Starting phenix.real_space_refine on Fri Dec 8 12:42:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3k_32283/12_2023/7w3k_32283_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3k_32283/12_2023/7w3k_32283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3k_32283/12_2023/7w3k_32283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3k_32283/12_2023/7w3k_32283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3k_32283/12_2023/7w3k_32283_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3k_32283/12_2023/7w3k_32283_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 10 5.49 5 S 641 5.16 5 C 69965 2.51 5 N 18989 2.21 5 O 21051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 110657 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 389} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3207 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 389} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 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: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3133 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1867 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1933 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 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': 6} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1813 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1890 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1521 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "O" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 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: "g" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1879 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 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: {'PTRANS': 9, '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: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1549 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "s" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1650 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "x" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3929 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "y" 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: "C" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3105 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 379} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 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: "U" Number of atoms: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6828 Classifications: {'peptide': 872} Link IDs: {'PTRANS': 31, 'TRANS': 840} Chain breaks: 1 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: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3202 Classifications: {'peptide': 389} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 379} 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: "f" Number of atoms: 6866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6866 Classifications: {'peptide': 889} Link IDs: {'PTRANS': 34, 'TRANS': 854} 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: "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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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 k 120 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA k 120 " occ=0.50 residue: pdb=" N GLU k 175 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU k 175 " 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 ASN p 18 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN p 18 " occ=0.50 residue: pdb=" N GLU p 78 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU p 78 " occ=0.50 residue: pdb=" N GLY p 79 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY p 79 " occ=0.50 residue: pdb=" N HIS q 99 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS q 99 " 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 ... (remaining 9 not shown) Time building chain proxies: 40.47, per 1000 atoms: 0.37 Number of scatterers: 110657 At special positions: 0 Unit cell: (329.485, 220.57, 222.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 641 16.00 P 10 15.00 O 21051 8.00 N 18989 7.00 C 69965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " 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: 30.38 Conformation dependent library (CDL) restraints added in 14.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26338 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: 516 helices and 89 sheets defined 54.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 51.99 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 removed outlier: 4.805A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 62 removed outlier: 3.681A pdb=" N LYS A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 6.042A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 85' Processing helix chain 'A' and resid 86 through 94 removed outlier: 5.258A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix No H-bonds generated for 'chain 'A' and resid 86 through 94' Processing helix chain 'A' and resid 158 through 166 removed outlier: 4.050A pdb=" N THR A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N MET A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.497A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 5.213A 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 192 removed outlier: 3.853A pdb=" N LYS A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 4.791A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 4.113A pdb=" N ALA A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.908A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLN A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 247' Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.719A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.785A pdb=" N GLY A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 308 removed outlier: 3.500A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.517A pdb=" N LEU A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.635A pdb=" N LEU A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 338' Processing helix chain 'A' and resid 348 through 361 removed outlier: 3.510A pdb=" N THR A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.761A 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 399 removed outlier: 3.863A pdb=" N MET A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'B' and resid 58 through 82 removed outlier: 3.623A pdb=" N LEU B 62 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.654A pdb=" N LEU B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 4.668A pdb=" N LEU B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 170 through 176 removed outlier: 4.884A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 206 removed outlier: 4.578A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 208 through 215 removed outlier: 4.455A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 243 removed outlier: 3.690A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.701A pdb=" N LYS B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.893A pdb=" N GLN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 4.531A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.544A pdb=" N LYS B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.553A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.551A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU B 432 " --> pdb=" O TYR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 4.897A pdb=" N TYR B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 440' Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.531A pdb=" N LYS B 38 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 53 removed outlier: 3.894A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.677A pdb=" N LEU E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 5.576A 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 126 removed outlier: 5.388A pdb=" N ASP E 126 " --> pdb=" O MET E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 5.337A 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: 3.869A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 6.619A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU E 214 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.482A pdb=" N ILE E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.595A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 318 Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 339 through 358 removed outlier: 4.894A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 382 removed outlier: 3.535A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.696A pdb=" N ILE E 135 " --> pdb=" O TYR E 132 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLY E 136 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 removed outlier: 5.636A pdb=" N SER E 202 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ILE E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL E 204 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP E 205 " --> pdb=" O SER E 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 205' Processing helix chain 'F' and resid 26 through 35 removed outlier: 4.136A pdb=" N GLU F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 85 removed outlier: 4.330A pdb=" N ARG F 44 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG F 46 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER F 50 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE F 54 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 5.266A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.615A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.391A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.011A 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: 5.292A 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 Processing helix chain 'F' and resid 232 through 245 removed outlier: 4.889A pdb=" N LEU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 279 removed outlier: 4.803A pdb=" N ASP F 270 " --> pdb=" O LYS F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 293 removed outlier: 4.322A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 318 removed outlier: 6.404A pdb=" N GLU F 305 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL F 306 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG F 308 " --> pdb=" O ARG F 304 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 4.031A pdb=" N LEU F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 339 through 344' Processing helix chain 'F' and resid 358 through 372 removed outlier: 6.481A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 4.332A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.821A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.311A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 4.972A 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: 3.796A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.816A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.862A pdb=" N LEU G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.558A pdb=" N ILE G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 211 through 216' Processing helix chain 'G' and resid 231 through 245 removed outlier: 3.531A pdb=" N ARG G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 12 removed outlier: 4.372A pdb=" N PHE G 9 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP G 10 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG G 11 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS G 12 " --> pdb=" O PHE G 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 12' Processing helix chain 'H' and resid 3 through 10 removed outlier: 5.829A pdb=" N SER H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE H 8 " --> pdb=" O ARG H 4 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER H 9 " --> pdb=" O GLY H 5 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU H 10 " --> pdb=" O TYR H 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3 through 10' Processing helix chain 'H' and resid 19 through 32 removed outlier: 3.770A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 63 removed outlier: 4.883A pdb=" N VAL H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 5.228A 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 removed outlier: 4.233A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 124 removed outlier: 4.115A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 4.866A 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: 3.972A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.626A pdb=" N GLY h 31 " --> pdb=" O ALA h 27 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 102 removed outlier: 3.750A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 124 removed outlier: 3.701A pdb=" N TYR h 121 " --> pdb=" O VAL h 117 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 4.306A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 234 Processing helix chain 'I' and resid 18 through 32 removed outlier: 5.236A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY I 29 " --> pdb=" O MET I 25 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.483A 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: 3.774A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN I 123 " --> pdb=" O GLN I 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.813A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN I 177 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 202 removed outlier: 5.728A pdb=" N ASP I 202 " --> pdb=" O ASN I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 212 removed outlier: 4.056A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.644A 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 249 removed outlier: 