X 75 - end of helix Processing helix chain 'X' and resid 81 through 100 removed outlier: 4.632A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU X 100 " --> pdb=" O PHE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 removed outlier: 4.014A pdb=" N GLU X 106 " --> pdb=" O ALA X 102 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 141 removed outlier: 3.628A pdb=" N ASP X 139 " --> pdb=" O SER X 135 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR X 140 " --> pdb=" O LEU X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 161 removed outlier: 5.075A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG X 155 " --> pdb=" O SER X 151 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 5.720A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 198 removed outlier: 4.115A pdb=" N ASN X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 222 removed outlier: 4.736A pdb=" N ALA X 208 " --> pdb=" O PRO X 204 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU X 221 " --> pdb=" O ILE X 217 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU X 222 " --> pdb=" O HIS X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.461A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR X 229 " --> pdb=" O TRP X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 3.980A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER X 250 " --> pdb=" O LYS X 246 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 273 Processing helix chain 'X' and resid 274 through 280 removed outlier: 4.495A pdb=" N ARG X 278 " --> pdb=" O LYS X 274 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR X 279 " --> pdb=" O LEU X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 310 Processing helix chain 'X' and resid 320 through 340 removed outlier: 3.574A pdb=" N GLU X 332 " --> pdb=" O ASP X 328 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 Processing helix chain 'X' and resid 357 through 372 removed outlier: 4.268A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 422 removed outlier: 5.098A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU X 402 " --> pdb=" O GLU X 398 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS X 417 " --> pdb=" O SER X 413 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 316 removed outlier: 5.614A pdb=" N ASP X 316 " --> pdb=" O ALA X 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 311 through 316' Processing helix chain 'Y' and resid 12 through 28 removed outlier: 4.480A pdb=" N LEU Y 17 " --> pdb=" O LYS Y 13 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG Y 18 " --> pdb=" O ASN Y 14 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE Y 19 " --> pdb=" O PRO Y 15 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA Y 20 " --> pdb=" O ASP Y 16 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN Y 21 " --> pdb=" O LEU Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 47 removed outlier: 4.436A pdb=" N VAL Y 37 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N MET Y 42 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA Y 43 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 60 removed outlier: 4.684A pdb=" N TYR Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR Y 54 " --> pdb=" O MET Y 50 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU Y 57 " --> pdb=" O TYR Y 53 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS Y 58 " --> pdb=" O TYR Y 54 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS Y 59 " --> pdb=" O GLU Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 85 removed outlier: 3.758A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG Y 83 " --> pdb=" O ASP Y 79 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU Y 84 " --> pdb=" O GLU Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 114 removed outlier: 6.035A pdb=" N MET Y 105 " --> pdb=" O ARG Y 101 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA Y 106 " --> pdb=" O ASP Y 102 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU Y 109 " --> pdb=" O MET Y 105 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TYR Y 110 " --> pdb=" O ALA Y 106 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 131 removed outlier: 3.784A pdb=" N LYS Y 126 " --> pdb=" O THR Y 122 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 3.665A pdb=" N ARG Y 137 " --> pdb=" O ALA Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 167 removed outlier: 3.645A pdb=" N ILE Y 157 " --> pdb=" O ASP Y 153 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR Y 158 " --> pdb=" O ASN Y 154 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG Y 159 " --> pdb=" O ASP Y 155 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN Y 160 " --> pdb=" O LEU Y 156 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 174 through 190 removed outlier: 5.790A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG Y 179 " --> pdb=" O ASP Y 175 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYS Y 181 " --> pdb=" O ARG Y 177 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N VAL Y 182 " --> pdb=" O ASN Y 178 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N TYR Y 183 " --> pdb=" O ARG Y 179 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN Y 184 " --> pdb=" O LEU Y 180 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR Y 187 " --> pdb=" O TYR Y 183 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL Y 189 " --> pdb=" O GLY Y 185 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA Y 190 " --> pdb=" O LEU Y 186 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 208 removed outlier: 4.513A pdb=" N GLU Y 199 " --> pdb=" O LYS Y 195 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU Y 200 " --> pdb=" O GLN Y 196 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE Y 201 " --> pdb=" O ALA Y 197 " (cutoff:3.500A) Processing helix chain 'Y' and resid 217 through 231 removed outlier: 4.125A pdb=" N MET Y 228 " --> pdb=" O VAL Y 224 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA Y 230 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU Y 231 " --> pdb=" O SER Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 240 Processing helix chain 'Y' and resid 243 through 254 Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.922A pdb=" N SER Y 262 " --> pdb=" O GLN Y 258 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR Y 264 " --> pdb=" O LEU Y 260 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU Y 265 " --> pdb=" O PHE Y 261 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 286 removed outlier: 3.787A pdb=" N VAL Y 277 " --> pdb=" O GLN Y 273 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TRP Y 286 " --> pdb=" O MET Y 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 310 removed outlier: 4.093A pdb=" N HIS Y 291 " --> pdb=" O LEU Y 287 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ARG Y 293 " --> pdb=" O ALA Y 289 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR Y 294 " --> pdb=" O PRO Y 290 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU Y 298 " --> pdb=" O TYR Y 294 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 322 removed outlier: 3.886A pdb=" N MET Y 319 " --> pdb=" O THR Y 315 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 3.676A pdb=" N GLY Y 341 " --> pdb=" O PHE Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 388 removed outlier: 3.976A pdb=" N GLN Y 365 " --> pdb=" O SER Y 361 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP Y 374 " --> pdb=" O ILE Y 370 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG Y 385 " --> pdb=" O GLN Y 381 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 95 removed outlier: 4.058A pdb=" N ASN Y 94 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU Y 95 " --> pdb=" O GLU Y 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 28 removed outlier: 3.586A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL Z 20 " --> pdb=" O LEU Z 16 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP Z 21 " --> pdb=" O LEU Z 17 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS Z 22 " --> pdb=" O SER Z 18 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 102 through 117 removed outlier: 4.446A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS Z 116 " --> pdb=" O MET Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix Processing helix chain 'Z' and resid 165 through 178 removed outlier: 3.801A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG Z 177 " --> pdb=" O GLU Z 173 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASP Z 178 " --> pdb=" O HIS Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 218 removed outlier: 6.329A pdb=" N ARG Z 190 " --> pdb=" O THR Z 186 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE Z 191 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY Z 218 " --> pdb=" O LYS Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 225 through 237 removed outlier: 4.390A pdb=" N GLN Z 229 " --> pdb=" O GLN Z 225 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN Z 231 " --> pdb=" O ILE Z 227 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU Z 236 " --> pdb=" O ASP Z 232 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU Z 237 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 243 through 290 removed outlier: 4.327A pdb=" N LYS Z 247 " --> pdb=" O GLN Z 243 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN Z 254 " --> pdb=" O TYR Z 250 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP Z 255 " --> pdb=" O LEU Z 251 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN Z 274 " --> pdb=" O VAL Z 270 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU Z 275 " --> pdb=" O ALA Z 271 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA Z 281 " --> pdb=" O ASN Z 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 15 removed outlier: 3.992A pdb=" N ASN a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER a 14 " --> pdb=" O GLN a 10 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY a 15 " --> pdb=" O SER a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 32 removed outlier: 4.956A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR a 29 " --> pdb=" O LEU a 25 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS a 31 " --> pdb=" O GLU a 27 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS a 32 " --> pdb=" O LEU a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 5.389A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR a 38 " --> pdb=" O TRP a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 removed outlier: 3.660A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 removed outlier: 4.040A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 105 removed outlier: 3.765A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 125 removed outlier: 4.687A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE a 125 " --> pdb=" O LEU a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 142 removed outlier: 5.027A pdb=" N VAL a 130 " --> pdb=" O GLY a 126 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR a 131 " --> pdb=" O ASP a 127 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS a 132 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU a 133 " --> pdb=" O GLN a 129 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE a 135 " --> pdb=" O THR a 131 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU a 136 " --> pdb=" O LYS a 132 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 164 removed outlier: 6.542A pdb=" N HIS a 152 " --> pdb=" O VAL a 148 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN a 164 " --> pdb=" O SER a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 184 removed outlier: 6.299A pdb=" N TYR a 172 " --> pdb=" O ASN a 168 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU a 177 " --> pdb=" O TYR a 173 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 5.120A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 219 removed outlier: 3.788A pdb=" N LEU a 217 " --> pdb=" O PHE a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 220 through 230 removed outlier: 5.510A pdb=" N SER a 224 " --> pdb=" O PRO a 220 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG a 230 " --> pdb=" O ARG a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 243 Processing helix chain 'a' and resid 246 through 258 removed outlier: 4.515A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 265 removed outlier: 6.370A pdb=" N ALA a 263 " --> pdb=" O PRO a 259 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU a 265 " --> pdb=" O LEU a 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 259 through 265' Processing helix chain 'a' and resid 266 through 285 removed outlier: 4.160A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG a 284 " --> pdb=" O MET a 280 " (cutoff:3.500A) Proline residue: a 285 - end of helix Processing helix chain 'a' and resid 292 through 301 removed outlier: 3.590A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 318 removed outlier: 4.764A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 376 removed outlier: 3.715A pdb=" N ASP a 359 " --> pdb=" O PHE a 355 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU a 375 " --> pdb=" O ALA a 371 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 67 through 76 removed outlier: 4.727A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 3.857A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG b 100 " --> pdb=" O ALA b 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 removed outlier: 3.716A pdb=" N LYS b 133 " --> pdb=" O LYS b 129 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU b 134 " --> pdb=" O ARG b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 162 removed outlier: 6.680A pdb=" N ALA b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE b 156 " --> pdb=" O LYS b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 removed outlier: 4.373A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'b' and resid 13 through 18 removed outlier: 3.539A pdb=" N MET b 16 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN b 18 " --> pdb=" O TYR b 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 49 removed outlier: 3.790A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 103 removed outlier: 3.676A pdb=" N ALA c 93 " --> pdb=" O PRO c 89 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR c 102 " --> pdb=" O MET c 98 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 removed outlier: 3.571A pdb=" N ASN c 128 " --> pdb=" O GLY c 124 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR c 129 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN c 130 " --> pdb=" O ASP c 126 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN c 131 " --> pdb=" O ILE c 127 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 195 removed outlier: 4.397A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 220 removed outlier: 3.721A pdb=" N ASN c 219 " --> pdb=" O LYS c 215 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU c 220 " --> pdb=" O MET c 216 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 removed outlier: 4.252A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR c 230 " --> pdb=" O MET c 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 224 through 230' Processing helix chain 'c' and resid 234 through 259 removed outlier: 3.983A pdb=" N CYS c 238 " --> pdb=" O TYR c 234 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS c 257 " --> pdb=" O LYS c 253 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 276 removed outlier: 3.864A pdb=" N VAL c 275 " --> pdb=" O ALA c 271 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY c 276 " --> pdb=" O ILE c 272 " (cutoff:3.500A) Processing helix chain 'c' and resid 280 through 310 removed outlier: 5.520A pdb=" N LEU c 284 " --> pdb=" O PRO c 280 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU c 285 " --> pdb=" O LYS c 281 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS c 287 " --> pdb=" O HIS c 283 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP c 289 " --> pdb=" O GLU c 285 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL c 290 " --> pdb=" O GLU c 286 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 34 removed outlier: 4.415A pdb=" N CYS d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY d 20 " --> pdb=" O LEU d 16 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU d 33 " --> pdb=" O VAL d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 66 removed outlier: 4.453A pdb=" N LYS d 45 " --> pdb=" O THR d 41 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLN d 46 " --> pdb=" O LYS d 42 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 84 removed outlier: 3.607A pdb=" N PHE d 71 " --> pdb=" O ASP d 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN d 77 " --> pdb=" O ARG d 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 110 Processing helix chain 'd' and resid 111 through 121 removed outlier: 3.678A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix removed outlier: 4.238A pdb=" N GLU d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 155 removed outlier: 4.531A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE d 152 " --> pdb=" O TYR d 148 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 185 removed outlier: 4.226A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA d 185 " --> pdb=" O CYS d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 197 Processing helix chain 'd' and resid 204 through 212 Processing helix chain 'd' and resid 236 through 255 removed outlier: 4.506A pdb=" N THR d 240 " --> pdb=" O THR d 236 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU d 241 " --> pdb=" O ILE d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 124 through 129 removed outlier: 3.619A pdb=" N THR d 129 " --> pdb=" O ALA d 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 124 through 129' Processing helix chain 'e' and resid 51 through 64 removed outlier: 4.658A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY e 64 " --> pdb=" O LEU e 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 7 through 20 removed outlier: 5.216A pdb=" N VAL f 11 " --> pdb=" O ASP f 7 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN f 12 " --> pdb=" O LYS f 8 " (cutoff:3.500A) Proline residue: f 13 - end of helix Proline residue: f 17 - end of helix Processing helix chain 'f' and resid 21 through 27 removed outlier: 5.779A pdb=" N GLU f 26 " --> pdb=" O GLY f 22 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS f 27 " --> pdb=" O GLY f 23 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 46 removed outlier: 3.721A pdb=" N LYS f 41 " --> pdb=" O GLY f 37 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 59 removed outlier: 4.094A pdb=" N MET f 58 " --> pdb=" O ASP f 54 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU f 59 " --> pdb=" O GLU f 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 54 through 59' Processing helix chain 'f' and resid 61 through 72 removed outlier: 4.521A pdb=" N LYS f 66 " --> pdb=" O ARG f 62 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 99 removed outlier: 3.931A pdb=" N VAL f 92 " --> pdb=" O SER f 88 " (cutoff:3.500A) Proline residue: f 93 - end of helix removed outlier: 5.756A pdb=" N LEU f 96 " --> pdb=" O VAL f 92 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU f 99 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 110 removed outlier: 4.031A pdb=" N ILE f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 120 through 125 removed outlier: 4.748A pdb=" N ASP f 124 " --> pdb=" O ARG f 120 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE f 125 " --> pdb=" O PHE f 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 120 through 125' Processing helix chain 'f' and resid 128 through 148 removed outlier: 4.674A pdb=" N THR f 132 " --> pdb=" O VAL f 128 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS f 139 " --> pdb=" O GLY f 135 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU f 140 " --> pdb=" O GLU f 136 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR f 142 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) Processing helix chain 'f' and resid 153 through 173 removed outlier: 4.397A pdb=" N GLU f 157 " --> pdb=" O SER f 153 " (cutoff:3.500A) Processing helix chain 'f' and resid 178 through 191 removed outlier: 4.739A pdb=" N GLU f 182 " --> pdb=" O LYS f 178 " (cutoff:3.500A) Proline residue: f 183 - end of helix removed outlier: 4.419A pdb=" N VAL f 188 " --> pdb=" O LEU f 184 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU f 190 " --> pdb=" O THR f 186 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE f 191 " --> pdb=" O LEU f 187 " (cutoff:3.500A) Processing helix chain 'f' and resid 193 through 206 Processing helix chain 'f' and resid 212 through 227 removed outlier: 4.274A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA f 225 " --> pdb=" O ILE f 221 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR f 226 " --> pdb=" O ASP f 222 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 247 removed outlier: 3.995A pdb=" N THR f 234 " --> pdb=" O CYS f 230 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER f 235 " --> pdb=" O LEU f 231 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS f 236 " --> pdb=" O TYR f 232 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 4.707A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) Processing helix chain 'f' and resid 253 through 263 removed outlier: 4.016A pdb=" N ARG f 257 " --> pdb=" O LEU f 253 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS f 258 " --> pdb=" O GLY f 254 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE f 262 " --> pdb=" O LYS f 258 " (cutoff:3.500A) Proline residue: f 263 - end of helix Processing helix chain 'f' and resid 269 through 277 removed outlier: 5.180A pdb=" N ASN f 273 " --> pdb=" O ALA f 269 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU f 276 " --> pdb=" O LEU f 272 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU f 277 " --> pdb=" O ASN f 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 284 through 294 removed outlier: 4.108A pdb=" N VAL f 288 " --> pdb=" O SER f 284 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN f 291 " --> pdb=" O ASP f 287 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 296 through 308 removed outlier: 3.690A pdb=" N ARG f 300 " --> pdb=" O PHE f 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY f 302 " --> pdb=" O LEU f 298 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL f 303 " --> pdb=" O GLY f 299 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE f 304 " --> pdb=" O ARG f 300 " (cutoff:3.500A) Processing helix chain 'f' and resid 313 through 322 Processing helix chain 'f' and resid 323 through 336 removed