4.029A pdb=" N GLN I 235 " --> pdb=" O LYS I 231 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG I 249 " --> pdb=" O ALA I 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 28 removed outlier: 4.175A pdb=" N GLU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 98 Processing helix chain 'J' and resid 103 through 122 removed outlier: 3.735A pdb=" N TYR J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN J 120 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASN J 122 " --> pdb=" O TYR J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.596A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 removed outlier: 4.147A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 199 removed outlier: 3.933A 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 'j' and resid 16 through 30 removed outlier: 5.171A pdb=" N SER j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.607A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.447A 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: 3.605A pdb=" N ILE j 107 " --> pdb=" O THR j 103 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 4.482A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN j 175 " --> pdb=" O PHE j 171 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 182 removed outlier: 4.593A pdb=" N ILE j 181 " --> pdb=" O THR j 177 " (cutoff:3.500A) removed outlier: 4.378A 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: 3.648A pdb=" N THR j 187 " --> pdb=" O THR j 183 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU j 197 " --> pdb=" O LYS j 193 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 201 through 206 removed outlier: 7.286A pdb=" N ASN j 205 " --> pdb=" O SER j 201 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE j 206 " --> pdb=" O GLY j 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 201 through 206' Processing helix chain 'j' and resid 221 through 240 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.764A pdb=" N ASP K 9 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 5 through 10' Processing helix chain 'K' and resid 21 through 35 removed outlier: 3.507A pdb=" N GLU K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 103 removed outlier: 4.327A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 122 removed outlier: 4.185A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.820A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 211 through 216 removed outlier: 4.118A pdb=" N ILE K 215 " --> pdb=" O ASN K 211 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU K 216 " --> pdb=" O ALA K 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 211 through 216' Processing helix chain 'K' and resid 230 through 241 removed outlier: 4.227A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 130 removed outlier: 3.670A pdb=" N ALA K 128 " --> pdb=" O GLU K 125 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP K 129 " --> pdb=" O GLU K 126 " (cutoff:3.500A) Proline residue: K 130 - end of helix No H-bonds generated for 'chain 'K' and resid 125 through 130' Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.941A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 4.646A 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: 4.157A 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 165 through 180 removed outlier: 5.519A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.922A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 4.303A pdb=" N VAL L 210 " --> pdb=" O THR L 206 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER L 211 " --> pdb=" O THR L 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 206 through 211' Processing helix chain 'L' and resid 225 through 237 removed outlier: 3.888A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 3.513A pdb=" N GLU L 234 " --> pdb=" O SER L 230 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 9 removed outlier: 4.004A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP L 9 " --> pdb=" O TYR L 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.812A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.775A 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 125 removed outlier: 4.031A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 180 removed outlier: 3.581A pdb=" N ALA M 172 " --> pdb=" O ALA M 168 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLN M 180 " --> pdb=" O ILE M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 202 removed outlier: 4.627A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 removed outlier: 3.537A pdb=" N LEU M 243 " --> pdb=" O ALA M 239 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS M 244 " --> pdb=" O LYS M 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 91 removed outlier: 3.527A pdb=" N TYR N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.552A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (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: 3.520A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.933A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 removed outlier: 3.557A pdb=" N ASN O 165 " --> pdb=" O ALA O 161 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.717A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.860A 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: 3.688A pdb=" N TYR P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 4.060A 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: 4.366A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 153 removed outlier: 4.296A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 3.950A pdb=" N GLU P 165 " --> pdb=" O ASP P 161 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP P 176 " --> pdb=" O LEU P 172 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 5.194A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.939A 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: 4.264A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 153 removed outlier: 3.832A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.171A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 72 removed outlier: 3.842A pdb=" N THR Q 53 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 93 removed outlier: 3.880A pdb=" N CYS Q 91 " --> pdb=" O ASN Q 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU Q 92 " --> pdb=" O LEU Q 88 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.549A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 5.436A 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 49 through 72 removed outlier: 3.738A pdb=" N THR q 53 " --> pdb=" O GLU q 49 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 93 removed outlier: 4.041A pdb=" N CYS q 91 " --> pdb=" O ASN q 87 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU q 92 " --> pdb=" O LEU q 88 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.578A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.593A 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: 3.883A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.987A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG R 141 " --> pdb=" O GLY R 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY R 142 " --> pdb=" O VAL R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 201 removed outlier: 4.389A 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: 3.992A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.954A pdb=" N GLY r 137 " --> pdb=" O VAL r 133 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL r 138 " --> pdb=" O TYR r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 removed outlier: 3.740A pdb=" N ALA r 152 " --> pdb=" O GLU r 148 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR r 153 " --> pdb=" O VAL r 149 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP r 154 " --> pdb=" O GLU r 150 " (cutoff:3.500A) 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 101 removed outlier: 3.855A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N PHE S 101 " --> pdb=" O TYR S 97 " (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: 4.460A pdb=" N GLU S 184 " --> pdb=" O ILE S 180 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP S 186 " --> pdb=" O ALA S 182 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 79 removed outlier: 3.552A pdb=" N THR s 63 " --> pdb=" O GLY s 59 " (cutoff:3.500A) Processing helix chain 's' and resid 84 through 101 removed outlier: 3.965A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE s 101 " --> pdb=" O TYR s 97 " (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: 4.094A pdb=" N GLU s 184 " --> pdb=" O ILE s 180 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 4.190A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 Processing helix chain 'T' and resid 140 through 158 removed outlier: 4.327A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.788A 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 210 through 216 removed outlier: 4.432A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER T 216 " --> pdb=" O ALA T 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 210 through 216' Processing helix chain 't' and resid 56 through 78 removed outlier: 3.587A pdb=" N PHE t 60 " --> pdb=" O ASP t 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.621A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 158 removed outlier: 4.563A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 5.053A 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 210 through 216 removed outlier: 4.650A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER t 216 " --> pdb=" O ALA t 212 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 210 through 216' Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.942A pdb=" N ALA g 28 " --> pdb=" O GLN g 24 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE g 29 " --> pdb=" O VAL g 25 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS g 30 " --> pdb=" O GLU g 26 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.233A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.136A 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: 3.984A pdb=" N TYR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR g 126 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN g 127 " --> pdb=" O GLN g 123 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN g 128 " --> pdb=" O VAL g 124 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 4.289A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 3.607A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 211 through 216 removed outlier: 4.346A pdb=" N ILE g 215 " --> pdb=" O LYS g 211 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU g 216 " --> pdb=" O PRO g 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 211 through 216' Processing helix chain 'g' and resid 231 through 245 removed outlier: 3.747A pdb=" N ARG g 245 " --> pdb=" O ALA g 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 7 removed outlier: 3.517A pdb=" N ASP i 6 " --> pdb=" O SER i 2 " (cutoff:3.500A) removed outlier: 6.088A 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: 3.916A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.591A pdb=" N ALA i 83 " --> pdb=" O ILE i 79 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN i 84 " --> pdb=" O THR i 80 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL i 85 " --> pdb=" O SER i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.531A pdb=" N LEU i 110 " --> pdb=" O PRO i 106 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE i 124 " --> pdb=" O ALA i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 removed outlier: 3.535A pdb=" N GLN i 177 " --> pdb=" O SER i 173 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 202 removed outlier: 3.613A pdb=" N ALA i 189 " --> pdb=" O THR i 185 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET i 201 " --> pdb=" O LEU i 197 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP i 202 " --> pdb=" O ASN i 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 229 through 251 removed outlier: 3.852A pdb=" N LYS i 251 " --> pdb=" O ALA i 247 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 34 removed outlier: 3.550A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.798A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 4.019A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.757A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL k 184 " --> pdb=" O SER k 180 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 removed outlier: 3.631A pdb=" N ALA k 194 " --> pdb=" O THR k 190 " (cutoff:3.500A) Processing helix chain 'k' and resid 211 through 216 removed outlier: 4.350A pdb=" N ILE k 215 " --> pdb=" O ASN k 211 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLU k 216 " --> pdb=" O ALA k 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 211 through 216' Processing helix chain 'k' and resid 230 through 241 removed outlier: 3.866A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 65 removed outlier: 3.571A pdb=" N SER k 63 " --> pdb=" O GLU k 60 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU k 65 " --> pdb=" O SER k 62 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 4.003A pdb=" N LYS l 30 " --> pdb=" O MET l 26 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 removed outlier: 3.505A pdb=" N ALA l 81 " --> pdb=" O LEU l 77 " (cutoff:3.500A) Processing helix chain 'l' and resid 104 through 123 removed outlier: 4.039A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix removed outlier: 6.467A pdb=" N TYR l 123 " --> pdb=" O PRO l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 164 through 180 removed outlier: 4.538A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 4.076A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 4.113A 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 234 removed outlier: 3.799A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 4.323A pdb=" N GLU l 234 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 33 removed outlier: 3.860A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 5.097A 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: 4.195A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 3.754A pdb=" N GLU m 177 " --> pdb=" O LYS m 173 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 201 removed outlier: 4.003A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS m 201 " --> pdb=" O ILE m 197 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 removed outlier: 3.641A pdb=" N LYS m 244 " --> pdb=" O LYS m 240 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 71 Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.572A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.800A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.572A 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 'x' and resid 25 through 37 removed outlier: 3.979A pdb=" N PHE x 29 " --> pdb=" O PRO x 25 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 45 removed outlier: 3.642A pdb=" N GLN x 44 " --> pdb=" O GLN x 40 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS x 45 " --> pdb=" O PRO x 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 40 through 45' Processing helix chain 'x' and resid 93 through 102 removed outlier: 3.775A pdb=" N LEU x 97 " --> pdb=" O THR x 93 " (cutoff:3.500A) Processing helix chain 'x' and resid 113 through 127 removed outlier: 3.677A pdb=" N VAL x 126 " --> pdb=" O CYS x 122 " (cutoff:3.500A) Proline residue: x 127 - end of helix Processing helix chain 'x' and resid 128 through 137 removed outlier: 5.032A pdb=" N ALA x 137 " --> pdb=" O LEU x 133 " (cutoff:3.500A) Processing helix chain 'x' and resid 147 through 167 removed outlier: 3.910A pdb=" N TYR x 151 " --> pdb=" O ALA x 147 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA x 154 " --> pdb=" O GLN x 150 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP x 164 " --> pdb=" O PHE x 160 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS x 165 " --> pdb=" O ASP x 161 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER x 167 " --> pdb=" O MET x 163 " (cutoff:3.500A) Processing helix chain 'x' and resid 172 through 184 Proline residue: x 184 - end of helix Processing helix chain 'x' and resid 199 through 213 removed outlier: 3.598A pdb=" N CYS x 203 " --> pdb=" O ASP x 199 " (cutoff:3.500A) Processing helix chain 'x' and resid 220 through 227 removed outlier: 4.371A pdb=" N LYS x 224 " --> pdb=" O ASP x 220 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR x 226 " --> pdb=" O SER x 222 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP x 227 " --> pdb=" O VAL x 223 " (cutoff:3.500A) Processing helix chain 'x' and resid 241 through 248 Processing helix chain 'x' and resid 285 through 296 removed outlier: 3.830A pdb=" N GLN x 295 " --> pdb=" O LYS x 291 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLU x 296 " --> pdb=" O LEU x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 360 through 372 removed outlier: 3.625A pdb=" N PHE x 370 " --> pdb=" O LYS x 366 " (cutoff:3.500A) Processing helix chain 'x' and resid 374 through 385 removed outlier: 4.791A pdb=" N GLU x 378 " --> pdb=" O PHE x 374 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN x 383 " --> pdb=" O ASP x 379 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN x 384 " --> pdb=" O LYS x 380 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN x 385 " --> pdb=" O LYS x 381 " (cutoff:3.500A) Processing helix chain 'x' and resid 459 through 467 removed outlier: 4.202A pdb=" N SER x 467 " --> pdb=" O ILE x 463 " (cutoff:3.500A) Processing helix chain 'y' and resid 22 through 34 Processing helix chain 'y' and resid 55 through 60 removed outlier: 3.975A pdb=" N TYR y 59 " --> pdb=" O THR y 55 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN y 60 " --> pdb=" O LEU y 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 55 through 60' Processing helix chain 'C' and resid 11 through 68 removed outlier: 3.559A pdb=" N LYS C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 171 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 179 removed outlier: 3.570A pdb=" N GLU C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 removed outlier: 4.883A pdb=" N ASP C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 242 removed outlier: 6.676A pdb=" N ALA C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 280 Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.919A pdb=" N ARG C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.877A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 374 removed outlier: 7.016A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.626A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 removed outlier: 3.631A pdb=" N SER C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU C 396 " --> pdb=" O GLN C 392 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 397' Processing helix chain 'C' and resid 400 through 406 removed outlier: 3.815A pdb=" N LEU C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS C 406 " --> pdb=" O LYS C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 406' Processing helix chain 'D' and resid 44 through 83 removed outlier: 3.724A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.782A pdb=" N LEU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 5.567A 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 144 through 149 removed outlier: 4.409A pdb=" N ASP D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 149' Processing helix chain 'D' and resid 170 through 187 removed outlier: 3.645A pdb=" N LYS D 174 " --> pdb=" O MET D 170 " (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 224 removed outlier: 3.519A pdb=" N ALA D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.888A pdb=" N ARG D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.802A pdb=" N ILE D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N THR D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 299 removed outlier: 3.526A pdb=" N ARG D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.797A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 5.268A 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 337 through 352 Processing helix chain 'D' and resid 359 through 367 removed outlier: 4.539A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 4.416A 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 Processing helix chain 'D' and resid 395 through 404 removed outlier: 3.632A pdb=" N LYS D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 14 removed outlier: 3.821A pdb=" N LEU U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP U 13 " --> pdb=" O ILE U 9 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU U 14 " --> pdb=" O SER U 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 7 through 14' Processing helix chain 'U' and resid 16 through 35 removed outlier: 4.114A pdb=" N LYS U 26 " --> pdb=" O PHE U 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU U 27 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASN U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP U 35 " --> pdb=" O VAL U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 42 removed outlier: 4.248A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 52 removed outlier: 5.300A pdb=" N GLU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 Processing helix chain 'U' and resid 86 through 91 removed outlier: 4.638A pdb=" N VAL U 90 " --> pdb=" O ASP U 86 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 86 through 91' Processing helix chain 'U' and resid 94 through 119 removed outlier: 3.599A pdb=" N LEU U 118 " --> pdb=" O GLU U 114 " (cutoff:3.500A) Proline residue: U 119 - end of helix Processing helix chain 'U' and resid 127 through 145 removed outlier: 3.616A pdb=" N GLU U 131 " --> pdb=" O ASP U 127 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N HIS U 145 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 158 removed outlier: 4.003A pdb=" N ILE U 151 " --> pdb=" O TYR U 147 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU U 156 " --> pdb=" O GLY U 152 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR U 157 " --> pdb=" O ILE U 153 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 170 removed outlier: 4.454A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU U 164 " --> pdb=" O LEU U 160 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N SER U 170 " --> pdb=" O THR U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 187 removed outlier: 4.184A pdb=" N TYR U 179 " --> pdb=" O GLY U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 192 through 209 removed outlier: 5.097A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL U 197 " --> pdb=" O PHE U 193 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN U 207 " --> pdb=" O LYS U 203 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU U 209 " --> pdb=" O TYR U 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 4.549A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU U 220 " --> pdb=" O VAL U 216 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 3.505A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU U 239 " --> pdb=" O LYS U 235 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 256 Processing helix chain 'U' and resid 258 through 270 removed outlier: 6.359A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR U 270 " --> pdb=" O GLN U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 removed outlier: 3.944A pdb=" N LYS U 324 " --> pdb=" O ASP U 320 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 346 Processing helix chain 'U' and resid 349 through 360 Processing helix chain 'U' and resid 364 through 378 removed outlier: 3.638A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS U 377 " --> pdb=" O ASN U 373 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 390 removed outlier: 5.184A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU U 390 " --> pdb=" O LEU U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 391 through 397 removed outlier: 4.037A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR U 397 " --> pdb=" O LEU U 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 398 through 413 removed outlier: 6.294A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR U 403 " --> pdb=" O TRP U 399 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS U 412 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing helix chain 'U' and resid 418 through 432 removed outlier: 4.542A pdb=" N TYR U 426 " --> pdb=" O LEU U 422 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU U 427 " --> pdb=" O MET U 423 " (cutoff:3.500A) Proline residue: U 428 - end of helix removed outlier: 4.361A pdb=" N THR U 431 " --> pdb=" O LEU U 427 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER U 432 " --> pdb=" O PRO U 428 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 451 removed outlier: 3.857A pdb=" N GLY U 440 " --> pdb=" O ALA U 436 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA U 451 " --> pdb=" O GLY U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 3.955A pdb=" N GLN U 464 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 486 removed outlier: 4.027A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 4.466A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 505 through 521 removed outlier: 4.114A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET U 520 " --> pdb=" O LEU U 516 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU U 521 " --> pdb=" O GLY U 517 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 4.324A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 556 removed outlier: 4.480A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 561 through 573 removed outlier: 4.661A pdb=" N ALA U 565 " --> pdb=" O GLU U 561 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU U 566 " --> pdb=" O GLU U 562 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG U 572 " --> pdb=" O GLU U 568 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.765A pdb=" N CYS U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 removed outlier: 4.206A pdb=" N VAL U 607 " --> pdb=" O LEU U 603 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP U 609 " --> pdb=" O VAL U 605 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 627 removed outlier: 4.116A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 643 removed outlier: 3.608A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 3.967A pdb=" N VAL U 637 " --> pdb=" O CYS U 633 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER U 638 " --> pdb=" O PRO U 634 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 removed outlier: 3.914A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA U 661 " --> pdb=" O GLY U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 677 removed outlier: 6.385A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN U 670 " --> pdb=" O LYS U 666 " (cutoff:3.500A) Proline residue: U 674 - end of helix removed outlier: 4.844A pdb=" N ASN U 677 " --> pdb=" O GLU U 673 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.507A pdb=" N MET U 695 " --> pdb=" O SER U 691 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 704 through 719 removed outlier: 3.833A pdb=" N GLN U 708 " --> pdb=" O PRO U 704 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN U 718 " --> pdb=" O SER U 714 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP U 719 " --> pdb=" O LYS U 715 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 739 Processing helix chain 'U' and resid 756 through 773 removed outlier: 4.244A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TRP