outlier: 3.527A pdb=" N ASN f 327 " --> pdb=" O ASN f 323 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER f 328 " --> pdb=" O VAL f 324 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 351 removed outlier: 3.551A pdb=" N LYS f 350 " --> pdb=" O ASP f 346 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR f 351 " --> pdb=" O ASP f 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 346 through 351' Processing helix chain 'f' and resid 354 through 359 removed outlier: 3.642A pdb=" N GLY f 359 " --> pdb=" O ASN f 355 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 383 Processing helix chain 'f' and resid 395 through 402 removed outlier: 4.892A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 403 through 419 removed outlier: 3.989A pdb=" N LEU f 408 " --> pdb=" O ASP f 404 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 423 through 436 removed outlier: 3.647A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER f 435 " --> pdb=" O LYS f 431 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N SER f 436 " --> pdb=" O TYR f 432 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 3.730A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 471 removed outlier: 4.377A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU f 465 " --> pdb=" O PRO f 461 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 removed outlier: 3.609A pdb=" N GLY f 480 " --> pdb=" O THR f 476 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE f 482 " --> pdb=" O ARG f 478 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU f 485 " --> pdb=" O SER f 481 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 508 removed outlier: 3.639A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) Proline residue: f 503 - end of helix removed outlier: 5.211A pdb=" N SER f 508 " --> pdb=" O VAL f 504 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 527 removed outlier: 3.942A pdb=" N ALA f 515 " --> pdb=" O SER f 511 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 545 removed outlier: 3.942A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS f 545 " --> pdb=" O THR f 541 " (cutoff:3.500A) Processing helix chain 'f' and resid 546 through 551 removed outlier: 3.632A pdb=" N LEU f 550 " --> pdb=" O SER f 546 " (cutoff:3.500A) Processing helix chain 'f' and resid 555 through 567 Proline residue: f 559 - end of helix Processing helix chain 'f' and resid 572 through 584 removed outlier: 4.496A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU f 577 " --> pdb=" O ILE f 573 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL f 583 " --> pdb=" O ALA f 579 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER f 584 " --> pdb=" O LEU f 580 " (cutoff:3.500A) Processing helix chain 'f' and resid 586 through 601 removed outlier: 4.797A pdb=" N PHE f 590 " --> pdb=" O PRO f 586 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR f 593 " --> pdb=" O SER f 589 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 623 removed outlier: 5.140A pdb=" N CYS f 616 " --> pdb=" O LEU f 612 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER f 617 " --> pdb=" O LEU f 613 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER f 622 " --> pdb=" O GLU f 618 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS f 623 " --> pdb=" O HIS f 619 " (cutoff:3.500A) Processing helix chain 'f' and resid 627 through 641 removed outlier: 4.728A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS f 637 " --> pdb=" O GLU f 633 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP f 638 " --> pdb=" O LYS f 634 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS f 639 " --> pdb=" O LYS f 635 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS f 640 " --> pdb=" O ASP f 636 " (cutoff:3.500A) Processing helix chain 'f' and resid 645 through 658 removed outlier: 5.897A pdb=" N HIS f 649 " --> pdb=" O ASP f 645 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN f 650 " --> pdb=" O MET f 646 " (cutoff:3.500A) Processing helix chain 'f' and resid 671 through 680 removed outlier: 5.491A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU f 679 " --> pdb=" O PHE f 675 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG f 680 " --> pdb=" O GLY f 676 " (cutoff:3.500A) Processing helix chain 'f' and resid 686 through 696 removed outlier: 5.671A pdb=" N VAL f 690 " --> pdb=" O LEU f 686 " (cutoff:3.500A) Proline residue: f 691 - end of helix removed outlier: 3.581A pdb=" N LEU f 694 " --> pdb=" O VAL f 690 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA f 695 " --> pdb=" O PRO f 691 " (cutoff:3.500A) Processing helix chain 'f' and resid 701 through 717 removed outlier: 4.033A pdb=" N THR f 709 " --> pdb=" O ASN f 705 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER f 714 " --> pdb=" O LEU f 710 " (cutoff:3.500A) Processing helix chain 'f' and resid 723 through 733 removed outlier: 5.070A pdb=" N GLY f 733 " --> pdb=" O MET f 729 " (cutoff:3.500A) Processing helix chain 'f' and resid 742 through 751 Processing helix chain 'f' and resid 771 through 784 removed outlier: 4.240A pdb=" N THR f 777 " --> pdb=" O LYS f 773 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N CYS f 779 " --> pdb=" O THR f 775 " (cutoff:3.500A) Proline residue: f 780 - end of helix removed outlier: 4.310A pdb=" N ASP f 784 " --> pdb=" O PRO f 780 " (cutoff:3.500A) Processing helix chain 'f' and resid 797 through 803 removed outlier: 4.886A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER f 802 " --> pdb=" O THR f 798 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE f 803 " --> pdb=" O VAL f 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 797 through 803' Processing helix chain 'f' and resid 664 through 669 Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'u' and resid 37 through 42 removed outlier: 3.827A pdb=" N GLN u 41 " --> pdb=" O PRO u 37 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 37 through 42' Processing helix chain 'u' and resid 55 through 60 Processing helix chain 'x' and resid 25 through 37 Processing sheet with id= 1, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.733A pdb=" N PHE A 121 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG A 139 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 236 through 240 removed outlier: 4.297A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 270 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 212 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 215 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 107 through 113 removed outlier: 4.213A pdb=" N CYS B 148 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 114 through 117 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'B' and resid 245 through 250 removed outlier: 3.531A pdb=" N THR B 246 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 94 through 97 removed outlier: 7.071A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N CYS C 112 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG C 113 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 125 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 209 through 214 removed outlier: 3.576A pdb=" N SER C 244 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 290 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET C 248 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 294 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 313 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 109 through 114 removed outlier: 4.291A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA D 128 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER D 129 " --> pdb=" O LEU D 143 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 226 through 230 removed outlier: 4.378A pdb=" N ALA D 226 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 265 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 78 through 82 removed outlier: 7.405A pdb=" N ILE E 70 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR E 96 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 194 through 198 removed outlier: 5.658A pdb=" N ASN E 194 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS E 168 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 95 through 98 removed outlier: 3.601A pdb=" N CYS F 121 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 246 through 251 removed outlier: 3.521A pdb=" N ASP F 286 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS F 327 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 121 through 126 removed outlier: 3.891A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.461A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.915A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.363A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'g' and resid 165 through 169 removed outlier: 5.799A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.468A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 160 through 164 removed outlier: 5.416A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.459A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'h' and resid 160 through 164 removed outlier: 5.315A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 65 through 68 removed outlier: 6.539A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 161 through 165 removed outlier: 5.167A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'i' and resid 65 through 68 removed outlier: 6.720A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'i' and resid 161 through 165 removed outlier: 5.198A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 69 through 75 removed outlier: 4.473A pdb=" N THR J 152 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 158 through 162 removed outlier: 5.239A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'j' and resid 69 through 75 removed outlier: 3.936A pdb=" N ALA j 131 " --> pdb=" O THR j 147 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY j 135 " --> pdb=" O ARG j 143 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP j 148 " --> pdb=" O THR j 152 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'j' and resid 158 through 162 removed outlier: 5.464A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASN j 205 " --> pdb=" O LYS j 47 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.470A pdb=" N LYS K 66 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 167 through 171 removed outlier: 5.580A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASN K 214 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'k' and resid 66 through 70 removed outlier: 6.526A pdb=" N LYS k 66 " --> pdb=" O MET k 78 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'k' and resid 167 through 171 removed outlier: 5.692A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASN k 214 " --> pdb=" O LYS k 52 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.477A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 158 through 162 removed outlier: 4.724A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASN L 209 " --> pdb=" O LYS L 50 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.532A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU l 132 " --> pdb=" O THR l 147 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'l' and resid 158 through 162 removed outlier: 5.384A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 65 through 69 removed