U 770 " --> pdb=" O PHE U 766 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE U 771 " --> pdb=" O THR U 767 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP U 772 " --> pdb=" O GLN U 768 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE U 773 " --> pdb=" O PHE U 769 " (cutoff:3.500A) Processing helix chain 'U' and resid 774 through 783 removed outlier: 5.064A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR U 783 " --> pdb=" O LEU U 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 774 through 783' Processing helix chain 'U' and resid 835 through 851 removed outlier: 4.638A pdb=" N ALA U 839 " --> pdb=" O ILE U 835 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS U 849 " --> pdb=" O GLU U 845 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU U 850 " --> pdb=" O LYS U 846 " (cutoff:3.500A) Processing helix chain 'U' and resid 864 through 872 removed outlier: 5.680A pdb=" N LYS U 868 " --> pdb=" O GLU U 864 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU U 870 " --> pdb=" O GLU U 866 " (cutoff:3.500A) Proline residue: U 871 - end of helix Processing helix chain 'U' and resid 885 through 892 removed outlier: 3.931A pdb=" N VAL U 891 " --> pdb=" O ALA U 887 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 36 Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 40 through 58 removed outlier: 3.738A pdb=" N ILE W 44 " --> pdb=" O LEU W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 78 removed outlier: 3.889A pdb=" N THR W 63 " --> pdb=" O ASP W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 94 removed outlier: 4.167A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG W 94 " --> pdb=" O LEU W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 115 removed outlier: 3.859A pdb=" N VAL W 101 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU W 114 " --> pdb=" O THR W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 133 removed outlier: 3.527A pdb=" N THR W 132 " --> pdb=" O LEU W 128 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU W 133 " --> pdb=" O ARG W 129 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 156 removed outlier: 4.939A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 176 removed outlier: 4.394A pdb=" N ALA W 162 " --> pdb=" O ASP W 158 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU W 169 " --> pdb=" O ILE W 165 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 197 removed outlier: 4.227A pdb=" N VAL W 183 " --> pdb=" O LYS W 179 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 212 removed outlier: 4.168A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS W 212 " --> pdb=" O LYS W 208 " (cutoff:3.500A) Processing helix chain 'W' and resid 221 through 238 removed outlier: 4.017A pdb=" N LYS W 225 " --> pdb=" O LYS W 221 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU W 233 " --> pdb=" O LEU W 229 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 258 removed outlier: 5.159A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS W 244 " --> pdb=" O TYR W 240 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 5.060A 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 277 removed outlier: 3.667A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 292 removed outlier: 5.012A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 295 through 300 removed outlier: 4.979A pdb=" N ILE W 299 " --> pdb=" O LYS W 295 " (cutoff:3.500A) Proline residue: W 300 - end of helix No H-bonds generated for 'chain 'W' and resid 295 through 300' Processing helix chain 'W' and resid 301 through 310 removed outlier: 3.774A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR W 310 " --> pdb=" O LEU W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 324 removed outlier: 4.262A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR W 324 " --> pdb=" O LEU W 320 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 330 removed outlier: 3.982A pdb=" N ARG W 329 " --> pdb=" O GLY W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 344 through 370 removed outlier: 3.772A pdb=" N GLU W 348 " --> pdb=" O THR W 344 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS W 368 " --> pdb=" O ARG W 364 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 removed outlier: 3.923A pdb=" N MET W 378 " --> pdb=" O THR W 374 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 400 removed outlier: 3.772A pdb=" N ASN W 399 " --> pdb=" O ASN W 395 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 456 Processing helix chain 'X' and resid 44 through 61 removed outlier: 3.806A pdb=" N GLN X 48 " --> pdb=" O GLN X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 removed outlier: 4.693A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 80 removed outlier: 4.226A pdb=" N ILE X 80 " --> pdb=" O PHE X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 100 removed outlier: 3.506A pdb=" N ALA X 85 " --> pdb=" O SER X 81 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU X 100 " --> pdb=" O PHE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 removed outlier: 3.597A pdb=" N GLU X 106 " --> pdb=" O ALA X 102 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 141 Processing helix chain 'X' and resid 143 through 161 removed outlier: 4.387A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 4.891A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 199 removed outlier: 5.310A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 222 removed outlier: 4.037A pdb=" N ALA X 208 " --> pdb=" O PRO X 204 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR X 209 " --> pdb=" O LYS X 205 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.526A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP X 240 " --> pdb=" O PHE X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 3.775A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 273 removed outlier: 4.440A pdb=" N VAL X 267 " --> pdb=" O THR X 263 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA X 269 " --> pdb=" O GLU X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 274 through 280 Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.511A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 317 through 340 removed outlier: 5.899A pdb=" N THR X 321 " --> pdb=" O PRO X 317 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 Processing helix chain 'X' and resid 357 through 372 removed outlier: 4.175A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP X 371 " --> pdb=" O GLN X 367 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS X 372 " --> pdb=" O MET X 368 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 408 removed outlier: 3.913A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) Processing helix chain 'X' and resid 410 through 420 removed outlier: 4.769A pdb=" N LEU X 414 " --> pdb=" O VAL X 410 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS X 417 " --> pdb=" O SER X 413 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA X 418 " --> pdb=" O LEU X 414 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS X 420 " --> pdb=" O ASN X 416 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 28 Proline residue: Y 15 - end of helix removed outlier: 3.735A pdb=" N ARG Y 18 " --> pdb=" O ASN Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 45 removed outlier: 4.872A pdb=" N ARG Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 58 removed outlier: 3.811A pdb=" N TYR Y 54 " --> pdb=" O MET Y 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS Y 58 " --> pdb=" O TYR Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 92 removed outlier: 5.993A pdb=" N LEU Y 69 " --> pdb=" O ILE Y 65 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU Y 92 " --> pdb=" O LEU Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 114 removed outlier: 4.032A pdb=" N ASP Y 102 " --> pdb=" O SER Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 131 removed outlier: 3.934A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 Processing helix chain 'Y' and resid 153 through 167 Processing helix chain 'Y' and resid 174 through 188 removed outlier: 4.089A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG Y 179 " --> pdb=" O ASP Y 175 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS Y 181 " --> pdb=" O ARG Y 177 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL Y 182 " --> pdb=" O ASN Y 178 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN Y 184 " --> pdb=" O LEU Y 180 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY Y 185 " --> pdb=" O LYS Y 181 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU Y 186 " --> pdb=" O VAL Y 182 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR Y 187 " --> pdb=" O TYR Y 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 203 removed outlier: 5.097A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP Y 203 " --> pdb=" O GLU Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 4.063A pdb=" N PHE Y 219 " --> pdb=" O ASP Y 215 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 240 removed outlier: 3.507A pdb=" N LYS Y 239 " --> pdb=" O ASP Y 235 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL Y 240 " --> pdb=" O LEU Y 236 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'Y' and resid 267 through 283 removed outlier: 4.193A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) Processing helix chain 'Y' and resid 295 through 309 removed outlier: 5.133A pdb=" N MET Y 299 " --> pdb=" O TYR Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 323 removed outlier: 4.153A pdb=" N MET Y 319 " --> pdb=" O THR Y 315 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 Processing helix chain 'Y' and resid 360 through 388 removed outlier: 4.531A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 28 removed outlier: 6.370A pdb=" N LEU Z 17 " --> pdb=" O PRO Z 13 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER Z 18 " --> pdb=" O LEU Z 14 " (cutoff:3.500A) removed outlier: 4.331A 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: 4.880A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 3.625A 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 167 through 177 removed outlier: 4.006A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 218 removed outlier: 3.588A pdb=" N GLY Z 218 " --> pdb=" O LYS Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 225 through 237 removed outlier: 4.804A pdb=" N GLN Z 229 " --> pdb=" O GLN Z 225 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU Z 230 " --> pdb=" O ILE Z 226 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN Z 231 " --> pdb=" O ILE Z 227 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE Z 234 " --> pdb=" O LEU Z 230 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 249 removed outlier: 4.154A pdb=" N VAL Z 246 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 290 removed outlier: 3.587A pdb=" N ALA Z 263 " --> pdb=" O VAL Z 259 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY Z 290 " --> pdb=" O GLU Z 286 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 14 removed outlier: 3.747A pdb=" N LEU a 8 " --> pdb=" O VAL a 4 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER a 14 " --> pdb=" O GLN a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 32 removed outlier: 4.245A pdb=" N VAL a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS a 31 " --> pdb=" O GLU a 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS a 32 " --> pdb=" O LEU a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 5.058A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN a 46 " --> pdb=" O LEU a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 Processing helix chain 'a' and resid 72 through 88 removed outlier: 4.930A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL a 83 " --> pdb=" O ILE a 79 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR a 88 " --> pdb=" O VAL a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 105 removed outlier: 4.217A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 126 removed outlier: 4.401A pdb=" N ILE a 112 " --> pdb=" O ASP a 108 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE a 125 " --> pdb=" O LEU a 121 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY a 126 " --> pdb=" O LYS a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 143 removed outlier: 4.069A pdb=" N VAL a 138 " --> pdb=" O THR a 134 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N MET a 141 " --> pdb=" O ASP a 137 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU a 142 " --> pdb=" O VAL a 138 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 163 removed outlier: 6.095A pdb=" N HIS a 152 " --> pdb=" O VAL a 148 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR a 163 " --> pdb=" O SER a 159 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 184 removed outlier: 4.973A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 5.184A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 220 removed outlier: 6.921A pdb=" N MET a 218 " --> pdb=" O GLY a 214 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N HIS a 219 " --> pdb=" O GLU a 215 " (cutoff:3.500A) Proline residue: a 220 - end of helix No H-bonds generated for 'chain 'a' and resid 214 through 220' Processing helix chain 'a' and resid 221 through 227 removed outlier: 5.579A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.228A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.631A pdb=" N TRP a 255 " --> pdb=" O LEU a 251 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN a 257 " --> pdb=" O THR a 253 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 283 removed outlier: 4.698A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET a 280 " --> pdb=" O CYS a 276 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR a 281 " --> pdb=" O LEU a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 292 through 301 Processing helix chain 'a' and resid 304 through 318 removed outlier: 4.867A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 376 removed outlier: 4.470A pdb=" N MET a 349 " --> pdb=" O GLN a 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP a 359 " --> pdb=" O PHE a 355 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER a 362 " --> pdb=" O THR a 358 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 68 through 76 removed outlier: 4.192A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 4.545A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG b 100 " --> pdb=" O ALA b 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 Processing helix chain 'b' and resid 150 through 162 Processing helix chain 'b' and resid 179 through 185 removed outlier: 3.533A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 18 removed outlier: 3.807A pdb=" N ARG b 17 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 49 removed outlier: 3.627A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 103 removed outlier: 3.880A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 146 through 151 removed outlier: 3.676A pdb=" N SER c 150 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL c 151 " --> pdb=" O PRO c 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 146 through 151' Processing helix chain 'c' and resid 166 through 171 removed outlier: 3.911A pdb=" N GLY c 171 " --> pdb=" O MET c 167 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 185 removed outlier: 5.676A pdb=" N LEU c 184 " --> pdb=" O ASN c 180 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN c 185 " --> pdb=" O LEU c 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 185' Processing helix chain 'c' and resid 188 through 194 Processing helix chain 'c' and resid 195 through 201 removed outlier: 4.425A pdb=" N HIS c 199 " --> pdb=" O GLY c 195 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR c 200 " --> pdb=" O LEU c 196 " (cutoff:3.500A) Processing helix chain 'c' and resid 212 through 223 removed outlier: 4.756A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS c 223 " --> pdb=" O ASN c 219 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 260 Processing helix chain 'c' and resid 266 through 275 removed outlier: 4.396A pdb=" N LEU c 270 " --> pdb=" O THR c 266 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS c 273 " --> pdb=" O GLN c 269 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 310 removed outlier: 3.747A pdb=" N PHE c 309 " --> pdb=" O ASP c 305 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 29 removed outlier: 4.337A pdb=" N GLU d 21 " --> pdb=" O SER d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 66 Processing helix chain 'd' and resid 67 through 84 removed outlier: 3.923A pdb=" N ASP d 84 " --> pdb=" O CYS d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 110 removed outlier: 3.752A pdb=" N LEU d 98 " --> pdb=" O TYR d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 123 removed outlier: 5.122A pdb=" N PHE d 115 " --> pdb=" O ARG d 111 " (cutoff:3.500A) Proline residue: d 123 - end of helix Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix removed outlier: 3.836A pdb=" N GLU d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 156 removed outlier: 4.922A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 164 through 186 removed outlier: 4.666A pdb=" N ASP d 168 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA d 185 " --> pdb=" O CYS d 181 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR d 186 " --> pdb=" O ILE d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 196 Processing helix chain 'd' and resid 203 through 212 removed outlier: 4.991A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 254 removed outlier: 4.404A pdb=" N SER d 239 " --> pdb=" O THR d 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 11 Proline residue: f 10 - end of helix No H-bonds generated for 'chain 'f' and resid 6 through 11' Processing helix chain 'f' and resid 12 through 24 Proline residue: f 17 - end of helix Proline residue: f 21 - end of helix Processing helix chain 'f' and resid 27 through 49 removed outlier: 4.901A pdb=" N ARG f 34 " --> pdb=" O GLY f 30 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU f 48 " --> pdb=" O GLU f 44 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP f 49 " --> pdb=" O LEU f 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 59 Processing helix chain 'f' and resid 62 through 75 removed outlier: 5.448A pdb=" N LYS f 66 " --> pdb=" O ARG f 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR f 68 " --> pdb=" O GLY f 64 " (cutoff:3.500A) Proline residue: f 73 - end of helix Processing helix chain 'f' and resid 80 through 91 removed outlier: 4.411A pdb=" N SER f 84 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 removed outlier: 4.392A pdb=" N LYS f 97 " --> pdb=" O PRO f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 104 Processing helix chain 'f' and resid 106 through 111 removed outlier: 3.602A pdb=" N GLU f 111 " --> pdb=" O LYS f 107 " (cutoff:3.500A) Processing helix chain 'f' and resid 115 through 123 removed outlier: 5.691A pdb=" N LYS f 119 " --> pdb=" O PRO f 115 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG f 120 " --> pdb=" O GLY f 116 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N PHE f 121 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA f 122 " --> pdb=" O ASN f 118 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 148 removed outlier: 5.691A pdb=" N THR f 132 " --> pdb=" O VAL f 128 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET f 133 " --> pdb=" O LEU f 129 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU f 136 " --> pdb=" O THR f 132 " (cutoff:3.500A) Processing helix chain 'f' and resid 153 through 170 Processing helix chain 'f' and resid 176 through 182 removed outlier: 4.177A pdb=" N GLN f 180 " --> pdb=" O ALA f 176 " (cutoff:3.500A) Processing helix chain 'f' and resid 193 through 208 removed outlier: 4.256A pdb=" N ALA f 197 " --> pdb=" O PRO f 193 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN f 199 " --> pdb=" O ASN f 195 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA f 200 " --> pdb=" O MET f 196 " (cutoff:3.500A) Processing helix chain 'f' and resid 209 through 227 removed outlier: 4.593A pdb=" N GLN f 213 " --> pdb=" O MET f 209 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL f 214 " --> pdb=" O GLU f 210 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP f 215 " --> pdb=" O ILE f 211 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR f 226 " --> pdb=" O ASP f 222 " (cutoff:3.500A) Processing helix chain 'f' and resid 231 through 236 removed outlier: 3.987A pdb=" N SER f 235 " --> pdb=" O LEU f 231 " (cutoff:3.500A) Processing helix chain 'f' and resid 237 through 246 Proline residue: f 241 - end of helix removed outlier: 5.198A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN f 245 " --> pdb=" O PRO f 241 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER f 246 " --> pdb=" O GLU f 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 237 through 246' Processing helix chain 'f' and resid 253 through 264 removed outlier: 3.724A pdb=" N ARG f 257 " --> pdb=" O LEU f 253 " (cutoff:3.500A) removed outlier: 3.938A 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 268 through 275 removed outlier: 4.189A pdb=" N MET f 275 " --> pdb=" O MET f 271 " (cutoff:3.500A) Processing helix chain 'f' and resid 279 through 285 removed outlier: 4.652A pdb=" N THR f 283 " --> pdb=" O GLU f 279 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS f 285 " --> pdb=" O ILE f 281 " (cutoff:3.500A) Processing helix chain 'f' and resid 286 through 294 removed outlier: 3.907A pdb=" N VAL f 290 " --> pdb=" O LYS f 286 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 295 through 304 removed outlier: 4.023A pdb=" N GLY f 299 " --> pdb=" O ALA f 295 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N HIS f 301 " --> pdb=" O MET f 297 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLY f 302 " --> pdb=" O LEU f 298 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL f 303 " --> pdb=" O GLY f 299 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE f 304 " --> pdb=" O ARG f 300 " (cutoff:3.500A) Processing helix chain 'f' and resid 313 through 318 removed outlier: 3.747A pdb=" N LEU f 317 " --> pdb=" O GLU f 313 " (cutoff:3.500A) Processing helix chain 'f' and resid 325 through 336 removed outlier: 4.080A pdb=" N ASN f 329 " --> pdb=" O GLN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 347 through 354 removed outlier: 4.230A pdb=" N LEU f 353 " --> pdb=" O TYR f 349 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU f 354 " --> pdb=" O LYS f 350 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 383 Processing helix chain 'f' and resid 395 through 402 removed outlier: 4.544A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 403 through 419 removed outlier: 4.157A pdb=" N LEU f 408 " --> pdb=" O ASP f 404 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER f 409 " --> pdb=" O HIS f 405 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 423 through 436 removed outlier: 4.020A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER f 435 " --> pdb=" O LYS f 431 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER f 436 " --> pdb=" O TYR f 432 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 456 removed outlier: 3.565A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY f 454 " --> pdb=" O ILE f 450 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL f 455 " --> pdb=" O VAL f 451 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 472 removed outlier: 4.941A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU f 465 " --> pdb=" O PRO f 461 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU f 466 " --> pdb=" O ALA f 462 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER f 467 " --> pdb=" O LEU f 463 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR f 469 " --> pdb=" O LEU f 465 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HIS f 472 " --> pdb=" O ASP f 468 " (cutoff:3.500A) Processing helix chain 'f' and resid 475 through 490 removed outlier: 3.721A pdb=" N ALA f 490 " --> pdb=" O GLY f 486 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 507 removed outlier: 3.848A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 511 through 527 removed outlier: 4.027A pdb=" N ALA f 526 " --> pdb=" O CYS f 522 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 544 removed outlier: 3.731A pdb=" N VAL f 534 " --> pdb=" O CYS f 530 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR f 535 " --> pdb=" O ASN f 531 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER f 536 " --> pdb=" O GLY f 532 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 551 removed outlier: 4.014A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (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 573 through 583 removed outlier: 3.503A pdb=" N LEU f 577 " --> pdb=" O ILE f 573 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA f 579 " --> pdb=" O ALA f 575 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU f 580 " --> pdb=" O ILE f 576 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU f 581 " --> pdb=" O LEU f 577 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL f 583 " --> pdb=" O ALA f 579 " (cutoff:3.500A) Processing helix chain 'f' and resid 588 through 601 removed outlier: 4.003A pdb=" N THR f 593 " --> pdb=" O SER f 589 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 614 removed outlier: 3.750A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) Processing helix chain 'f' and resid 618 through 624 removed outlier: 3.793A pdb=" N SER f 622 " --> pdb=" O GLU f 618 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS f 623 " --> pdb=" O HIS f 619 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU f 624 " --> pdb=" O PHE f 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 618 through 624' Processing helix chain 'f' and resid 642 through 647 removed outlier: 7.081A pdb=" N MET f 646 " --> pdb=" O ALA f 642 " (cutoff:3.500A) Processing helix chain 'f' and resid 648 through 658 Processing helix chain 'f' and resid 671 through 680 removed outlier: 5.140A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU f 679 " --> pdb=" O PHE f 675 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG f 680 " --> pdb=" O GLY f 676 " (cutoff:3.500A) Processing helix chain 'f' and resid 688 through 698 removed outlier: 4.326A pdb=" N LEU f 696 " --> pdb=" O LEU f 692 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE f 697 " --> pdb=" O ALA f 693 " (cutoff:3.500A) Processing helix chain 'f' and resid 701 through 717 removed outlier: 5.545A pdb=" N PHE f 713 " --> pdb=" O THR f 709 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER f 714 " --> pdb=" O LEU f 710 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N HIS f 715 " --> pdb=" O SER f 711 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP f 716 " --> pdb=" O LYS f 712 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA f 717 " --> pdb=" O PHE f 713 " (cutoff:3.500A) Processing helix chain 'f' and resid 725 through 734 removed outlier: 4.747A pdb=" N MET f 729 " --> pdb=" O SER f 725 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL f 732 " --> pdb=" O ALA f 728 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLY f 733 " --> pdb=" O MET f 729 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N SER f 734 " --> pdb=" O GLY f 730 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 753 removed outlier: 3.911A pdb=" N LEU f 745 " --> pdb=" O LEU f 741 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG f 