outlier: 6.694A pdb=" N ARG M 65 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL M 69 " --> pdb=" O VAL M 73 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY M 138 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP M 152 " --> pdb=" O VAL M 156 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL M 156 " --> pdb=" O ASP M 152 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'M' and resid 161 through 166 removed outlier: 6.469A pdb=" N TRP M 161 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'm' and resid 65 through 69 removed outlier: 6.537A pdb=" N ARG m 65 " --> pdb=" O VAL m 77 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU m 148 " --> pdb=" O TYR m 160 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP m 152 " --> pdb=" O VAL m 156 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL m 156 " --> pdb=" O ASP m 152 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'm' and resid 161 through 166 removed outlier: 6.242A pdb=" N TRP m 161 " --> pdb=" O ARG m 40 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.554A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.476A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER N 18 " --> pdb=" O VAL N 173 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.621A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL n 111 " --> pdb=" O GLN n 123 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.255A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.348A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.196A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.488A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.141A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'P' and resid 42 through 45 removed outlier: 6.018A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.317A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS P 194 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.318A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.262A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS p 194 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.404A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS Q 99 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Q' and resid 129 through 132 removed outlier: 6.756A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.388A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS q 99 " --> pdb=" O GLU q 49 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'q' and resid 129 through 132 removed outlier: 6.477A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'R' and resid 34 through 37 removed outlier: 6.591A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.070A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY R 183 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.665A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.173A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL r 12 " --> pdb=" O VAL r 179 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.638A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.481A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 's' and resid 43 through 46 removed outlier: 6.605A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 's' and resid 135 through 139 removed outlier: 5.861A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.655A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.377A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA T 23 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG T 186 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 't' and resid 42 through 45 removed outlier: 6.671A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 't' and resid 136 through 139 removed outlier: 4.285A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG t 186 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'U' and resid 788 through 792 removed outlier: 3.502A pdb=" N LEU U 914 " --> pdb=" O LEU U 791 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ARG U 899 " --> pdb=" O THR U 917 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'U' and resid 801 through 805 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'V' and resid 449 through 453 Processing sheet with id= 74, first strand: chain 'W' and resid 404 through 408 Processing sheet with id= 75, first strand: chain 'X' and resid 376 through 380 Processing sheet with id= 76, first strand: chain 'Y' and resid 345 through 349 removed outlier: 3.848A pdb=" N ILE Y 353 " --> pdb=" O ASP Y 348 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 37 through 40 Processing sheet with id= 78, first strand: chain 'Z' and resid 47 through 50 removed outlier: 7.224A pdb=" N GLN Z 7 " --> pdb=" O HIS Z 157 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR Z 159 " --> pdb=" O GLN Z 7 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'a' and resid 321 through 326 removed outlier: 6.915A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'b' and resid 48 through 54 removed outlier: 4.039A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR b 6 " --> pdb=" O ASN b 48 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG b 108 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP b 11 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY b 114 " --> pdb=" O ASP b 11 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'c' and resid 29 through 33 Processing sheet with id= 82, first strand: chain 'c' and resid 52 through 58 removed outlier: 4.712A pdb=" N VAL c 53 " --> pdb=" O SER c 114 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY c 110 " --> pdb=" O MET c 57 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP c 111 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA c 140 " --> pdb=" O LEU c 162 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU c 162 " --> pdb=" O ALA c 140 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS c 199 " --> pdb=" O ILE c 163 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'f' and resid 812 through 815 Processing sheet with id= 84, first strand: chain 'u' and resid 11 through 17 removed outlier: 4.522A pdb=" N LYS u 11 " --> pdb=" O THR u 7 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET u 1 " --> pdb=" O VAL u 17 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER u 65 " --> pdb=" O GLN u 2 " (cutoff:3.500A) 5635 hydrogen bonds defined for protein. 16833 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: 45.12 Time building geometry restraints manager: 30.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 34718 1.34 - 1.46: 20365 1.46 - 1.58: 52146 1.58 - 1.70: 16 1.70 - 1.82: 1031 Bond restraints: 108276 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 bond pdb=" C5 ATP D 501 " pdb=" N7 ATP D 501 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.04e+01 bond pdb=" C8 ATP D 501 " pdb=" N7 ATP D 501 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.83e+01 bond pdb=" C4 ATP D 501 " pdb=" N9 ATP D 501 " ideal model delta sigma weight residual 1.374 1.339 0.035 1.00e-02 1.00e+04 1.24e+01 ... (remaining 108271 not shown) Histogram of bond angle deviations from ideal: 94.64 - 103.65: 1346 103.65 - 112.65: 57079 112.65 - 121.66: 64055 121.66 - 130.66: 23377 130.66 - 139.67: 428 Bond angle restraints: 146285 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 123.64 16.23 1.00e+00 1.00e+00 2.63e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 122.71 14.12 1.00e+00 1.00e+00 1.99e+02 angle pdb=" C5 ATP D 501 " pdb=" C4 ATP D 501 " pdb=" N3 ATP D 501 " ideal model delta sigma weight residual 126.80 117.91 8.89 1.00e+00 1.00e+00 7.90e+01 angle pdb=" N3 ATP D 501 " pdb=" C4 ATP D 501 " pdb=" N9 ATP D 501 " ideal model delta sigma weight residual 127.04 136.04 -9.00 1.15e+00 7.59e-01 6.15e+01 angle pdb=" C GLU g 223 " pdb=" N ASN g 224 " pdb=" CA ASN g 224 " ideal model delta sigma weight residual 122.26 129.86 -7.60 1.10e+00 8.26e-01 4.78e+01 ... (remaining 146280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.72: 64291 30.72 - 61.43: 1761 61.43 - 92.15: 104 92.15 - 122.87: 2 122.87 - 153.58: 1 Dihedral angle restraints: 66159 sinusoidal: 26835 harmonic: 39324 Sorted by residual: dihedral pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -150.87 64.87 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 93.59 -153.58 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 62.83 -122.83 1 2.00e+01 2.50e-03 3.70e+01 ... (remaining 66156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 15176 0.092 - 0.185: 1336 0.185 - 0.277: 50 0.277 - 0.369: 4 0.369 - 0.461: 1 Chirality restraints: 16567 Sorted by residual: chirality pdb=" CG LEU U 764 " pdb=" CB LEU U 764 " pdb=" CD1 LEU U 764 " pdb=" CD2 LEU U 764 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CB THR U 629 " pdb=" CA THR U 629 " pdb=" OG1 THR U 629 " pdb=" CG2 THR U 629 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB VAL Y 325 " pdb=" CA VAL Y 325 " pdb=" CG1 VAL Y 325 " pdb=" CG2 VAL Y 325 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 16564 not shown) Planarity restraints: 18851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 255 " 0.031 2.00e-02 2.50e+03 3.25e-02 2.65e+01 pdb=" CG TRP a 255 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP a 255 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP a 255 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 255 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP a 255 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 255 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 255 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 255 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP a 255 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 215 " 0.025 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP M 215 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP M 215 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP M 215 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 215 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 215 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 215 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP M 215 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU d 198 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU d 198 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU d 198 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE d 199 " 0.021 2.00e-02 2.50e+03 ... (remaining 18848 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.14: 11 2.14 - 2.83: 33272 2.83 - 3.52: 146139 3.52 - 4.21: 239423 4.21 - 4.90: 426080 Nonbonded interactions: 844925 Sorted by model distance: nonbonded pdb=" C GLY u 76 " pdb=" NZ LYS v 25 " model vdw 1.455 3.350 nonbonded pdb=" O2B ATP D 501 " pdb="MG MG D 502 " model vdw 1.762 2.170 nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 502 " model vdw 1.889 2.170 nonbonded pdb=" OG1 THR A 223 " pdb="MG MG A 502 " model vdw 2.049 2.170 nonbonded pdb=" O1B ADP F 501 " pdb="MG MG F 502 " model vdw 2.080 2.170 ... (remaining 844920 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 'G' and (resid 2 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 195 or (resid 196 and (n \ ame N or name CA or name C or name O or name CB )) or resid 197 through 222 or ( \ resid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 \ through 245)) selection = (chain 