746 " --> pdb=" O ALA f 742 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA f 749 " --> pdb=" O LEU f 745 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN f 750 " --> pdb=" O ARG f 746 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR f 751 " --> pdb=" O GLN f 747 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N HIS f 752 " --> pdb=" O LEU f 748 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA f 753 " --> pdb=" O ALA f 749 " (cutoff:3.500A) Processing helix chain 'f' and resid 771 through 787 removed outlier: 4.517A pdb=" N THR f 775 " --> pdb=" O LEU f 771 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU f 776 " --> pdb=" O GLY f 772 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR f 777 " --> pdb=" O LYS f 773 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS f 779 " --> pdb=" O THR f 775 " (cutoff:3.500A) Proline residue: f 780 - end of helix removed outlier: 4.920A pdb=" N SER f 783 " --> pdb=" O CYS f 779 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP f 784 " --> pdb=" O PRO f 780 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG f 785 " --> pdb=" O TYR f 781 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU f 787 " --> pdb=" O SER f 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 771 through 787' Processing helix chain 'f' and resid 797 through 803 removed outlier: 4.877A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER f 802 " --> pdb=" O THR f 798 " (cutoff:3.500A) removed outlier: 4.851A 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 'V' and resid 54 through 89 Processing helix chain 'V' and resid 91 through 108 Proline residue: V 102 - end of helix removed outlier: 4.198A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG V 107 " --> pdb=" O SER V 103 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU V 108 " --> pdb=" O THR V 104 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 122 removed outlier: 4.324A pdb=" N THR V 122 " --> pdb=" O GLN V 118 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.760A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix removed outlier: 5.275A pdb=" N GLU V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 158 removed outlier: 3.567A pdb=" N THR V 157 " --> pdb=" O LYS V 153 " (cutoff:3.500A) Proline residue: V 158 - end of helix Processing helix chain 'V' and resid 160 through 179 Processing helix chain 'V' and resid 181 through 199 removed outlier: 3.579A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 204 through 222 removed outlier: 3.969A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.271A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 removed outlier: 3.612A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 removed outlier: 4.087A pdb=" N LYS V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 345 through 350 removed outlier: 4.218A pdb=" N GLN V 350 " --> pdb=" O LEU V 346 " (cutoff:3.500A) 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: 3.690A 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: 3.844A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 3.929A pdb=" N ILE V 422 " --> pdb=" O SER V 418 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA V 423 " --> pdb=" O LEU V 419 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN V 424 " --> pdb=" O ALA V 420 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 removed outlier: 3.742A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 494 removed outlier: 4.679A pdb=" N THR V 469 " --> pdb=" O ASP V 465 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG V 470 " --> pdb=" O ILE V 466 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 5.158A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE V 480 " --> pdb=" O PHE V 476 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER V 481 " --> pdb=" O HIS V 477 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 64 removed outlier: 4.956A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 removed outlier: 4.120A pdb=" N ASP e 46 " --> pdb=" O TRP e 43 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 96 through 100 removed outlier: 6.518A pdb=" N GLY A 141 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN A 148 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 111 through 114 removed outlier: 3.836A pdb=" N TYR A 111 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 212 through 216 Processing sheet with id= 4, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.561A pdb=" N ASP A 275 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS A 316 " --> pdb=" O CYS A 270 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 114 through 117 removed outlier: 3.564A pdb=" N GLU B 114 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER B 108 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU B 151 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 110 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER B 149 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU B 112 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 220 through 225 removed outlier: 6.737A pdb=" N LYS B 220 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 327 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 222 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 280 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 326 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 330 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 119 through 125 removed outlier: 6.177A pdb=" N ASN B 119 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 68 through 72 removed outlier: 3.604A pdb=" N VAL E 81 " --> pdb=" O PHE E 69 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 194 through 198 removed outlier: 5.994A pdb=" N ASN E 194 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS E 228 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 274 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA E 278 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS E 168 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET E 275 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 88 through 92 removed outlier: 3.524A pdb=" N SER F 91 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY F 152 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU F 159 " --> pdb=" O ASN F 154 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 95 through 99 removed outlier: 3.745A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 122 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 246 through 252 removed outlier: 3.823A pdb=" N LYS F 327 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 350 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE F 354 " --> pdb=" O TYR F 226 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.741A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET G 80 " --> pdb=" O HIS G 68 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET G 138 " --> pdb=" O CYS G 154 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.026A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.541A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS H 71 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.685A pdb=" N GLU H 49 " --> pdb=" O PRO H 34 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ASN H 207 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.555A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS h 71 " --> pdb=" O TRP h 139 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'h' and resid 160 through 164 removed outlier: 3.719A pdb=" N GLU h 49 " --> pdb=" O PRO h 34 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN h 207 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 64 through 68 removed outlier: 6.607A pdb=" N LYS I 64 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 161 through 165 removed outlier: 5.072A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.507A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASN J 68 " --> pdb=" O PHE J 136 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE J 136 " --> pdb=" O ASN J 68 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 158 through 162 removed outlier: 5.321A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'j' and resid 62 through 65 removed outlier: 6.218A pdb=" N VAL j 69 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN j 68 " --> pdb=" O PHE j 136 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'j' and resid 158 through 162 removed outlier: 5.320A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY j 44 " --> pdb=" O VAL j 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL j 42 " --> pdb=" O VAL j 35 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU j 208 " --> pdb=" O LEU j 220 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 67 through 70 removed outlier: 6.579A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N HIS K 73 " --> pdb=" O VAL K 146 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR K 161 " --> pdb=" O ASP K 157 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 166 through 171 removed outlier: 6.541A pdb=" N ASP K 166 " --> pdb=" O GLN K 41 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.531A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 158 through 162 removed outlier: 3.892A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 66 through 69 removed outlier: 6.487A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 76 " --> pdb=" O MET M 136 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE M 135 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER M 141 " --> pdb=" O GLY M 145 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 162 through 166 removed outlier: 5.086A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.487A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.438A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER N 18 " --> pdb=" O VAL N 173 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.523A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY O 101 " --> pdb=" O TYR O 42 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.339A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.643A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.206A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 42 through 45 removed outlier: 5.678A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.167A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.904A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'p' and resid 136 through 140 removed outlier: 5.921A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.380A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Q' and resid 129 through 132 removed outlier: 3.904A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.207A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'q' and resid 129 through 132 removed outlier: 6.529A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL q 180 " --> pdb=" O LEU q 191 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU q 191 " --> pdb=" O VAL q 180 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'R' and resid 34 through 37 removed outlier: 6.804A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS R 102 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR R 44 " --> pdb=" O MET R 100 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.262A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL R 174 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER R 189 " --> pdb=" O VAL R 174 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'r' and resid 34 through 37 removed outlier: 3.853A pdb=" N ILE r 35 " --> pdb=" O GLY r 43 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE r 37 " --> pdb=" O LEU r 41 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS r 102 " --> pdb=" O LEU r 42 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR r 44 " --> pdb=" O MET r 100 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.403A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL r 12 " --> pdb=" O VAL r 179 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL r 174 " --> pdb=" O SER r 189 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER r 189 " --> pdb=" O VAL r 174 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.541A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.430A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 's' and resid 43 through 46 removed outlier: 6.650A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 's' and resid 135 through 139 removed outlier: 5.805A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.631A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER T 54 " --> pdb=" O THR T 109 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.219A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 't' and resid 42 through 45 removed outlier: 6.711A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR t 109 " --> pdb=" O SER t 54 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 't' and resid 136 through 139 removed outlier: 4.639A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA t 23 " --> pdb=" O LEU t 12 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 69 through 72 removed outlier: 6.560A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY g 77 " --> pdb=" O ILE g 141 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET g 138 " --> pdb=" O CYS g 154 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'g' and resid 165 through 169 removed outlier: 5.138A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 65 through 68 removed outlier: 6.410A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL i 132 " --> pdb=" O PRO i 152 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN i 149 " --> pdb=" O TYR i 156 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR i 156 " --> pdb=" O