'g' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 245)) } ncs_group { reference = (chain 'H' and (resid 3 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 199 or (resid 200 and (name N or \ name CA or name C or name O or name CB )) or resid 201 through 234)) selection = (chain 'h' and (resid 3 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 175 or (resid 176 and (name N or na \ me CA or name C or name O or name CB )) or resid 177 through 234)) } ncs_group { reference = (chain 'I' and (resid 2 through 6 or resid 8 through 198 or (resid 199 and (name \ N or name CA or name C or name O or name CB )) or resid 200 through 204 or (res \ id 205 and (name N or name CA or name C or name O or name CB )) or resid 206 thr \ ough 251)) selection = (chain 'i' and (resid 2 through 6 or resid 8 through 228 or (resid 229 and (name \ N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and ( \ name N or name CA or name C or name O or name CB )) or resid 232 through 251)) } ncs_group { reference = (chain 'J' and (resid 2 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 223 or (resid 22 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or re \ sid 233 through 238 or (resid 239 through 240 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'j' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 240)) } ncs_group { reference = (chain 'K' and (resid 8 through 240 or (resid 241 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)))) selection = (chain 'k' and (resid 8 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 241)) } ncs_group { reference = (chain 'L' and (resid 4 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 241)) selection = (chain 'l' and (resid 4 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 241)) } ncs_group { reference = chain 'M' selection = (chain 'm' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 187 or (resid 188 and (name N or name CA or name C or name \ O or name CB )) or resid 189 through 244)) } ncs_group { reference = (chain 'N' and (resid 1 through 149 or (resid 150 and (name N or name CA or name \ C or name O or name CB )) or resid 151 through 202)) selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 through 202 or (resid 203 and (name N or \ name CA or name C or name O or name CB )) or resid 204 through 220)) } ncs_group { reference = chain 'P' selection = (chain 'p' and (resid 2 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 205)) } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = (chain 's' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 213)) } ncs_group { reference = chain 'T' selection = (chain 't' and (resid 1 through 205 or (resid 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 through 216)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 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: 51.060 Check model and map are aligned: 1.180 Set scattering table: 0.720 Process input model: 264.260 Find NCS groups from input model: 6.430 Set up NCS constraints: 0.690 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 335.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.004 0.082 108276 Z= 0.278 Angle : 0.815 16.231 146285 Z= 0.428 Chirality : 0.051 0.461 16567 Planarity : 0.006 0.070 18851 Dihedral : 13.533 153.583 40850 Min Nonbonded Distance : 1.455 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.90 % Favored : 94.05 % Rotamer: Outliers : 0.15 % Allowed : 0.57 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 13433 helix: 0.32 (0.06), residues: 6321 sheet: 0.40 (0.12), residues: 2001 loop : -1.91 (0.08), residues: 5111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP a 255 HIS 0.013 0.001 HIS c 183 PHE 0.034 0.002 PHE d 199 TYR 0.033 0.002 TYR Y 292 ARG 0.009 0.000 ARG F 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 453 time to evaluate : 9.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8211 (ptm) cc_final: 0.7800 (ptp) REVERT: B 74 MET cc_start: 0.7624 (mmt) cc_final: 0.7088 (ttm) REVERT: C 293 MET cc_start: 0.7853 (mmm) cc_final: 0.7465 (tpt) REVERT: C 391 MET cc_start: 0.8244 (mmp) cc_final: 0.7617 (mmt) REVERT: L 26 MET cc_start: 0.8519 (tpt) cc_final: 0.7721 (tpt) REVERT: P 34 MET cc_start: 0.8197 (tmm) cc_final: 0.7983 (tmm) REVERT: Q 1 MET cc_start: 0.8883 (ppp) cc_final: 0.7966 (ppp) REVERT: U 351 MET cc_start: 0.8638 (tpp) cc_final: 0.8317 (tpt) REVERT: V 494 MET cc_start: 0.9286 (tpp) cc_final: 0.8677 (tpt) REVERT: W 16 MET cc_start: 0.3544 (tpt) cc_final: 0.2201 (tmm) REVERT: X 99 MET cc_start: 0.6485 (ppp) cc_final: 0.5834 (ppp) REVERT: X 254 MET cc_start: 0.8869 (ptp) cc_final: 0.8254 (mtm) REVERT: X 368 MET cc_start: 0.8801 (mmm) cc_final: 0.8216 (mpp) REVERT: a 141 MET cc_start: 0.8879 (ppp) cc_final: 0.8451 (ppp) REVERT: c 167 MET cc_start: 0.7919 (mmp) cc_final: 0.7627 (mtp) REVERT: f 1 MET cc_start: 0.0580 (mpp) cc_final: 0.0158 (ttp) REVERT: f 131 MET cc_start: 0.4661 (mtt) cc_final: 0.2644 (ttt) REVERT: f 505 MET cc_start: 0.3747 (ppp) cc_final: 0.3452 (ppp) REVERT: f 524 MET cc_start: 0.7334 (ppp) cc_final: 0.6935 (ptt) REVERT: f 788 MET cc_start: 0.6722 (mpp) cc_final: 0.6324 (mpp) REVERT: f 829 MET cc_start: 0.7002 (tpp) cc_final: 0.6688 (tpp) REVERT: i 174 MET cc_start: 0.8981 (ptm) cc_final: 0.8162 (ppp) REVERT: p 131 MET cc_start: 0.6889 (mmt) cc_final: 0.6569 (tpp) REVERT: x 48 VAL cc_start: 0.3013 (t) cc_final: 0.2195 (t) REVERT: x 67 MET cc_start: 0.3523 (mpp) cc_final: 0.2737 (tmm) outliers start: 16 outliers final: 7 residues processed: 469 average time/residue: 0.8399 time to fit residues: 709.3039 Evaluate side-chains 438 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 431 time to evaluate : 9.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain a residue 123 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1126 optimal weight: 10.0000 chunk 1011 optimal weight: 0.0980 chunk 561 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 682 optimal weight: 3.9990 chunk 540 optimal weight: 6.9990 chunk 1045 optimal weight: 10.0000 chunk 404 optimal weight: 0.9980 chunk 635 optimal weight: 20.0000 chunk 778 optimal weight: 20.0000 chunk 1211 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN Q 27 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 464 GLN ** U 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN Z 273 HIS ** d 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 GLN ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 790 GLN ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 108276 Z= 0.141 Angle : 0.536 14.748 146285 Z= 0.276 Chirality : 0.041 0.165 16567 Planarity : 0.004 0.056 18851 Dihedral : 6.015 161.575 14934 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.10 (0.07), residues: 13433 helix: 1.27 (0.07), residues: 6344 sheet: 0.55 (0.12), residues: 1992 loop : -1.72 (0.08), residues: 5097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP a 255 HIS 0.007 0.001 HIS a 372 PHE 0.020 0.001 PHE f 713 TYR 0.023 0.001 TYR Y 292 ARG 0.003 0.000 ARG e 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 436 time to evaluate : 9.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.7970 (ptm) cc_final: 0.7568 (ptp) REVERT: B 74 MET cc_start: 0.7554 (mmt) cc_final: 0.7070 (ttm) REVERT: D 246 MET cc_start: 0.8754 (tmm) cc_final: 0.8420 (tmm) REVERT: E 275 MET cc_start: 0.8412 (mmm) cc_final: 0.8043 (mmm) REVERT: E 277 MET cc_start: 0.8684 (mmt) cc_final: 0.8326 (mmt) REVERT: L 26 MET cc_start: 0.8527 (tpt) cc_final: 0.7779 (tpt) REVERT: Q 1 MET cc_start: 0.8787 (ppp) cc_final: 0.7879 (ppp) REVERT: U 351 MET cc_start: 0.8682 (tpp) cc_final: 0.8414 (tpp) REVERT: V 494 MET cc_start: 0.9233 (tpp) cc_final: 0.8621 (tpt) REVERT: W 16 MET cc_start: 0.3570 (tpt) cc_final: 0.2692 (mmp) REVERT: X 99 MET cc_start: 0.6394 (ppp) cc_final: 0.5706 (ppp) REVERT: X 254 MET cc_start: 0.8758 (ptp) cc_final: 0.8420 (ptt) REVERT: Y 214 MET cc_start: 0.2999 (tpt) cc_final: 0.2457 (tpt) REVERT: c 167 MET cc_start: 0.7864 (mmp) cc_final: 0.7604 (mtp) REVERT: f 1 MET cc_start: 0.0601 (mpp) cc_final: 0.0114 (ttp) REVERT: f 131 MET cc_start: 0.4862 (mtt) cc_final: 0.2802 (ttt) REVERT: f 370 MET cc_start: 0.7706 (mmt) cc_final: 0.7220 (tmm) REVERT: f 407 MET cc_start: 0.7493 (mtt) cc_final: 0.7035 (mmt) REVERT: f 505 MET cc_start: 0.3776 (ppp) cc_final: 0.3499 (ppp) REVERT: i 72 MET cc_start: 0.8898 (mtp) cc_final: 0.8684 (ttm) REVERT: i 184 MET cc_start: 0.8593 (mmm) cc_final: 0.8339 (mmt) REVERT: p 131 MET cc_start: 0.6956 (mmt) cc_final: 0.6634 (tpp) REVERT: x 47 MET cc_start: -0.1034 (ptm) cc_final: -0.3064 (mtp) REVERT: x 48 VAL cc_start: 0.3046 (t) cc_final: 0.2752 (t) outliers start: 27 outliers final: 9 residues processed: 446 average time/residue: 0.8462 time to fit residues: 682.1661 Evaluate side-chains 438 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 429 time to evaluate : 9.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 248 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 673 optimal weight: 1.9990 chunk 375 optimal weight: 20.0000 chunk 1008 optimal weight: 4.9990 chunk 824 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 chunk 1213 optimal weight: 30.0000 chunk 1311 optimal weight: 9.9990 chunk 1080 optimal weight: 20.0000 chunk 1203 optimal weight: 5.9990 chunk 413 optimal weight: 0.8980 chunk 973 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN F 116 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 HIS Z 104 ASN Z 109 ASN ** d 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 220 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 108276 Z= 0.198 Angle : 0.529 11.382 146285 Z= 0.274 Chirality : 0.041 0.178 16567 Planarity : 0.004 0.052 18851 Dihedral : 5.777 169.236 14931 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 0.49 % Allowed : 8.51 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.48 (0.08), residues: 13433 helix: 1.71 (0.07), residues: 6337 sheet: 0.56 (0.12), residues: 2008 loop : -1.64 (0.08), residues: 5088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP a 255 HIS 0.006 0.001 HIS f 715 PHE 0.022 0.001 PHE d 199 TYR 0.022 0.001 TYR W 369 ARG 0.004 0.000 ARG Z 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 431 time to evaluate : 9.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.7532 (mmt) cc_final: 0.7178 (ttm) REVERT: D 246 MET cc_start: 0.8825 (tmm) cc_final: 0.8449 (tmm) REVERT: E 277 MET cc_start: 0.8677 (mmt) cc_final: 0.8364 (mmt) REVERT: L 26 MET cc_start: 0.8588 (tpt) cc_final: 0.7785 (tpt) REVERT: N 116 MET cc_start: 0.8108 (mmt) cc_final: 0.7771 (mmt) REVERT: Q 1 MET cc_start: 0.8728 (ppp) cc_final: 0.7847 (ppp) REVERT: U 351 MET cc_start: 0.8721 (tpp) cc_final: 0.8488 (tpp) REVERT: U 885 MET cc_start: 0.7975 (mtm) cc_final: 0.7694 (mtm) REVERT: U 894 MET cc_start: 0.6607 (tpp) cc_final: 0.6322 (tpp) REVERT: V 494 MET cc_start: 0.9205 (tpp) cc_final: 0.8512 (tpt) REVERT: W 16 MET cc_start: 0.3475 (tpt) cc_final: 0.2735 (mmp) REVERT: X 99 MET cc_start: 0.6389 (ppp) cc_final: 0.5615 (ppp) REVERT: X 254 MET cc_start: 0.8832 (ptp) cc_final: 0.8489 (ptt) REVERT: b 107 MET cc_start: 0.8204 (mmp) cc_final: 0.7962 (mmp) REVERT: c 131 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8629 (pm20) REVERT: c 167 MET cc_start: 0.7814 (mmp) cc_final: 0.7555 (mtp) REVERT: f 1 MET cc_start: 0.0517 (mpp) cc_final: 0.0043 (ttp) REVERT: f 131 MET cc_start: 0.4894 (mtt) cc_final: 0.2944 (ttt) REVERT: f 407 MET cc_start: 0.7481 (mtt) cc_final: 0.7061 (mmt) REVERT: f 505 MET cc_start: 0.3730 (ppp) cc_final: 0.3484 (ppp) REVERT: f 646 MET cc_start: 0.6998 (ppp) cc_final: 0.6586 (ppp) REVERT: p 131 MET cc_start: 0.6948 (mmt) cc_final: 0.6628 (tpp) REVERT: x 48 VAL cc_start: 0.3074 (t) cc_final: 0.2419 (t) REVERT: x 67 MET cc_start: 0.2942 (mpp) cc_final: 0.2217 (tmm) outliers start: 55 outliers final: 17 residues processed: 468 average time/residue: 0.8211 time to fit residues: 694.9225 Evaluate side-chains 447 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 429 time to evaluate : 8.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 315 MET Chi-restraints excluded: chain X residue 237 GLU Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain c residue 131 GLN Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain p residue 12 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1199 optimal weight: 0.5980 chunk 912 optimal weight: 20.0000 chunk 629 optimal weight: 0.0010 chunk 134 optimal weight: 9.9990 chunk 579 optimal weight: 5.9990 chunk 814 optimal weight: 40.0000 chunk 1217 optimal weight: 40.0000 chunk 1289 optimal weight: 20.0000 chunk 636 optimal weight: 0.0980 chunk 1154 optimal weight: 10.0000 chunk 347 optimal weight: 3.9990 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN ** d 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 108276 Z= 0.129 Angle : 0.497 13.662 146285 Z= 0.255 Chirality : 0.040 0.166 16567 Planarity : 0.003 0.052 18851 Dihedral : 5.570 174.541 14927 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 0.66 % Allowed : 10.25 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.66 (0.08), residues: 13433 helix: 1.87 (0.07), residues: 6327 sheet: 0.60 (0.12), residues: 2015 loop : -1.56 (0.08), residues: 5091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP a 255 HIS 0.005 0.001 HIS f 715 PHE 0.017 0.001 PHE d 199 TYR 0.016 0.001 TYR Y 292 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 431 time to evaluate : 9.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.7505 (mmt) cc_final: 0.7133 (ttm) REVERT: C 237 MET cc_start: 0.9060 (mmm) cc_final: 0.8644 (tpt) REVERT: C 293 MET cc_start: 0.7651 (tpt) cc_final: 0.7106 (tpt) REVERT: D 246 MET cc_start: 0.8750 (tmm) cc_final: 0.8394 (tmm) REVERT: E 277 MET cc_start: 0.8659 (mmt) cc_final: 0.8432 (mmt) REVERT: L 26 MET cc_start: 0.8577 (tpt) cc_final: 0.7791 (tpt) REVERT: N 116 MET cc_start: 0.8216 (mmt) cc_final: 0.7848 (mmt) REVERT: Q 1 MET cc_start: 0.8640 (ppp) cc_final: 0.7840 (ppp) REVERT: U 351 MET cc_start: 0.8676 (tpp) cc_final: 0.8469 (tpp) REVERT: U 894 MET cc_start: 0.6670 (tpp) cc_final: 0.6398 (tpp) REVERT: V 175 MET cc_start: 0.9024 (mmm) cc_final: 0.8774 (mmm) REVERT: V 494 MET cc_start: 0.9206 (tpp) cc_final: 0.8467 (tpt) REVERT: W 16 MET cc_start: 0.3506 (tpt) cc_final: 0.2759 (mmp) REVERT: W 73 MET cc_start: 0.9102 (ppp) cc_final: 0.8863 (ppp) REVERT: W 177 MET cc_start: 0.7517 (mmm) cc_final: 0.7255 (mmt) REVERT: X 99 MET cc_start: 0.6420 (ppp) cc_final: 0.5629 (ppp) REVERT: X 254 MET cc_start: 0.8812 (ptp) cc_final: 0.8405 (ptt) REVERT: Y 214 MET cc_start: 0.3406 (tpt) cc_final: 0.2834 (tpt) REVERT: c 131 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8562 (pm20) REVERT: c 167 MET cc_start: 0.7765 (mmp) cc_final: 0.7530 (mtp) REVERT: d 190 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8733 (tt) REVERT: f 1 MET cc_start: 0.0479 (mpp) cc_final: 0.0014 (ttp) REVERT: f 131 MET cc_start: 0.4861 (mtt) cc_final: 0.3020 (ttt) REVERT: f 407 MET cc_start: 0.7435 (mtt) cc_final: 0.7032 (mmt) REVERT: f 416 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6921 (tmm) REVERT: f 505 MET cc_start: 0.3642 (ppp) cc_final: 0.3404 (ppp) REVERT: f 512 MET cc_start: 0.5291 (tmm) cc_final: 0.4028 (ppp) REVERT: f 646 MET cc_start: 0.6939 (ppp) cc_final: 0.6535 (ppp) REVERT: l 26 MET cc_start: 0.6858 (tpt) cc_final: 0.6486 (tpt) REVERT: n 95 MET cc_start: 0.8702 (tpp) cc_final: 0.8008 (tpp) REVERT: n 116 MET cc_start: 0.8540 (mtm) cc_final: 0.8274 (mtt) REVERT: p 131 MET cc_start: 0.6952 (mmt) cc_final: 0.6632 (tpp) REVERT: x 48 VAL cc_start: 0.3147 (t) cc_final: 0.2495 (t) REVERT: x 67 MET cc_start: 0.2771 (mpp) cc_final: 0.2057 (tmm) outliers start: 75 outliers final: 26 residues processed: 484 average time/residue: 0.8242 time to fit residues: 720.5727 Evaluate side-chains 456 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 427 time to evaluate : 9.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 315 MET Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain Y residue 105 MET Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain c residue 131 GLN Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain t residue 117 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1073 optimal weight: 20.0000 chunk 731 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 960 optimal weight: 7.9990 chunk 532 optimal weight: 5.9990 chunk 1100 optimal weight: 30.0000 chunk 891 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 658 optimal weight: 30.0000 chunk 1157 optimal weight: 20.0000 chunk 325 optimal weight: 0.8980 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS G 172 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN R 29 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 GLN ** V 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN b 158 ASN ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 102 ASN ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 108276 Z= 0.249 Angle : 0.552 13.540 146285 Z= 0.286 Chirality : 0.041 0.182 16567 Planarity : 0.004 0.052 18851 Dihedral : 5.656 176.478 14927 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 1.03 % Allowed : 11.47 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.67 (0.08), residues: 13433 helix: 1.90 (0.07), residues: 6353 sheet: 0.51 (0.12), residues: 2045 loop : -1.55 (0.09), residues: 5035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP a 255 HIS 0.007 0.001 HIS c 183 PHE 0.020 0.001 PHE d 199 TYR 0.019 0.001 TYR Y 292 ARG 0.005 0.000 ARG Z 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 432 time to evaluate : 9.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.7482 (mmt) cc_final: 0.7062 (ttm) REVERT: C 248 MET cc_start: 0.8575 (pmm) cc_final: 0.8159 (pmm) REVERT: D 246 MET cc_start: 0.8820 (tmm) cc_final: 0.8516 (tmm) REVERT: E 277 MET cc_start: 0.8705 (mmt) cc_final: 0.8443 (mmt) REVERT: F 366 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8305 (mpp) REVERT: L 26 MET cc_start: 0.8632 (tpt) cc_final: 0.7759 (tpt) REVERT: N 116 MET cc_start: 0.8104 (mmt) cc_final: 0.7848 (mmp) REVERT: Q 1 MET cc_start: 0.8669 (ppp) cc_final: 0.7866 (ppp) REVERT: U 351 MET cc_start: 0.8713 (tpp) cc_final: 0.8504 (tpp) REVERT: V 494 MET cc_start: 0.9176 (tpp) cc_final: 0.8397 (tpt) REVERT: W 16 MET cc_start: 0.3200 (tpt) cc_final: 0.2553 (mmp) REVERT: W 177 MET cc_start: 0.7847 (mmm) cc_final: 0.7642 (mmt) REVERT: W 413 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9032 (pt) REVERT: W 456 GLN cc_start: 0.5400 (pm20) cc_final: 0.4518 (mm-40) REVERT: X 254 MET cc_start: 0.8934 (ptp) cc_final: 0.8552 (ptt) REVERT: Y 389 MET cc_start: 0.7584 (mmp) cc_final: 0.7322 (mmt) REVERT: Z 17 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9475 (mm) REVERT: b 16 MET cc_start: 0.8549 (mmt) cc_final: 0.8269 (mmm) REVERT: c 167 MET cc_start: 0.7754 (mmp) cc_final: 0.7514 (mtp) REVERT: d 190 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8731 (tt) REVERT: f 1 MET cc_start: 0.0486 (mpp) cc_final: 0.0032 (ttp) REVERT: f 131 MET cc_start: 0.4890 (mtt) cc_final: 0.3784 (mtp) REVERT: f 407 MET cc_start: 0.7496 (mtt) cc_final: 0.7103 (mmt) REVERT: f 416 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6968 (tmm) REVERT: f 505 MET cc_start: 0.3905 (ppp) cc_final: 0.3669 (ppp) REVERT: f 670 MET cc_start: 0.3860 (mmm) cc_final: 0.3564 (mmm) REVERT: f 718 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6555 (p0) REVERT: g 73 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8240 (p) REVERT: l 26 MET cc_start: 0.7169 (tpt) cc_final: 0.6664 (tpt) REVERT: p 131 MET cc_start: 0.6917 (mmt) cc_final: 0.6589 (tpp) REVERT: x 48 VAL cc_start: 0.3427 (t) cc_final: 0.2425 (t) REVERT: x 67 MET cc_start: 0.2864 (mpp) cc_final: 0.2043 (tmm) outliers start: 117 outliers final: 41 residues processed: 523 average time/residue: 0.8287 time to fit residues: 786.2024 Evaluate side-chains 478 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 430 time to evaluate : 9.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 366 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 315 MET Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 214 VAL Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain p residue 12 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 433 optimal weight: 9.9990 chunk 1161 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 757 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 1290 optimal weight: 9.9990 chunk 1071 optimal weight: 30.0000 chunk 597 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 426 optimal weight: 20.0000 chunk 677 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN a 86 GLN c 274 ASN ** d 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 108276 Z= 0.223 Angle : 0.535 12.933 146285 Z= 0.276 Chirality : 0.041 0.177 16567 Planarity : 0.003 0.053 18851 Dihedral : 5.622 168.391 14927 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.63 % Favored : 94.35 % Rotamer: Outliers : 1.06 % Allowed : 12.37 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.71 (0.08), residues: 13433 helix: 1.94 (0.07), residues: 6345 sheet: 0.49 (0.12), residues: 2017 loop : -1.53 (0.09), residues: 5071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP a 255 HIS 0.006 0.001 HIS c 183 PHE 0.019 0.001 PHE d 199 TYR 0.019 0.001 TYR Y 292 ARG 0.004 0.000 ARG Z 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 430 time to evaluate : 9.