GLN i 149 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP i 151 " --> pdb=" O GLY i 154 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'i' and resid 161 through 165 removed outlier: 4.831A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL i 43 " --> pdb=" O LEU i 216 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS i 210 " --> pdb=" O ARG i 49 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 67 through 70 removed outlier: 6.391A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'k' and resid 167 through 171 removed outlier: 5.134A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 63 through 66 removed outlier: 3.681A pdb=" N VAL l 66 " --> pdb=" O ILE l 70 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 158 through 162 removed outlier: 5.322A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE l 212 " --> pdb=" O TYR l 224 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'm' and resid 73 through 79 Processing sheet with id= 66, first strand: chain 'm' and resid 162 through 166 removed outlier: 4.909A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU m 50 " --> pdb=" O THR m 35 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.536A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL n 111 " --> pdb=" O GLN n 123 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.397A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'x' and resid 250 through 255 removed outlier: 6.852A pdb=" N GLU x 250 " --> pdb=" O SER x 318 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS x 316 " --> pdb=" O GLU x 252 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER x 302 " --> pdb=" O GLN x 306 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN x 308 " --> pdb=" O LYS x 300 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS x 300 " --> pdb=" O ASN x 308 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'x' and resid 323 through 327 removed outlier: 3.562A pdb=" N TYR x 480 " --> pdb=" O LEU x 324 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'x' and resid 331 through 335 Processing sheet with id= 72, first strand: chain 'x' and resid 447 through 451 removed outlier: 3.764A pdb=" N SER x 438 " --> pdb=" O PHE x 450 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU x 424 " --> pdb=" O TYR x 476 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE x 474 " --> pdb=" O HIS x 426 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'y' and resid 1 through 4 Processing sheet with id= 74, first strand: chain 'C' and resid 71 through 75 Processing sheet with id= 75, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.864A pdb=" N PHE C 95 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 87 through 91 Processing sheet with id= 77, first strand: chain 'D' and resid 99 through 104 removed outlier: 5.359A pdb=" N ASN D 99 " --> pdb=" O ILE D 115 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 260 through 265 removed outlier: 4.078A pdb=" N VAL D 202 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET D 309 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR D 205 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 333 " --> pdb=" O TYR D 205 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'W' and resid 404 through 408 removed outlier: 3.687A pdb=" N LYS W 405 " --> pdb=" O ASN W 414 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN W 414 " --> pdb=" O LYS W 405 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'X' and resid 376 through 380 Processing sheet with id= 81, first strand: chain 'Y' and resid 345 through 349 Processing sheet with id= 82, first strand: chain 'Z' and resid 35 through 39 removed outlier: 4.985A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY Z 93 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL Z 122 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE Z 124 " --> pdb=" O HIS Z 96 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP Z 125 " --> pdb=" O PRO Z 134 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'Z' and resid 48 through 51 removed outlier: 4.245A pdb=" N LEU Z 48 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL Z 10 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU Z 161 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Z 11 " --> pdb=" O GLU Z 161 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'Z' and resid 58 through 61 No H-bonds generated for sheet with id= 84 Processing sheet with id= 85, first strand: chain 'a' and resid 319 through 325 removed outlier: 6.984A pdb=" N LEU a 319 " --> pdb=" O VAL a 336 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER a 323 " --> pdb=" O HIS a 332 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG a 330 " --> pdb=" O ASP a 325 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'b' and resid 47 through 53 removed outlier: 4.134A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE b 52 " --> pdb=" O VAL b 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE b 112 " --> pdb=" O CYS b 9 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP b 139 " --> pdb=" O ILE b 109 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'c' and resid 65 through 69 removed outlier: 3.984A pdb=" N GLN c 30 " --> pdb=" O TYR c 65 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR c 204 " --> pdb=" O GLU c 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'c' and resid 141 through 145 Processing sheet with id= 89, first strand: chain 'f' and resid 869 through 872 removed outlier: 6.633A pdb=" N GLU f 881 " --> pdb=" O VAL f 872 " (cutoff:3.500A) 5526 hydrogen bonds defined for protein. 16473 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: 44.17 Time building geometry restraints manager: 33.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 27100 1.33 - 1.45: 22159 1.45 - 1.58: 62220 1.58 - 1.70: 15 1.70 - 1.83: 1073 Bond restraints: 112567 Sorted by residual: bond pdb=" CA LEU E 111 " pdb=" C LEU E 111 " ideal model delta sigma weight residual 1.519 1.556 -0.037 9.50e-03 1.11e+04 1.50e+01 bond pdb=" C SER b 186 " pdb=" N PRO b 187 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.46e+01 bond pdb=" C PRO A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.333 1.376 -0.043 1.20e-02 6.94e+03 1.29e+01 bond pdb=" C ILE l 118 " pdb=" N PRO l 119 " ideal model delta sigma weight residual 1.337 1.371 -0.034 9.80e-03 1.04e+04 1.21e+01 bond pdb=" C CYS f 779 " pdb=" N PRO f 780 " ideal model delta sigma weight residual 1.340 1.417 -0.077 2.76e-02 1.31e+03 7.71e+00 ... (remaining 112562 not shown) Histogram of bond angle deviations from ideal: 95.62 - 104.46: 1620 104.46 - 113.29: 61856 113.29 - 122.12: 68222 122.12 - 130.95: 19931 130.95 - 139.79: 422 Bond angle restraints: 152051 Sorted by residual: angle pdb=" N ARG E 113 " pdb=" CA ARG E 113 " pdb=" C ARG E 113 " ideal model delta sigma weight residual 108.45 118.63 -10.18 1.26e+00 6.30e-01 6.53e+01 angle pdb=" C THR W 310 " pdb=" N THR W 311 " pdb=" CA THR W 311 " ideal model delta sigma weight residual 122.08 129.67 -7.59 1.47e+00 4.63e-01 2.67e+01 angle pdb=" N VAL Z 240 " pdb=" CA VAL Z 240 " pdb=" C VAL Z 240 " ideal model delta sigma weight residual 111.88 106.41 5.47 1.06e+00 8.90e-01 2.66e+01 angle pdb=" N ILE p 30 " pdb=" CA ILE p 30 " pdb=" C ILE p 30 " ideal model delta sigma weight residual 110.05 104.62 5.43 1.09e+00 8.42e-01 2.48e+01 angle pdb=" CB MET A 263 " pdb=" CG MET A 263 " pdb=" SD MET A 263 " ideal model delta sigma weight residual 112.70 127.49 -14.79 3.00e+00 1.11e-01 2.43e+01 ... (remaining 152046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 61648 17.92 - 35.85: 5892 35.85 - 53.77: 1011 53.77 - 71.69: 180 71.69 - 89.61: 80 Dihedral angle restraints: 68811 sinusoidal: 27891 harmonic: 40920 Sorted by residual: dihedral pdb=" CA VAL Z 144 " pdb=" C VAL Z 144 " pdb=" N HIS Z 145 " pdb=" CA HIS Z 145 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA VAL g 222 " pdb=" C VAL g 222 " pdb=" N GLU g 223 " pdb=" CA GLU g 223 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PRO G 133 " pdb=" C PRO G 133 " pdb=" N LEU G 134 " pdb=" CA LEU G 134 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 68808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 17043 0.144 - 0.288: 155 0.288 - 0.432: 8 0.432 - 0.576: 0 0.576 - 0.720: 1 Chirality restraints: 17207 Sorted by residual: chirality pdb=" CG LEU Z 176 " pdb=" CB LEU Z 176 " pdb=" CD1 LEU Z 176 " pdb=" CD2 LEU Z 176 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB ILE d 256 " pdb=" CA ILE d 256 " pdb=" CG1 ILE d 256 " pdb=" CG2 ILE d 256 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB VAL W 131 " pdb=" CA VAL W 131 " pdb=" CG1 VAL W 131 " pdb=" CG2 VAL W 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 17204 not shown) Planarity restraints: 19611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 111 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO E 112 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 215 " 0.021 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP m 215 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP m 215 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP m 215 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP m 215 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP m 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP m 215 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 215 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 215 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP m 215 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE W 214 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C PHE W 214 " 0.054 2.00e-02 2.50e+03 pdb=" O PHE W 214 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN W 215 " -0.018 2.00e-02 2.50e+03 ... (remaining 19608 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 155 2.37 - 3.01: 54644 3.01 - 3.64: 171029 3.64 - 4.27: 241782 4.27 - 4.90: 404489 Nonbonded interactions: 872099 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 1.743 2.230 nonbonded pdb=" CG ASP c 126 " pdb="ZN ZN c 401 " model vdw 1.875 2.460 nonbonded pdb=" O LEU i 38 " pdb=" OH TYR i 179 " model vdw 2.228 2.440 nonbonded pdb=" O THR g 190 " pdb=" OG1 THR g 194 " model vdw 2.244 2.440 nonbonded pdb=" O GLN U 632 " pdb=" OG SER U 635 " model vdw 2.247 2.440 ... (remaining 872094 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 6 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 6 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 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 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 name CA or name C or name O or name CB )) or resid 177 through 234)) } ncs_group { reference = (chain 'I' and (resid 4 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 (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 251)) selection = (chain 'i' and (resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 228 or (resid 229 and (name N or na \ me CA or name C or name O or name CB )) or resid 230 or (resid 231 and (name N o \ r name CA or name C or name O or name CB )) or resid 232 through 238 or (resid 2 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 240 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 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 173 or (resid 174 and (name N or na \ me CA or name C or name O or name CB )) or resid 175 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 188 \ or (resid 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 217 or (resid 218 and (name N or name CA or name C or name O or nam \ e CB )) or resid 219 through 240)) } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 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 207 or (resid 208 an \ d (name N or name CA or name C or name O or name CB )) or resid 209 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' and resid 5 through 244) selection = (chain 'm' and (resid 5 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 179 or (resid 180 and (name N or name CA or name \ C or name O or name CB )) or resid 181 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 20 \ 3 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' and (resid 1 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 199)) selection = chain 'q' } ncs_group { reference = (chain 'R' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 88 or (resid 89 and (name N or name C \ A or name C or name O or name CB )) or resid 90 through 201)) selection = chain 'r' } ncs_group { reference = (chain 'S' and (resid 1 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 213)) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 51.380 Check model and map are aligned: 1.200 Set scattering table: 0.760 Process input model: 268.770 Find NCS groups from input model: 6.650 Set up NCS constraints: 0.490 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: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 340.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 0.089 112567 Z= 0.245 Angle : 0.818 14.790 152051 Z= 0.425 Chirality : 0.050 0.720 17207 Planarity : 0.005 0.103 19611 Dihedral : 14.416 89.614 42467 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.98 % Favored : 93.93 % Rotamer: Outliers : 0.18 % Allowed : 0.49 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % 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: -1.19 (0.07), residues: 13990 helix: -0.01 (0.06), residues: 6148 sheet: -0.02 (0.12), residues: 1918 loop : -1.87 (0.08), residues: 5924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP m 215 HIS 0.016 0.001 HIS c 172 PHE 0.038 0.002 PHE D 299 TYR 0.030 0.001 TYR d 249 ARG 0.015 0.000 ARG W 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 465 time to evaluate : 9.