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.7492 (mmt) cc_final: 0.7046 (ttm) REVERT: B 319 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7467 (p90) REVERT: C 237 MET cc_start: 0.9072 (mmm) cc_final: 0.8615 (tpt) REVERT: C 248 MET cc_start: 0.8428 (pmm) cc_final: 0.7734 (pmm) REVERT: D 246 MET cc_start: 0.8802 (tmm) cc_final: 0.8535 (tmm) REVERT: L 26 MET cc_start: 0.8622 (tpt) cc_final: 0.7745 (tpt) REVERT: N 116 MET cc_start: 0.8144 (mmt) cc_final: 0.7887 (mmp) REVERT: Q 1 MET cc_start: 0.8636 (ppp) cc_final: 0.7874 (ppp) REVERT: U 351 MET cc_start: 0.8699 (tpp) cc_final: 0.8497 (tpp) REVERT: V 175 MET cc_start: 0.9000 (mmm) cc_final: 0.8457 (mmm) REVERT: V 494 MET cc_start: 0.9167 (tpp) cc_final: 0.8383 (tpt) REVERT: W 16 MET cc_start: 0.3174 (tpt) cc_final: 0.2542 (mmp) REVERT: W 312 MET cc_start: 0.4063 (OUTLIER) cc_final: 0.3523 (mmt) REVERT: W 413 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9114 (pt) REVERT: X 254 MET cc_start: 0.8929 (ptp) cc_final: 0.8538 (ptt) REVERT: X 263 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7738 (p) REVERT: Y 129 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8816 (p0) REVERT: Y 214 MET cc_start: 0.4074 (tpt) cc_final: 0.3470 (tpt) REVERT: Y 389 MET cc_start: 0.7566 (mmp) cc_final: 0.7242 (mmp) REVERT: Z 201 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8852 (tp) REVERT: a 211 PHE cc_start: 0.5640 (OUTLIER) cc_final: 0.4719 (m-80) REVERT: b 16 MET cc_start: 0.8512 (mmt) cc_final: 0.8221 (mmm) REVERT: c 167 MET cc_start: 0.7732 (mmp) cc_final: 0.7500 (mtp) REVERT: d 190 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8748 (tt) REVERT: f 1 MET cc_start: 0.0541 (mpp) cc_final: 0.0089 (ttp) REVERT: f 131 MET cc_start: 0.4943 (mtt) cc_final: 0.3878 (mtp) REVERT: f 416 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6991 (tmm) REVERT: f 505 MET cc_start: 0.4057 (ppp) cc_final: 0.3814 (ppp) REVERT: f 543 MET cc_start: 0.8260 (ppp) cc_final: 0.7940 (ppp) REVERT: f 646 MET cc_start: 0.7109 (ppp) cc_final: 0.6747 (ppp) REVERT: f 718 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6603 (p0) REVERT: g 73 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8280 (p) REVERT: h 121 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8043 (t80) REVERT: l 26 MET cc_start: 0.7184 (tpt) cc_final: 0.6681 (tpt) REVERT: p 131 MET cc_start: 0.6838 (mmt) cc_final: 0.6519 (tpp) REVERT: x 48 VAL cc_start: 0.3285 (t) cc_final: 0.2648 (t) REVERT: x 67 MET cc_start: 0.3040 (mpp) cc_final: 0.2146 (tmm) outliers start: 121 outliers final: 50 residues processed: 523 average time/residue: 0.8261 time to fit residues: 783.9539 Evaluate side-chains 492 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 430 time to evaluate : 9.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 243 ILE Chi-restraints excluded: chain W residue 312 MET Chi-restraints excluded: chain W residue 315 MET Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 121 TYR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain s residue 91 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1244 optimal weight: 9.9990 chunk 145 optimal weight: 30.0000 chunk 735 optimal weight: 1.9990 chunk 942 optimal weight: 50.0000 chunk 730 optimal weight: 40.0000 chunk 1086 optimal weight: 40.0000 chunk 720 optimal weight: 5.9990 chunk 1285 optimal weight: 9.9990 chunk 804 optimal weight: 10.0000 chunk 783 optimal weight: 0.9990 chunk 593 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN L 20 HIS ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 362 ASN ** U 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 GLN Z 189 GLN b 76 HIS ** d 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 108276 Z= 0.216 Angle : 0.537 12.867 146285 Z= 0.276 Chirality : 0.041 0.212 16567 Planarity : 0.003 0.052 18851 Dihedral : 5.577 160.504 14927 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.91 % Favored : 94.07 % Rotamer: Outliers : 1.07 % Allowed : 12.98 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.73 (0.08), residues: 13433 helix: 1.97 (0.07), residues: 6345 sheet: 0.52 (0.12), residues: 2012 loop : -1.53 (0.09), residues: 5076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP a 255 HIS 0.006 0.001 HIS c 183 PHE 0.020 0.001 PHE f 713 TYR 0.018 0.001 TYR Y 292 ARG 0.004 0.000 ARG W 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 431 time to evaluate : 9.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7270 (ptm) REVERT: B 74 MET cc_start: 0.7516 (mmt) cc_final: 0.7078 (ttm) REVERT: B 319 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7496 (p90) REVERT: C 248 MET cc_start: 0.8329 (pmm) cc_final: 0.7832 (pmm) REVERT: C 369 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: C 391 MET cc_start: 0.8258 (mmp) cc_final: 0.7542 (mmt) REVERT: D 246 MET cc_start: 0.8794 (tmm) cc_final: 0.8524 (tmm) REVERT: L 26 MET cc_start: 0.8624 (tpt) cc_final: 0.7710 (tpt) REVERT: N 116 MET cc_start: 0.8133 (mmt) cc_final: 0.7891 (mmp) REVERT: Q 1 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7869 (ppp) REVERT: U 351 MET cc_start: 0.8693 (tpp) cc_final: 0.8378 (tpt) REVERT: V 494 MET cc_start: 0.9162 (tpp) cc_final: 0.8335 (tpt) REVERT: W 16 MET cc_start: 0.3186 (tpt) cc_final: 0.2584 (mmp) REVERT: W 413 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9003 (pt) REVERT: W 456 GLN cc_start: 0.5617 (OUTLIER) cc_final: 0.5136 (mp10) REVERT: X 254 MET cc_start: 0.8932 (ptp) cc_final: 0.8536 (ptt) REVERT: X 263 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7713 (p) REVERT: Y 129 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8840 (p0) REVERT: Y 389 MET cc_start: 0.7509 (mmp) cc_final: 0.7194 (mmp) REVERT: b 16 MET cc_start: 0.8491 (mmt) cc_final: 0.8215 (mmm) REVERT: c 167 MET cc_start: 0.7741 (mmp) cc_final: 0.7480 (mtp) REVERT: d 171 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8698 (tt) REVERT: d 190 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8762 (tt) REVERT: f 1 MET cc_start: 0.0507 (mpp) cc_final: 0.0054 (ttp) REVERT: f 48 GLU cc_start: 0.1897 (OUTLIER) cc_final: 0.1203 (tt0) REVERT: f 131 MET cc_start: 0.4899 (mtt) cc_final: 0.3858 (mtp) REVERT: f 340 MET cc_start: 0.4545 (mtt) cc_final: 0.4197 (pmm) REVERT: f 416 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6991 (tmm) REVERT: f 505 MET cc_start: 0.3986 (ppp) cc_final: 0.3757 (ppp) REVERT: f 512 MET cc_start: 0.5407 (tmm) cc_final: 0.4089 (ppp) REVERT: f 646 MET cc_start: 0.7066 (ppp) cc_final: 0.6694 (ppp) REVERT: f 718 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6576 (p0) REVERT: g 73 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8304 (p) REVERT: h 121 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8074 (t80) REVERT: l 26 MET cc_start: 0.7196 (tpt) cc_final: 0.6668 (tpt) REVERT: p 131 MET cc_start: 0.6867 (mmt) cc_final: 0.6548 (tpp) REVERT: x 48 VAL cc_start: 0.3424 (t) cc_final: 0.2752 (t) REVERT: x 67 MET cc_start: 0.3012 (mpp) cc_final: 0.2134 (tpt) outliers start: 122 outliers final: 61 residues processed: 527 average time/residue: 0.8220 time to fit residues: 784.9945 Evaluate side-chains 506 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 430 time to evaluate : 9.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain O residue 24 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 315 MET Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain W residue 456 GLN Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain X residue 389 ASP Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 47 ASN Chi-restraints excluded: chain f residue 48 GLU Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 214 VAL Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 121 TYR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain t residue 117 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 795 optimal weight: 9.9990 chunk 513 optimal weight: 9.9990 chunk 767 optimal weight: 20.0000 chunk 387 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 817 optimal weight: 7.9990 chunk 875 optimal weight: 20.0000 chunk 635 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 1010 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN R 89 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 453 HIS a 227 ASN b 76 HIS ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 752 HIS ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 108276 Z= 0.259 Angle : 0.568 13.397 146285 Z= 0.292 Chirality : 0.042 0.201 16567 Planarity : 0.004 0.052 18851 Dihedral : 5.640 144.042 14927 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 1.07 % Allowed : 13.29 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.67 (0.08), residues: 13433 helix: 1.90 (0.07), residues: 6368 sheet: 0.50 (0.12), residues: 2015 loop : -1.54 (0.09), residues: 5050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP a 255 HIS 0.008 0.001 HIS c 183 PHE 0.022 0.001 PHE d 199 TYR 0.021 0.001 TYR Y 292 ARG 0.005 0.000 ARG W 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 427 time to evaluate : 9.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.7494 (mmt) cc_final: 0.7025 (ttm) REVERT: B 319 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7490 (p90) REVERT: C 369 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8178 (m-10) REVERT: D 246 MET cc_start: 0.8803 (tmm) cc_final: 0.8518 (tmm) REVERT: L 26 MET cc_start: 0.8608 (tpt) cc_final: 0.7692 (tpt) REVERT: N 116 MET cc_start: 0.8179 (mmt) cc_final: 0.7949 (mmp) REVERT: Q 1 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7884 (ppp) REVERT: U 351 MET cc_start: 0.8723 (tpp) cc_final: 0.8344 (tpt) REVERT: V 494 MET cc_start: 0.9169 (tpp) cc_final: 0.8935 (tpp) REVERT: W 16 MET cc_start: 0.3011 (tpt) cc_final: 0.2610 (mmp) REVERT: W 334 GLU cc_start: 0.5297 (OUTLIER) cc_final: 0.4304 (tm-30) REVERT: W 413 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9099 (pt) REVERT: W 436 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8627 (mtm) REVERT: W 456 GLN cc_start: 0.5524 (OUTLIER) cc_final: 0.5199 (mp10) REVERT: X 254 MET cc_start: 0.8968 (ptp) cc_final: 0.8584 (ptt) REVERT: X 263 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7720 (p) REVERT: Y 129 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8893 (p0) REVERT: b 16 MET cc_start: 0.8464 (mmt) cc_final: 0.8219 (mmm) REVERT: c 167 MET cc_start: 0.7728 (mmp) cc_final: 0.7457 (mtp) REVERT: d 190 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8765 (tt) REVERT: f 1 MET cc_start: 0.0460 (mpp) cc_final: -0.0007 (ttp) REVERT: f 48 GLU cc_start: 0.1985 (OUTLIER) cc_final: 0.1316 (tt0) REVERT: f 131 MET cc_start: 0.4842 (mtt) cc_final: 0.3874 (mtp) REVERT: f 340 MET cc_start: 0.4631 (mtt) cc_final: 0.4340 (pmm) REVERT: f 416 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7036 (tmm) REVERT: f 505 MET cc_start: 0.4086 (ppp) cc_final: 0.3879 (ppp) REVERT: f 512 MET cc_start: 0.5491 (tmm) cc_final: 0.4083 (ppp) REVERT: f 543 MET cc_start: 0.8247 (ppp) cc_final: 0.7937 (ppp) REVERT: f 646 MET cc_start: 0.7065 (ppp) cc_final: 0.6621 (ppp) REVERT: f 718 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6429 (p0) REVERT: g 73 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8386 (p) REVERT: h 121 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8061 (t80) REVERT: l 26 MET cc_start: 0.7248 (tpt) cc_final: 0.6734 (tpt) REVERT: n 116 MET cc_start: 0.8592 (mtm) cc_final: 0.8313 (mtt) REVERT: p 131 MET cc_start: 0.6929 (mmt) cc_final: 0.6599 (tpp) REVERT: x 48 VAL cc_start: 0.3951 (t) cc_final: 0.3240 (t) REVERT: x 67 MET cc_start: 0.3215 (mpp) cc_final: 0.2311 (tpt) outliers start: 122 outliers final: 68 residues processed: 522 average time/residue: 0.8501 time to fit residues: 804.6367 Evaluate side-chains 510 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 427 time to evaluate : 9.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain S residue 91 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 258 TYR Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 315 MET Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 456 GLN Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain X residue 389 ASP Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 278 MET Chi-restraints excluded: chain a residue 319 LEU Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 47 ASN Chi-restraints excluded: chain f residue 48 GLU Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 214 VAL Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 121 TYR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain s residue 91 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1169 optimal weight: 10.0000 chunk 1231 optimal weight: 6.9990 chunk 1123 optimal weight: 6.9990 chunk 1198 optimal weight: 20.0000 chunk 721 optimal weight: 0.6980 chunk 521 optimal weight: 7.9990 chunk 940 optimal weight: 8.9990 chunk 367 optimal weight: 6.9990 chunk 1082 optimal weight: 9.9990 chunk 1133 optimal weight: 30.0000 chunk 1193 optimal weight: 9.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 ASN b 76 HIS d 60 GLN ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 108276 Z= 0.226 Angle : 0.555 13.023 146285 Z= 0.283 Chirality : 0.041 0.286 16567 Planarity : 0.003 0.052 18851 Dihedral : 5.580 127.881 14927 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 0.97 % Allowed : 13.48 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.70 (0.08), residues: 13433 helix: 1.93 (0.07), residues: 6348 sheet: 0.51 (0.12), residues: 2014 loop : -1.52 (0.09), residues: 5071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP a 255 HIS 0.009 0.001 HIS E 19 PHE 0.023 0.001 PHE d 199 TYR 0.020 0.001 TYR Y 292 ARG 0.004 0.000 ARG W 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 429 time to evaluate : 9.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.7513 (mmt) cc_final: 0.7043 (ttm) REVERT: B 319 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7484 (p90) REVERT: C 369 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8162 (m-10) REVERT: C 391 MET cc_start: 0.8263 (mmp) cc_final: 0.7558 (mmt) REVERT: D 246 MET cc_start: 0.8773 (tmm) cc_final: 0.8511 (tmm) REVERT: L 26 MET cc_start: 0.8611 (tpt) cc_final: 0.7693 (tpt) REVERT: N 116 MET cc_start: 0.8166 (mmt) cc_final: 0.7940 (mmp) REVERT: Q 1 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7865 (ppp) REVERT: U 351 MET cc_start: 0.8706 (tpp) cc_final: 0.8329 (tpt) REVERT: V 494 MET cc_start: 0.9168 (tpp) cc_final: 0.8930 (tpp) REVERT: W 16 MET cc_start: 0.2953 (tpt) cc_final: 0.2577 (mmp) REVERT: W 334 GLU cc_start: 0.5401 (OUTLIER) cc_final: 0.4417 (tm-30) REVERT: W 413 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9103 (pt) REVERT: W 436 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: X 254 MET cc_start: 0.8935 (ptp) cc_final: 0.8555 (ptt) REVERT: X 263 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7680 (p) REVERT: Y 129 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8881 (p0) REVERT: b 16 MET cc_start: 0.8441 (mmt) cc_final: 0.8216 (mmm) REVERT: c 167 MET cc_start: 0.7717 (mmp) cc_final: 0.7449 (mtp) REVERT: d 190 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8755 (tt) REVERT: f 1 MET cc_start: 0.0507 (mpp) cc_final: 0.0083 (ttp) REVERT: f 48 GLU cc_start: 0.1996 (OUTLIER) cc_final: 0.1328 (tt0) REVERT: f 131 MET cc_start: 0.4836 (mtt) cc_final: 0.3889 (mtp) REVERT: f 216 MET cc_start: 0.8350 (mpp) cc_final: 0.8023 (mpp) REVERT: f 340 MET cc_start: 0.4597 (mtt) cc_final: 0.4347 (pmm) REVERT: f 416 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7060 (tmm) REVERT: f 543 MET cc_start: 0.8295 (ppp) cc_final: 0.8010 (ppp) REVERT: f 718 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6435 (p0) REVERT: g 73 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8374 (p) REVERT: h 121 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8027 (t80) REVERT: l 26 MET cc_start: 0.7224 (tpt) cc_final: 0.6699 (tpt) REVERT: p 131 MET cc_start: 0.6894 (mmt) cc_final: 0.6559 (tpp) REVERT: x 48 VAL cc_start: 0.4049 (t) cc_final: 0.3335 (t) REVERT: x 67 MET cc_start: 0.3257 (mpp) cc_final: 0.2352 (tpt) outliers start: 110 outliers final: 73 residues processed: 514 average time/residue: 0.8546 time to fit residues: 797.2324 Evaluate side-chains 515 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 428 time to evaluate : 9.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain S residue 91 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain U residue 96 TYR Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 258 TYR Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 315 MET Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 389 ASP Chi-restraints excluded: chain Y residue 105 MET Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 189 GLN Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 278 MET Chi-restraints excluded: chain a residue 319 LEU Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 47 ASN Chi-restraints excluded: chain f residue 48 GLU Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 214 VAL Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain f residue 850 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 121 TYR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 786 optimal weight: 0.9990 chunk 1266 optimal weight: 6.9990 chunk 773 optimal weight: 5.9990 chunk 601 optimal weight: 0.7980 chunk 880 optimal weight: 0.1980 chunk 1329 optimal weight: 7.9990 chunk 1223 optimal weight: 5.9990 chunk 1058 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 817 optimal weight: 10.0000 chunk 648 optimal weight: 0.0020 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN G 172 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN Q 27 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 777 HIS W 228 ASN Y 14 ASN a 227 ASN b 76 HIS b 158 ASN ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 110 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 108276 Z= 0.129 Angle : 0.525 12.575 146285 Z= 0.264 Chirality : 0.040 0.192 16567 Planarity : 0.003 0.052 18851 Dihedral : 5.281 97.602 14927 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 0.72 % Allowed : 13.71 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.83 (0.08), residues: 13433 helix: 2.05 (0.07), residues: 6322 sheet: 0.61 (0.12), residues: 2017 loop : -1.47 (0.09), residues: 5094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP a 255 HIS 0.006 0.001 HIS Y 291 PHE 0.021 0.001 PHE d 199 TYR 0.022 0.001 TYR f 439 ARG 0.008 0.000 ARG f 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26866 Ramachandran restraints generated. 13433 Oldfield, 0 Emsley, 13433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 433 time to evaluate : 9.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 MET cc_start: 0.7562 (mmt) cc_final: 0.7084 (ttm) REVERT: C 391 MET cc_start: 0.8169 (mmp) cc_final: 0.7517 (mmt) REVERT: D 163 MET cc_start: 0.7709 (mmp) cc_final: 0.7452 (mmp) REVERT: L 26 MET cc_start: 0.8591 (tpt) cc_final: 0.7737 (tpt) REVERT: N 116 MET cc_start: 0.8154 (mmt) cc_final: 0.7869 (mmp) REVERT: Q 1 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7754 (ppp) REVERT: S 83 MET cc_start: 0.8756 (mtt) cc_final: 0.8510 (mtt) REVERT: U 351 MET cc_start: 0.8625 (tpp) cc_final: 0.8338 (tpt) REVERT: U 797 MET cc_start: 0.6619 (ppp) cc_final: 0.6400 (ppp) REVERT: U 885 MET cc_start: 0.7734 (mtm) cc_final: 0.7514 (mtt) REVERT: V 494 MET cc_start: 0.9164 (tpp) cc_final: 0.8292 (tpt) REVERT: W 16 MET cc_start: 0.2870 (tpt) cc_final: 0.2534 (mmp) REVERT: W 334 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.3809 (tm-30) REVERT: X 263 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7610 (p) REVERT: Y 129 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8857 (p0) REVERT: Y 214 MET cc_start: 0.4146 (tpt) cc_final: 0.3707 (tpt) REVERT: Z 257 MET cc_start: 0.9422 (mmm) cc_final: 0.9181 (mmp) REVERT: b 107 MET cc_start: 0.8031 (mmp) cc_final: 0.7783 (mmp) REVERT: c 167 MET cc_start: 0.7724 (mmp) cc_final: 0.7447 (mtp) REVERT: d 190 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8786 (tt) REVERT: f 1 MET cc_start: 0.0559 (mpp) cc_final: 0.0041 (ttp) REVERT: f 131 MET cc_start: 0.4660 (mtt) cc_final: 0.3976 (mtp) REVERT: f 216 MET cc_start: 0.8329 (mpp) cc_final: 0.8034 (mpp) REVERT: f 416 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7038 (tmm) REVERT: f 524 MET cc_start: 0.8063 (ppp) cc_final: 0.7562 (ppp) REVERT: f 543 MET cc_start: 0.8248 (ppp) cc_final: 0.7952 (ppp) REVERT: f 718 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6364 (p0) REVERT: g 73 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8270 (p) REVERT: h 121 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7971 (t80) REVERT: i 174 MET cc_start: 0.8691 (ppp) cc_final: 0.8324 (ppp) REVERT: j 177 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7448 (p) REVERT: k 133 MET cc_start: 0.6898 (mmm) cc_final: 0.6550 (mmm) REVERT: l 26 MET cc_start: 0.7202 (tpt) cc_final: 0.6756 (tpt) REVERT: p 131 MET cc_start: 0.6852 (mmt) cc_final: 0.6515 (tpp) REVERT: x 47 MET cc_start: -0.1140 (ptt) cc_final: -0.3024 (ttm) REVERT: x 48 VAL cc_start: 0.4008 (t) cc_final: 0.3317 (t) REVERT: x 67 MET cc_start: 0.3106 (mpp) cc_final: 0.2283 (tpt) outliers start: 82 outliers final: 57 residues processed: 496 average time/residue: 0.8426 time to fit residues: 756.5426 Evaluate side-chains 496 residues out of total 11550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 429 time to evaluate : 9.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain S residue 91 MET Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain U residue 333 MET Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 258 TYR Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 243 ILE Chi-restraints excluded: chain W residue 315 MET Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain Y residue 105 MET Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 319 LEU Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 95 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain f residue 151 LEU Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 416 MET Chi-restraints excluded: chain f residue 605 ASN Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 846 VAL Chi-restraints excluded: chain f residue 850 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 121 TYR Chi-restraints excluded: chain j residue 177 THR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain n residue 119 MET Chi-restraints excluded: chain s residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 840 optimal weight: 20.0000 chunk 1127 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 975 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 1059 optimal weight: 30.0000 chunk 443 optimal weight: 6.9990 chunk 1088 optimal weight: 20.0000 chunk 134 optimal weight: 0.6980 chunk 195 optimal weight: 5.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN G 172 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** S 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 228 ASN a 227 ASN c 180 ASN ** f 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.047034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.027391 restraints weight = 1088312.445| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 6.88 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 108276 Z= 0.211 Angle : 0.549 12.430 146285 Z= 0.278 Chirality : 0.041 0.213 16567 Planarity : 0.003 0.052 18851 Dihedral : 5.263 108.020 14927 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 0.72 % Allowed : 13.82 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % 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: 0.84 (0.08), residues: 13433 helix: 2.05 (0.07), residues: 6344 sheet: 0.59 (0.12), residues: 2025 loop : -1.47 (0.09), residues: 5064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP a 255 HIS 0.008 0.001 HIS c 183 PHE 0.021 0.001 PHE d 199 TYR 0.017 0.001 TYR Y 292 ARG 0.007 0.000 ARG W 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20301.71 seconds wall clock time: 358 minutes 50.27 seconds (21530.27 seconds total)