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 5 residues processed: 485 average time/residue: 0.9326 time to fit residues: 817.3241 Evaluate side-chains 449 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 444 time to evaluate : 9.408 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.7435 time to fit residues: 19.8341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1390 random chunks: chunk 1173 optimal weight: 9.9990 chunk 1053 optimal weight: 9.9990 chunk 584 optimal weight: 0.7980 chunk 359 optimal weight: 9.9990 chunk 710 optimal weight: 10.0000 chunk 562 optimal weight: 50.0000 chunk 1089 optimal weight: 8.9990 chunk 421 optimal weight: 10.0000 chunk 662 optimal weight: 20.0000 chunk 810 optimal weight: 7.9990 chunk 1262 optimal weight: 10.0000 overall best weight: 7.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN I 220 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 128 ASN k 178 GLN l 143 HIS x 197 GLN x 426 HIS x 473 HIS y 60 ASN C 392 GLN D 48 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 207 ASN U 647 HIS U 670 ASN W 106 GLN W 107 GLN W 228 ASN W 264 GLN ** W 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 144 ASN a 369 HIS ** b 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 238 ASN f 757 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 112567 Z= 0.221 Angle : 0.586 11.750 152051 Z= 0.304 Chirality : 0.042 0.190 17207 Planarity : 0.004 0.083 19611 Dihedral : 5.244 78.555 15434 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.62 % Favored : 94.31 % Rotamer: Outliers : 0.27 % Allowed : 5.80 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.07), residues: 13990 helix: 0.99 (0.07), residues: 6238 sheet: 0.06 (0.12), residues: 1928 loop : -1.73 (0.08), residues: 5824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP m 215 HIS 0.010 0.001 HIS c 172 PHE 0.027 0.001 PHE D 299 TYR 0.026 0.001 TYR Y 295 ARG 0.004 0.000 ARG n 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 446 time to evaluate : 9.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 460 average time/residue: 0.8997 time to fit residues: 746.2955 Evaluate side-chains 457 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 443 time to evaluate : 9.061 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 3 residues processed: 14 average time/residue: 0.7293 time to fit residues: 31.2373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1390 random chunks: chunk 701 optimal weight: 6.9990 chunk 391 optimal weight: 5.9990 chunk 1050 optimal weight: 5.9990 chunk 859 optimal weight: 0.0770 chunk 348 optimal weight: 0.0470 chunk 1264 optimal weight: 6.9990 chunk 1366 optimal weight: 10.0000 chunk 1126 optimal weight: 10.0000 chunk 1254 optimal weight: 0.2980 chunk 431 optimal weight: 20.0000 chunk 1014 optimal weight: 20.0000 overall best weight: 2.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN F 358 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 595 ASN ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 ASN X 416 ASN Y 363 ASN ** b 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 112567 Z= 0.134 Angle : 0.530 10.513 152051 Z= 0.271 Chirality : 0.041 0.174 17207 Planarity : 0.003 0.069 19611 Dihedral : 4.915 76.069 15434 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 0.38 % Allowed : 8.89 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % 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: 0.04 (0.07), residues: 13990 helix: 1.39 (0.07), residues: 6251 sheet: 0.24 (0.12), residues: 1884 loop : -1.61 (0.08), residues: 5855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP m 215 HIS 0.006 0.001 HIS c 172 PHE 0.025 0.001 PHE D 299 TYR 0.024 0.001 TYR Y 295 ARG 0.003 0.000 ARG V 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 445 time to evaluate : 9.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 18 residues processed: 478 average time/residue: 0.9026 time to fit residues: 779.7423 Evaluate side-chains 460 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 442 time to evaluate : 10.819 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 3 residues processed: 18 average time/residue: 0.7792 time to fit residues: 39.2219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1390 random chunks: chunk 1249 optimal weight: 30.0000 chunk 950 optimal weight: 10.0000 chunk 656 optimal weight: 30.0000 chunk 139 optimal weight: 40.0000 chunk 603 optimal weight: 30.0000 chunk 849 optimal weight: 20.0000 chunk 1269 optimal weight: 30.0000 chunk 1343 optimal weight: 9.9990 chunk 663 optimal weight: 30.0000 chunk 1202 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN E 45 ASN F 358 ASN G 12 HIS H 95 GLN H 169 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 163 HIS i 102 GLN l 90 GLN p 72 ASN x 281 GLN ** y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 171 ASN U 665 ASN ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 333 GLN Z 202 ASN ** b 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 790 GLN ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 112567 Z= 0.271 Angle : 0.601 14.448 152051 Z= 0.310 Chirality : 0.042 0.189 17207 Planarity : 0.004 0.065 19611 Dihedral : 5.021 76.716 15434 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.52 % Rotamer: Outliers : 0.67 % Allowed : 11.61 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % 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: 0.02 (0.07), residues: 13990 helix: 1.40 (0.07), residues: 6274 sheet: 0.13 (0.12), residues: 1945 loop : -1.64 (0.08), residues: 5771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP m 215 HIS 0.009 0.001 HIS r 178 PHE 0.023 0.002 PHE D 299 TYR 0.029 0.001 TYR Z 74 ARG 0.011 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 444 time to evaluate : 9.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 28 residues processed: 506 average time/residue: 0.8888 time to fit residues: 819.5037 Evaluate side-chains 469 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 441 time to evaluate : 9.689 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 3 residues processed: 28 average time/residue: 0.7601 time to fit residues: 53.4269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1390 random chunks: chunk 1118 optimal weight: 2.9990 chunk 762 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 1000 optimal weight: 30.0000 chunk 554 optimal weight: 9.9990 chunk 1146 optimal weight: 7.9990 chunk 928 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 686 optimal weight: 9.9990 chunk 1205 optimal weight: 50.0000 chunk 339 optimal weight: 20.0000 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 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 108 ASN h 102 GLN x 281 GLN ** y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 ASN ** b 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 790 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 112567 Z= 0.173 Angle : 0.537 10.734 152051 Z= 0.275 Chirality : 0.041 0.177 17207 Planarity : 0.003 0.056 19611 Dihedral : 4.857 76.071 15434 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 0.59 % Allowed : 13.25 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.07), residues: 13990 helix: 1.57 (0.07), residues: 6292 sheet: 0.23 (0.12), residues: 1910 loop : -1.59 (0.08), residues: 5788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP m 215 HIS 0.007 0.001 HIS c 199 PHE 0.023 0.001 PHE D 299 TYR 0.024 0.001 TYR Y 295 ARG 0.003 0.000 ARG f 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 440 time to evaluate : 9.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 21 residues processed: 492 average time/residue: 0.9386 time to fit residues: 835.2946 Evaluate side-chains 460 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 439 time to evaluate : 9.636 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 3 residues processed: 21 average time/residue: 0.7829 time to fit residues: 43.9115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1390 random chunks: chunk 452 optimal weight: 7.9990 chunk 1209 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 788 optimal weight: 7.9990 chunk 331 optimal weight: 20.0000 chunk 1344 optimal weight: 10.0000 chunk 1116 optimal weight: 40.0000 chunk 622 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 444 optimal weight: 8.9990 chunk 706 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN M 97 ASN ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 281 GLN ** y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 380 GLN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 112567 Z= 0.202 Angle : 0.552 10.619 152051 Z= 0.283 Chirality : 0.041 0.229 17207 Planarity : 0.003 0.056 19611 Dihedral : 4.835 77.196 15434 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.72 % Rotamer: Outliers : 0.72 % Allowed : 14.28 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % 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: 0.21 (0.07), residues: 13990 helix: 1.60 (0.07), residues: 6295 sheet: 0.21 (0.12), residues: 1916 loop : -1.59 (0.08), residues: 5779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP m 215 HIS 0.007 0.001 HIS c 199 PHE 0.022 0.001 PHE D 299 TYR 0.024 0.001 TYR Z 74 ARG 0.004 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 439 time to evaluate : 9.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 33 residues processed: 508 average time/residue: 0.9413 time to fit residues: 868.5809 Evaluate side-chains 472 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 439 time to evaluate : 9.609 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 3 residues processed: 33 average time/residue: 0.8177 time to fit residues: 64.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1390 random chunks: chunk 1296 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 766 optimal weight: 3.9990 chunk 982 optimal weight: 10.0000 chunk 760 optimal weight: 7.9990 chunk 1132 optimal weight: 5.9990 chunk 750 optimal weight: 6.9990 chunk 1339 optimal weight: 30.0000 chunk 838 optimal weight: 50.0000 chunk 816 optimal weight: 50.0000 chunk 618 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 92 GLN g 128 ASN h 109 GLN ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 281 GLN ** y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 178 ASN ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 GLN ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 198 HIS ** f 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 112567 Z= 0.181 Angle : 0.545 10.165 152051 Z= 0.278 Chirality : 0.041 0.196 17207 Planarity : 0.003 0.056 19611 Dihedral : 4.795 77.487 15434 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 0.42 % Allowed : 15.07 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % 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: 0.26 (0.07), residues: 13990 helix: 1.65 (0.07), residues: 6302 sheet: 0.24 (0.12), residues: 1914 loop : -1.58 (0.08), residues: 5774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP m 215 HIS 0.006 0.001 HIS c 199 PHE 0.022 0.001 PHE D 299 TYR 0.025 0.001 TYR Z 74 ARG 0.009 0.000 ARG V 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27980 Ramachandran restraints generated. 13990 Oldfield, 0 Emsley, 13990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 439 time to evaluate : 9.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 18 residues processed: 484 average time/residue: 0.9174 time to fit residues: 806.6454 Evaluate side-chains 457 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 439 time to evaluate : 9.503 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 3 residues processed: 18 average time/residue: 0.7551 time to fit residues: 38.8685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.8578 > 50: distance: 35 - 42: 33.682 distance: 42 - 43: 22.223 distance: 43 - 44: 21.352 distance: 43 - 46: 22.403 distance: 44 - 45: 7.749 distance: 44 - 51: 40.502 distance: 46 - 47: 26.271 distance: 47 - 48: 40.184 distance: 48 - 49: 41.099 distance: 49 - 50: 56.224 distance: 51 - 52: 56.182 distance: 52 - 53: 41.556 distance: 53 - 54: 39.611 distance: 53 - 57: 53.207 distance: 54 - 81: 55.712 distance: 55 - 56: 40.145 distance: 57 - 58: 39.083 distance: 58 - 59: 38.926 distance: 58 - 61: 41.057 distance: 59 - 60: 3.284 distance: 59 - 65: 40.792 distance: 60 - 90: 38.334 distance: 61 - 62: 39.466 distance: 62 - 64: 5.009 distance: 65 - 66: 11.852 distance: 66 - 67: 21.272 distance: 66 - 69: 42.610 distance: 67 - 68: 30.485 distance: 67 - 73: 25.719 distance: 68 - 101: 40.750 distance: 69 - 70: 7.106 distance: 69 - 71: 52.416 distance: 73 - 74: 24.445 distance: 74 - 75: 7.610 distance: 74 - 77: 24.214 distance: 75 - 76: 20.230 distance: 75 - 81: 20.925 distance: 76 - 112: 41.431 distance: 77 - 78: 43.917 distance: 78 - 79: 25.776 distance: 78 - 80: 59.615 distance: 81 - 82: 41.106 distance: 82 - 83: 51.877 distance: 82 - 85: 31.745 distance: 83 - 90: 40.112 distance: 85 - 86: 37.700 distance: 87 - 88: 41.132 distance: 90 - 91: 42.738 distance: 91 - 92: 16.198 distance: 91 - 94: 24.215 distance: 92 - 93: 12.998 distance: 92 - 101: 15.416 distance: 95 - 96: 14.926 distance: 96 - 98: 50.096 distance: 97 - 99: 22.812 distance: 98 - 100: 12.547 distance: 99 - 100: 43.741 distance: 101 - 102: 62.345 distance: 102 - 103: 28.156 distance: 103 - 104: 25.803 distance: 103 - 112: 13.447 distance: 105 - 106: 17.213 distance: 106 - 107: 22.541 distance: 106 - 108: 9.884 distance: 107 - 109: 9.668 distance: 108 - 110: 15.018 distance: 109 - 111: 17.532 distance: 110 - 111: 13.030 distance: 112 - 113: 55.777 distance: 113 - 114: 47.597 distance: 114 - 115: 42.677 distance: 114 - 116: 16.270 distance: 117 - 118: 40.228 distance: 117 - 120: 29.784 distance: 118 - 123: 34.831 distance: 120 - 121: 34.210 distance: 120 - 122: 30.900